Protein Data Bank Exchange macromolecular Crystallographic Information Framework, PDBx/mmCIF, provides the foundation for the deposition, annotation, and archiving of structural data across various experimental techniques.

PDBx/mmCIF uses data blocks to organize related information and data. A data block is a logical partition of a data file designated by a data_ record. A data block may be named by appending a text string after the data_ record and a data block is terminated by either another data_ record or by the end of the file.

An example of identifying data block at the beginning of the model file for the PDB entry 4HHB:

data_4HHB
#
_entry.id	4HHB
#
_audit_conform.dict_name	mmcif_pdbx.dic
_audit_conform.dict_version	5.367
_audit_conform.dict_location	http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
#

PDBx/mmCIF format utilizes the ASCII character set. All data items are identified by name, begin with the underscore character, and are composed of a category name followed by an attribute name. The category name is separated from the attribute name by a period.

An example of PDBx/mmCIF data item (_category.attribute):

_entity.id

Data items are presented in two styles: key-value and tabular.

An example of a key-value style where the PDBx/mmCIF item is followed directly by a corresponding value:

_cell.entry_id	4HHB
_cell.length_a	63.150
_cell.length_b	83.590
_cell.length_c	53.800
_cell.angle_alpha	90.00
_cell.angle_beta	99.34
_cell.angle_gamma	90.00
_cell.Z_PDB	4

An example of a tabular style used when there are multiple values for each item. In this style, a loop_ record is followed by rows of data item names and then white-space delimited data values:

loop_
_audit_author.name
_audit_author.pdbx_ordinal
_audit_author.identifier_ORCID
'Fermi, G.'	1	0000-000x-xxxx-xxxx
'Perutz, M.F'	2	0000-000x-xxxx-xxxx

The hash symbol (#) is used to separate categories to improve readability, but is not strictly necessary. It is also used to indicate comments.

Numbers and single-word data values (i.e., those not containing white space) are listed by themselves:

_cell.length_a

63.150

A single value composed of multiple words separated by white-space need to be quoted:

_audit_author.name

'Fermi, G.'

A single value encompassing multiple line data values can be listed on a new line within a pair of semicolons:

loop_

_entity_poly.entity_id

_entity_poly.type

_entity_poly.nstd_linkage

_entity_poly.nstd_monomer

_entity_poly.pdbx_seq_one_letter_code

_entity_poly.pdbx_seq_one_letter_code_can

_entity_poly.pdbx_strand_id

_entity_poly.pdbx_target_identifier

1 'polypeptide (L)' no no

;VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSD

LHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR

;

;VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSD

LHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR

;

A,C ?

There are two special characters used as placeholders for mmCIF item values which for some reason cannot be explicitly assigned. The question mark (?) is used to mark an item value as missing. A period (.) may be used to identify that there is no appropriate value for the item or that a value has been intentionally omitted.

The PDBx/mmCIF Dictionary supports primary data types (integers, real numbers, and text), defines boundary conditions and controlled vocabularies, and provides the ability to link data items together to express relationships (e.g., parent-child related data items).

For example, the entity identifier assigned to a molecule in the "parent" _entity data category (shown here) is referred to in the "child" categories (as shown in the subsequent example):

loop_
_entity.id
_entity.type
_entity.src_method
_entity.pdbx_description
_entity.formula_weight
_entity.pdbx_number_of_molecules
_entity.pdbx_ec
_entity.pdbx_mutation
_entity.pdbx_fragment
_entity.details
1	polymer	nat	'Hemoglobin subunit alpha'	14981.087	1	?	?	?	?
2	polymer	nat	'Hemoglobin subunit beta'	16032.274	1	?	?	?	?
3	non-polymer	syn	'PROTOPORPHYRIN IX CONTAINING FE'	616.487	2	?	?	?	?
4	water	nat	water	18.015	93	?	?	?	?

Example of a "child" category describing the source information for each polymer entity listed in the above "parent" category:

loop_
_entity_src_nat.entity_id
_entity_src_nat.pdbx_src_id
_entity_src_nat.pdbx_alt_source_flag
_entity_src_nat.pdbx_beg_seq_num
_entity_src_nat.pdbx_end_seq_num
_entity_src_nat.common_name
_entity_src_nat.pdbx_organism_scientific
_entity_src_nat.pdbx_ncbi_taxonomy_id
1	1	sample	1	140	horse	'Equus caballus'	9796
2	1	sample	1	146	horse	'Equus caballus'	9796

The primary PDBx/mmCIF resource mmcif.wwpdb.org contains all relevant data dictionaries and documentation, as well as a detailed description of the format's development and history. The below sections present some key PDBx/mmCIF categories with descriptions and examples, and aim to help users to understand and adopt the PDBx/mmCIF format.

PDBx/mmCIF category	Legacy PDB format records	Description
_struct_keywords	HEADER KEYWDS	Keywords that describe the structure.

Example:

_struct_keywords.entry_id	8HRI
_struct_keywords.text	'SARS-CoV-2, Delta, Spike protein, VIRAL PROTEIN'
_struct_keywords.pdbx_keywords	'VIRAL PROTEIN'

PDBx/mmCIF category	Legacy PDB format records	Description
_struct	TITLE	Structure title.

Example:

_struct.entry_id	8HYP
_struct.title	'Crystal structure of AtHPPD-Y18400 complex'

PDBx/mmCIF category	Legacy PDB format records	Description
_audit_author	AUTHOR	Structure author(s).

Example:

loop_
_audit_author.name
_audit_author.pdbx_ordinal
_audit_author.identifier_ORCID
'Fermi, G.'	1	?
'Perutz, M.F.'	2	?

PDBx/mmCIF category	Legacy PDB format record	Description
_citation	JRNL	Literature citations relevant to the contents of the entry.

Notes:

• The _citation.id 'primary' is used for the citation describing structure determination and refinement.
• The corresponding authors for each citation are listed in the 'child' _citation_author category (see below).

Example:

loop_

_citation.id

_citation.title

_citation.journal_abbrev

_citation.journal_volume

_citation.page_first

_citation.page_last

_citation.year

_citation.journal_id_ASTM

_citation.country

_citation.journal_id_ISSN

_citation.journal_id_CSD

_citation.book_publisher

_citation.pdbx_database_id_PubMed

_citation.pdbx_database_id_DOI

primary

'Interaction of coxsackievirus B3 with the full length coxsackievirus-adenovirus receptor.'

Nat.Struct.Biol.

8

874

878

2001

NSBIEW

US

1072-8368

2024

?

11573093

10.1038/nsb1001-874

1

'ISOLATION OF A COMMON RECEPTOR FOR COXSACKIE B VIRUSES AND ADENOVIRUSES 2 AND 5'

Science

275

1320

1323

1997

SCIEAS

US

0036-8075

0038

?

?

10.1126/science.275.5304.1320

PDBx/mmCIF category	Legacy PDB format records	Description
_citation_author	JRNL	Citation author(s).

Notes:

• The value in _citation_author.citation_id item points to the relevant citation information in the 'parent' _citation category (see above) linking citations with the corresponding authors.

Example:

loop_
_citation_author.citation_id
_citation_author.name
_citation_author.ordinal
_citation_author.identifier_ORCID
primary	'He, Y.'	1	?
primary	'Chipman, P.R.'	2	?
primary	'Howitt, J.'	3	?
primary	'Bator, C.M.'	4	?
primary	'Whitt, M.A.'	5	?
primary	'Baker, T.S.'	6	?
primary	'Kuhn, R.J.'	7	?
primary	'Anderson, C.W.'	8	?
primary	'Freimuth, P.'	9	?
primary	'Rossman, M.G.'	10	?
1	'Bergelson, J.M.'	11	?
1	'Cunningham, J.A.'	12	?
1	'Droguett, G.'	13	?
1	'Kurt-Jones, E.A.'	14	?
1	'Krithivas, A.'	15	?
1	'Hong, J.S.'	16	?
1	'Horwitz, M.S.'	17	?
1	'Crowell, R.L.'	18	?
1	'Finberg, R.W.'	19	?

PDBx/mmCIF category	Legacy PDB format records	Description
_exptl	EXPDTA	Experimental method used to collect data.

Example:

_exptl.entry_id	4HHB
_exptl.method	'X-RAY DIFFRACTION'
_exptl.crystals_number	?

Example:

loop_
_exptl.entry_id
_exptl.crystals_number
_exptl.details
_exptl.method
_exptl.method_details
8W48	1	?	'X-RAY DIFFRACTION'	?
8W48	?	?	'NEUTRON DIFFRACTION'	?

Entry Composition and Details

PDBx/mmCIF category	Legacy PDB format records	Description
_entity	COMPND	Details about each unique molecular entity (protein, nucleic acid, carbohydrate, small molecule) present in the structure.

Notes:

• _entity.id is a unique identifier of all unique polymer and non-polymer molecules in the structure. This value is referred to in many 'child' categories within the model file connecting all the information pertaining to a particular molecular entity together.
• _entity.type can be: polymer, branched, non-polymer, or water.
• Each polymer entity is expected to have a corresponding record in the _entity_poly, _entity_poly_seq, and _pdbx_poly_seq_scheme categories.
• _entity.src_method - defines the type of method by which the entity was produced: naturally obtained (nat), recombinantly expressed (man), or chemically synthesized (syn).
• Source information for each polymer entity must be provided in either _entity_src_nat (naturally obtained), _entity_src_gen (recombinantly expressed), or _pdbx_entity_src_syn (chemically synthesized).

Example:

loop_
_entity.id
_entity.type
_entity.src_method
_entity.pdbx_description
_entity.formula_weight
_entity.pdbx_number_of_molecules
_entity.pdbx_ec
_entity.pdbx_mutation
1	polymer	man	'Secreted effector kinase SteC'	19731.074	4	2.7.-.-	C276S
2	non-polymer	nat	'ADENOSINE MONOPHOSPHATE'	347.221	4	?	?
3	non-polymer	syn	'MAGNESIUM ION'	24.305	5	?	?
4	water	nat	water	18.015	167	?	?

---

Source and Expression System

PDBx/mmCIF category	Legacy PDB format records	Description
_entity_src_gen	SOURCE	Details of the source from which the entity was obtained in cases where the source was genetically manipulated, including the organism from which the gene was obtained and the host organism for gene expression and details about the host organism (e.g., the plasmid used).

Notes:

• _entity_src_gen.pdbx_gene_src_scientific_name corresponds to the scientific name of the organism from which the molecule originates.
• _entity_src_gen.pdbx_host_org_scientific_name corresponds to the scientific name of the organism that served as host for the production of the entity.

Example:

_entity_src_gen.entity_id	1
_entity_src_gen.pdbx_src_id	1
_entity_src_gen.pdbx_alt_source_flag	sample
_entity_src_gen.pdbx_seq_type	'Biological sequence'
_entity_src_gen.pdbx_beg_seq_num	1
_entity_src_gen.pdbx_end_seq_num	299
_entity_src_gen.pdbx_gene_src_scientific_name	'Severe acute respiratory syndrome coronavirus 2'
_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id	2697049
_entity_src_gen.pdbx_host_org_scientific_name	'Escherichia coli BL21 (DE3)'
_entity_src_gen.pdbx_host_org_ncbi_taxonomy_id	469008

PDBx/mmCIF category	Legacy PDB format records	Description
_entity_src_nat	SOURCE	Details of the source from which the entity was obtained in cases where the entity was isolated directly from a natural source.

Example:

_entity_src_nat	1
_entity_src_nat.pdbx_src_id	1
_entity_src_nat.pdbx_alt_source_flag	sample
_entity_src_nat.pdbx_beg_seq_num	1
_entity_src_nat.pdbx_end_seqe_num	129
_entity_src_nat.common_name	chicken
_entity_src_nat.pdbx_organism_scientific	'Gallus gallus'
_entity_src_nat.pdbx_ncbi_taxonomy_id	9031

PDBx/mmCIF category	Legacy PDB format records	Description
_pdbx_entity_src_syn	SOURCE	Details of the source from which the entity was obtained in cases where the entity was chemically synthesized.

Example:

_pdbx_entity_src_syn.entity_id	2
_pdbx_entity_src_syn.pdbx_src_id	1
_pdbx_entity_src_syn.pdbx_alt_source_flag	sample
_pdbx_entity_src_syn.pdbx_beg_seq_num	1
_pdbx_entity_src_syn.pdbx_end_seq_num	64
_pdbx_entity_src_syn.organism_scientific	'Mandarin fish ranavirus'
_pdbx_entity_src_syn.ncbi_taxonomy_id	2487147

---

Sample Sequence

PDBx/mmCIF category	Legacy PDB format records	Description
_entity_poly	SEQRES	Details about the polymer, such as polymer type, corresponding chain IDs and studied polymer sequence.

Notes:

• _entity_poly.pdbx_seq_one_letter_code describes the sequence of protein or nucleic acid polymers in standard one-letter codes of amino acids or nucleotides. Non-standard amino acids/nucleotides are represented by their Chemical Component Dictionary (CCD) codes in parenthesis. Deoxynucleotides are represented by the specially-assigned 2-letter CCD codes in parenthesis, with 'D' prefix added to their ribonucleotide counterparts. For hybrid polymers, each residue is represented by the code of its individual type. A cyclic polymer is represented in linear sequence from the chosen start to end.
• _entity_poly.pdbx_seq_one_letter_code_can describes the canonical sequence of protein or nucleic acid polymer in standard one-letter codes of amino acids or nucleotides, corresponding to the sequence in _entity_poly.pdbx_seq_one_letter_code. Non-standard amino acids/nucleotides are represented by the codes of their parents if parent is specified in _chem_comp.mon_nstd_parent_comp_id, or by letter 'X' if parent is not specified. Deoxynucleotides are represented by their canonical one-letter codes of A, C, G, or T. For modifications with several parent amino acids, all corresponding parent amino acid codes will be listed (ex. chromophores).

Example:

loop_
_entity_poly.entity_id
_entity_poly.type
_entity_poly.nstd_linkage
_entity_poly.nstd_monomer
_entity_poly.pdbx_seq_one_letter_code
_entity_poly.pdbx_seq_one_letter_code_can
_entity_poly.pdbx_strand_id
_entity_poly.pdbx_target_identifier
1	'polypeptide (L)'	no	no
;VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR
;
;VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR
;
A,C	?
2	'polypeptide (L)'	no	no
;VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH
;
;VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH
;
B,D	?

PDBx/mmCIF category	Legacy PDB format records	Description
_entity_poly_seq	SEQRES	Specifies the sequence of monomers in a polymer. Allowance is made for the possibility of microheterogeneity in a sample by allowing a given sequence number to be correlated with more than one monomer ID. The corresponding ATOM_SITE entries should reflect this heterogeneity.

Notes:

• _entity_poly_seq.hetero defines a flag to indicate whether this monomer in the polymer is heterogeneous in sequence.

Example:

loop_
_entity_poly_seq.entity_id
_entity_poly_seq.num
_entity_poly_seq.mon_id
_entity_poly_seq.hetero
1	1	VAL	n
1	2	LEU	n
1	3	SER	n
1	4	PRO	n
1	5	ALA	n
1	6	ASP	n
... (truncated for brevity)

PDBx/mmCIF category	Legacy PDB format records	Description
_pdbx_poly_seq_scheme	N/A	Residue level nomenclature mapping for polymer entities.

Notes:

• _pdbx_poly_seq_scheme.asym_id represents a unique and sequential identifier of each molecule in the model. Pointer to _atom_site.label_asym_id in the coordinate section.
• _pdbx_poly_seq_scheme.pdb_strand_id represents PDB chain ID.

Example:

loop_
_pdbx_poly_seq_scheme.asym_id
_pdbx_poly_seq_scheme.entity_id
_pdbx_poly_seq_scheme.seq_id
_pdbx_poly_seq_scheme.mon_id
_pdbx_poly_seq_scheme.ndb_seq_num
_pdbx_poly_seq_scheme.pdb_seq_num
_pdbx_poly_seq_scheme.auth_seq_num
_pdbx_poly_seq_scheme.pdb_mon_id
_pdbx_poly_seq_scheme.auth_mon_id
_pdbx_poly_seq_scheme.pdb_strand_id
_pdbx_poly_seq_scheme.pdb_ins_code
_pdbx_poly_seq_scheme.hetero
A	1	1	VAL	1	1	1	VAL	VAL	A	.	n
A	1	2	LEU	2	2	2	LEU	LEU	A	.	n
A	1	3	SER	3	3	3	SER	SER	A	.	n
A	1	4	PRO	4	4	4	PRO	PRO	A	.	n
A	1	5	ALA	5	5	5	ALA	ALA	A	.	n
A	1	6	ASP	6	6	6	ASP	ASP	A	.	n
A	1	7	LYS	7	7	7	LYS	LYS	A	.	n
A	1	8	THR	8	8	8	THR	THR	A	.	n
A	1	9	ASN	9	9	9	ASN	ASN	A	.	n
A	1	10	VAL	10	10	10	VAL	VAL	A	.	n
A	1	11	LYS	11	11	11	LYS	LYS	A	.	n
A	1	12	ALA	12	12	12	ALA	ALA	A	.	n
A	1	13	ALA	13	13	13	ALA	ALA	A	.	n
A	1	14	TRP	14	14	14	TRP	TRP	A	.	n
A	1	15	GLY	15	15	15	GLY	GLY	A	.	n
A	1	16	LYS	16	16	16	LYS	LYS	A	.	n
A	1	17	VAL	17	17	17	VAL	VAL	A	.	n
A	1	18	GLY	18	18	18	GLY	GLY	A	.	n
A	1	19	ALA	19	19	19	ALA	ALA	A	.	n
... (truncated for brevity)

PDBx/mmCIF category	Legacy PDB format records	Description
_struct_asym	N/A	Details about instances of molecular entities.

Notes:

• The category provides correspondence between molecule ASYM_ID (_struct_asym.id, a unique identifier of each molecule in the model) and corresponding Entity ID (_entity.id).
• ASYM_ID can be different from the author provided or PDB assigned chain identifier (chain ID), ASYM_ID is assigned sequentially starting from letter A to all polymer and non-polymer molecule instances in the structure.
• A group of water molecules associated with the same polymer chain is assigned one ASYM_ID.

Example:

loop_
_struct_asym.id
_struct_asym.pdbx_blank_PDB_chainid_flag
_struct_asym.pdbx_modified
_struct_asym.entity_id
_struct_asym.details
A	N	N	1	?
B	N	N	1	?
C	N	N	1	?
D	N	N	1	?
E	N	N	2	?
F	N	N	2	?
G	N	N	2	?
H	N	N	2	?

---

Sequence Reference

PDBx/mmCIF category	Legacy PDB format records	Description
_struct_ref	DBREF	Relates the sequence of the polymer entities described in the structure to the information archived in external sequence databases (UniProt, GeneBank, PDB, etc.).

Notes:

• _struct_ref.pdbx_seq_one_letter_code provides an external database sequence expressed as a string of one-letter amino acid codes. If no external database reference is provided, the PDB entry itself is used as a database reference (self-reference) in which case the studied sample sequence is provided here.

Example:

_struct_ref.id	1
_struct_ref.db_name	UNP
_struct_ref.db_code	Q93D82_RHIRD
_struct_ref.pdbx_db_accession	Q93D82
_struct_ref.pdbx_db_isoform	?
_struct_ref.entity_id	1
_struct_ref.pdbx_seq_one_letter_code
;TAIVTNVKHFGGMGSALRLSEAGHTVACHDESFKQKDELEAFAETYPQLKPMSEQEPAELIEAVTSAYGQVDVLVSNDIF APEFQPIDKYAVEDYRGAVEALQIRPFALVNAVASQMKKRKSGHIIFITSATPFGPWKELSTYTSARAGACTLANALSKE LGEYNIPVFAIGPNYLHSEDSPYFYPTEPWKTNPEHVAHVKKVTALQRLGTQKELGELVAFLASGSCDYLTGQVFWLAGG FPMIERWPGMPE
;
_struct_ref.pdbx_align_begin	3

PDBx/mmCIF category	Legacy PDB format records	Description
_struct_ref_seq	DBREF	Provides the residue ranges used for the alignment between the sequence of an entity described in the structure and the sequence in the referenced database entry.

Example:

loop_
_struct_ref_seq.align_id
_struct_ref_seq.ref_id
_struct_ref_seq.pdbx_PDB_id_code
_struct_ref_seq.pdbx_strand_id
_struct_ref_seq.seq_align_beg
_struct_ref_seq.pdbx_seq_align_beg_ins_code
_struct_ref_seq.seq_align_end
_struct_ref_seq.pdbx_seq_align_end_ins_code
_struct_ref_seq.pdbx_db_accession
_struct_ref_seq.db_align_beg
_struct_ref_seq.pdbx_db_align_beg_ins_code
_struct_ref_seq.db_align_end
_struct_ref_seq.pdbx_db_align_end_ins_code
_struct_ref_seq.pdbx_auth_seq_align_beg
_struct_ref_seq.pdbx_auth_seq_align_end
1	1	5KWE	A	20	?	271	?	Q93D82	3	?	254	?	3	254
2	1	5KWE	B	20	?	271	?	Q93D82	3	?	254	?	3	254
3	1	5KWE	C	20	?	271	?	Q93D82	3	?	254	?	3	254
4	1	5KWE	D	20	?	271	?	Q93D82	3	?	254	?	3	254

PDBx/mmCIF category	Legacy PDB format records	Description
_struct_ref_seq_dif	SEQADV	Lists differences (if any) between the sequence of the polymer entity described in the structure and the sequence of the referenced database entry with corresponding annotation (conflict, engineered mutation, variant, expression tag, etc.).

Example:

loop_

_struct_ref_seq_dif.align_id

_struct_ref_seq_dif.pdbx_pdb_id_code

_struct_ref_seq_dif.mon_id

_struct_ref_seq_dif.pdbx_pdb_strand_id

_struct_ref_seq_dif.seq_num

_struct_ref_seq_dif.pdbx_pdb_ins_code

_struct_ref_seq_dif.pdbx_seq_db_name

_struct_ref_seq_dif.pdbx_seq_db_accession_code

_struct_ref_seq_dif.db_mon_id

_struct_ref_seq_dif.pdbx_seq_db_seq_num

_struct_ref_seq_dif.details

_struct_ref_seq_dif.pdbx_auth_seq_num

_struct_ref_seq_dif.pdbx_ordinal

1

5KWE

MET

A

1

?

UNP

Q93D82

?

?

'initiating methionine'

-16

1

1

5KWE

GLY

A

2

?

UNP

Q93D82

?

?

'expression tag'

-15

2

1

5KWE

HIS

A

3

?

UNP

Q93D82

?

?

'expression tag'

-14

3

1

5KWE

HIS

A

4

?

UNP

Q93D82

?

?

'expression tag'

-13

4

1

5KWE

HIS

A

5

?

UNP

Q93D82

?

?

'expression tag'

-12

5

1

5KWE

HIS

A

6

?

UNP

Q93D82

?

?

'expression tag'

-11

6

1

5KWE

HIS

A

7

?

UNP

Q93D82

?

?

'expression tag'

-10

7

1

5KWE

HIS

A

8

?

UNP

Q93D82

?

?

'expression tag'

-9

8

1

5KWE

SER

A

9

?

UNP

Q93D82

?

?

'expression tag'

-8

9

1

5KWE

SER

A

10

?

UNP

Q93D82

?

?

'expression tag'

-7

10

1

5KWE

GLY

A

11

?

UNP

Q93D82

?

?

'expression tag'

-6

11

1

5KWE

LEU

A

12

?

UNP

Q93D82

?

?

'expression tag'

-5

12

1

5KWE

VAL

A

13

?

UNP

Q93D82

?

?

'expression tag'

-4

13

1

5KWE

PRO

A

14

?

UNP

Q93D82

?

?

'expression tag'

-3

14

1

5KWE

ARG

A

15

?

UNP

Q93D82

?

?

'expression tag'

-2

15

1

5KWE

GLY

A

16

?

UNP

Q93D82

?

?

'expression tag'

-1

16

1

5KWE

SER

A

17

?

UNP

Q93D82

?

?

'expression tag'

0

17

1

5KWE

HIS

A

18

?

UNP

Q93D82

?

?

'expression tag'

1

18

1

5KWE

ALA

A

19

?

UNP

Q93D82

?

?

'expression tag'

2

19

1

5KWE

ASN

A

170

?

UNP

Q93D82

CYS

153

'engineered mutation'

153

20

Entry Composition and Details

PDBx/mmCIF category	Legacy PDB format records	Description
_entity	COMPND	Details about each unique molecular entity (protein, nucleic acid, carbohydrate, small molecule) present in the structure.

Example:

loop_
_entity.id
_entity.type
_entity.src_method
_entity.pdbx_description
_entity.formula_weight
_entity.pdbx_number_of_molecules
_entity.pdbx_ec
_entity.pdbx_mutation
_entity.pdbx_fragment
_entity.details
1	polymer	man	'FUCOLECTIN-RELATED PROTEIN'	66769.758	1	?	YES	'CATALYTIC MODULE, RESIDUES 31-589'	?
2	branched	man	"alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose"	681.7	1	?	?	?	?
3	water	nat	water	18.015	334	?	?	?	?

PDBx/mmCIF category	Legacy PDB format records	Description
_pdbx_entity_branch	N/A	Specifies the list of branched entities and the type.

Example:

_pdbx_entity_branch.entity_id	2
_pdbx_entity_branch.type	oligosaccharide

PDBx/mmCIF category	Legacy PDB format records	Description
_pdbx_entity_branch_descriptor	N/A	Provides string descriptors of entity chemical structure.

Example:

loop_
_pdbx_entity_branch_descriptor.ordinal
_pdbx_entity_branch_descriptor.entity_id
_pdbx_entity_branch_descriptor.descriptor
_pdbx_entity_branch_descriptor.type
_pdbx_entity_branch_descriptor.program
_pdbx_entity_branch_descriptor.program_version
1	2	"LFucpa1-2DGalpb1-4[LFucpa1-3]DGlcpNAcb1-ROH"	"Glycam Condensed Sequence"	GMML	1.0
2	2	"WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-3-2/a3-b1_a4-c1_c2-d1"	WURCS	PDB2Glycan	1.1
3	2	"[][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}"	LINUCS	PDB-CARE	?

---

Sequence

PDBx/mmCIF category	Legacy PDB format records	Description
_pdbx_entity_branch_list	N/A	Specifies the list of monomers in a branched entity. Allowance is made for the possibility of microheterogeneity in a sample by allowing a given sequence number to be correlated with more than one monomer ID.

Example:

loop_
_pdbx_entity_branch_list.entity_id
_pdbx_entity_branch_list.comp_id
_pdbx_entity_branch_list.num
_pdbx_entity_branch_list.hetero
2	NAG	1	n
2	GAL	2	n
2	FUC	3	n
2	FUC	4	n

PDBx/mmCIF category	Legacy PDB format records	Description
_pdbx_branch_scheme	N/A	Residue level nomenclature mapping for branch chain entities.

Example:

loop_
_pdbx_branch_scheme.asym_id
_pdbx_branch_scheme.entity_id
_pdbx_branch_scheme.mon_id
_pdbx_branch_scheme.num
_pdbx_branch_scheme.pdb_asym_id
_pdbx_branch_scheme.pdb_mon_id
_pdbx_branch_scheme.pdb_seq_num
_pdbx_branch_scheme.auth_asym_id
_pdbx_branch_scheme.auth_mon_id
_pdbx_branch_scheme.auth_seq_num
_pdbx_branch_scheme.hetero
B	2	NAG	1	B	NAG	1	A	NAG	1592	n
B	2	GAL	2	B	GAL	2	A	GAL	1591	n
B	2	FUC	3	B	FUC	3	A	FUC	1590	n
B	2	FUC	4	B	FUC	4	A	FUC	1593	n

---

Connectivity

PDBx/mmCIF category	Legacy PDB format records	Description
_pdbx_entity_branch_link	N/A	Details about the linkages between components within a branched entity.

Example:

loop_

_pdbx_entity_branch_link.link_id

_pdbx_entity_branch_link.entity_id

_pdbx_entity_branch_link.entity_branch_list_num_1

_pdbx_entity_branch_link.comp_id_1

_pdbx_entity_branch_link.atom_id_1

_pdbx_entity_branch_link.leaving_atom_id_1

_pdbx_entity_branch_link.atom_stereo_config_1

_pdbx_entity_branch_link.entity_branch_list_num_2

_pdbx_entity_branch_link.comp_id_2

_pdbx_entity_branch_link.atom_id_2

_pdbx_entity_branch_link.leaving_atom_id_2

_pdbx_entity_branch_link.atom_stereo_config_2

_pdbx_entity_branch_link.value_order

_pdbx_entity_branch_link.details

1

2

2

GAL

C1

O1

1

NAG

O4

HO4

sing

?

?

?

2

2

3

FUC

C1

O1

2

GAL

O2

HO2

sing

?

?

?

3

2

4

FUC

C1

O1

1

NAG

O3

HO3

sing

?

?

?

PDBx/mmCIF category	Legacy PDB format records	Description
_struct_conn	LINK SSBOND	Details about the connections between portions of the structure. These can be covalent bonds, disulfide bridges, hydrogen bonds, and so on.

Example:

loop_

_struct_conn.id

_struct_conn.conn_type_id

_struct_conn.pdbx_leaving_atom_flag

_struct_conn.pdbx_PDB_id

_struct_conn.ptnr1_label_asym_id

_struct_conn.ptnr1_label_comp_id

_struct_conn.ptnr1_label_seq_id

_struct_conn.ptnr1_label_atom_id

_struct_conn.pdbx_ptnr1_label_alt_id

_struct_conn.pdbx_ptnr1_PDB_ins_code

_struct_conn.pdbx_ptnr1_standard_comp_id

_struct_conn.ptnr1_symmetry

_struct_conn.ptnr2_label_asym_id

_struct_conn.ptnr2_label_comp_id

_struct_conn.ptnr2_label_seq_id

_struct_conn.ptnr2_label_atom_id

_struct_conn.pdbx_ptnr2_label_alt_id

_struct_conn.pdbx_ptnr2_PDB_ins_code

_struct_conn.ptnr1_auth_asym_id

_struct_conn.ptnr1_auth_comp_id

_struct_conn.ptnr1_auth_seq_id

_struct_conn.ptnr2_auth_asym_id

_struct_conn.ptnr2_auth_comp_id

_struct_conn.ptnr2_auth_seq_id

_struct_conn.ptnr2_symmetry

_struct_conn.pdbx_ptnr3_label_atom_id

_struct_conn.pdbx_ptnr3_label_seq_id

_struct_conn.pdbx_ptnr3_label_comp_id

_struct_conn.pdbx_ptnr3_label_asym_id

_struct_conn.pdbx_ptnr3_label_alt_id

_struct_conn.pdbx_ptnr3_PDB_ins_code

_struct_conn.details

_struct_conn.pdbx_dist_value

_struct_conn.pdbx_value_order

_struct_conn.pdbx_role

covale1

covale

one

?

A

ASN

91

ND2

?

?

?

1_555

L

NAG

.

C1

?

?

B

ASN

91

B

NAG

409

1_555

?

?

?

?

?

?

?

1.440

?

N-Glycosylation

covale2

covale

one

?

A

ASN

207

ND2

?

?

?

1_555

C

NAG

.

C1

?

?

B

ASN

207

C

NAG

1

1_555

?

?

?

?

?

?

?

1.418

?

N-Glycosylation

covale3

covale

one

?

A

ASN

305

ND2

?

?

?

1_555

B

NAG

.

C1

?

?

B

ASN

305

A

NAG

1

1_555

?

?

?

?

?

?

?

1.451

?

N-Glycosylation

covale4

covale

both

?

B

NAG

.

O4

?

?

?

1_555

B

NAG

.

C1

?

?

A

NAG

1

A

NAG

2

1_555

?

?

?

?

?

?

?

1.357

?

?

covale5

covale

both

?

C

NAG

.

O4

?

?

?

1_555

C

NAG

.

C1

?

?

C

NAG

1

C

NAG

2

1_555

?

?

?

?

?

?

?

1.369

?

?

covale6

covale

both

?

C

NAG

.

O4

?

?

?

1_555

C

BMA

.

C1

?

?

C

NAG

2

C

BMA

3

1_555

?

?

?

?

?

?

?

1.374

?

?

covale7

covale

both

?

C

BMA

.

O6

?

?

?

1_555

C

MAN

.

C1

?

?

C

BMA

3

C

MAN

4

1_555

?

?

?

?

?

?

?

1.363

?

?

covale8

covale

both

?

C

BMA

.

O3

?

?

?

1_555

C

MAN

.

C1

?

?

C

BMA

3

C

MAN

6

1_555

?

?

?

?

?

?

?

1.353

?

?

covale9

covale

both

?

C

MAN

.

O3

?

?

?

1_555

C

MAN

.

C1

?

?

C

MAN

4

C

MAN

5

1_555

?

?

?

?

?

?

?

1.346

?

?

Entry composition & details

PDBx/mmCIF category	Legacy PDB format records	Description
_entity	COMPOUND	Details about each unique molecular entity (protein, nucleic acid, carbohydrate, small molecule) present in the structure.

Example:

loop_
_entity.id
_entity.type
_entity.src_method
_entity.pdbx_description
_entity.formula_weight
_entity.pdbx_number_of_molecules
_entity.pdbx_ec
_entity.pdbx_mutation
_entity.pdbx_fragment
_entity.details
1	polymer	man	'3C-like proteinase'	33825.547	1	3.4.22.69	?	?	?
2	non-polymer	syn
;(1R,2S,5S)-N-{(1E,2S)-1-imino-3[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-
3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide
;
501.542	1	?	?	?	?
3	water	nat	water	18.015	83	?	?	?	?

PDBx/mmCIF category	Legacy PDB format records	Description
_pdbx_entity_nonpoly	N/A	Provides mapping between entity and the non polymer component.

Example:

loop_
_pdbx_entity_nonpoly.entity_id
_pdbx_entity_nonpoly.name
_pdbx_entity_nonpoly.comp_id
2
;(1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl}-6,6-dimethyl-
3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide
;
4WI
3	water	HOH

PDBx/mmCIF category	Legacy PDB format records	Description
_chem_comp	HET HETNAM HETSYN FORMUL	Details about each of the chemical components from which the relevant chemical structures can be constructed, such as name, synonym, mass, or formula.

Example:

loop_
_chem_comp.id
_chem_comp.type
_chem_comp.mon_nstd_flag
_chem_comp.name
_chem_comp.pdbx_synonyms
_chem_comp.formula
_chem_comp.formula_weight
4WI	non-polymer	.
;(1R,2S,5S)-N{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-
3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide
;
'PF-07321332, bound form; nirmatrelvir, bound form; Paxlovid, bound form' 'C23 H34 F3
N5 O4' 501.542
ALA	'L-peptide linking'	y	ALANINE	?	'C3 H7 N O2'	89.093
ARG	'L-peptide linking'	y	ARGININE	?	'C6 H15 N4 O2 1'	175.209
ASN	'L-peptide linking'	y	ASPARAGINE	?	'C4 H8 N2 O3'	132.118
ASP	'L-peptide linking'	y	'ASPARTIC ACID'	?	'C4 H7 N O4'	133.103
... (truncated for brevity)

PDBx/mmCIF category	Legacy PDB format records	Description
_pdbx_nonpoly_scheme	N/A	Residue level nomenclature mapping for non-polymer entities.

Example:

loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.pdb_ins_code
B	2	4WI	1	401	1	4WI	UNL	A	.
C	3	HOH	1	501	12	HOH	HOH	A	.
C	3	HOH	2	502	85	HOH	HOH	A	.
C	3	HOH	3	503	52	HOH	HOH	A	.
C	3	HOH	4	504	27	HOH	HOH	A	.
C	3	HOH	5	505	29	HOH	HOH	A	.
C	3	HOH	6	506	3	HOH	HOH	A	.
C	3	HOH	7	507	23	HOH	HOH	A	.
C	3	HOH	8	508	55	HOH	HOH	A	.
C	3	HOH	9	509	42	HOH	HOH	A	.
C	3	HOH	10	510	53	HOH	HOH	A	.
... (truncated for brevity)

---

Connectivity

PDBx/mmCIF category	Legacy PDB format records	Description
_struct_conn	LINK	Details about the connections between portions of the structure. These can be covalent bonds, disulfide bridges, hydrogen bonds, and so on.

Example:

_struct_conn.id	covale1
_struct_conn.conn_type_id	covale
_struct_conn.pdbx_leaving_atom_flag	none
_struct_conn.pdbx_PDB_id	?
_struct_conn.ptnr1_label_asym_id	A
_struct_conn.ptnr1_label_comp_id	CYS
_struct_conn.ptnr1_label_seq_id	145
_struct_conn.ptnr1_label_atom_id	SG
_struct_conn.pdbx_ptnr1_label_alt_id	?
_struct_conn.pdbx_ptnr1_PDB_ins_code	?
_struct_conn.pdbx_ptnr1_standard_comp_id	?
_struct_conn.ptnr1_symmetry	1_555
_struct_conn.ptnr2_label_asym_id	B
_struct_conn.ptnr2_label_comp_id	4WI
_struct_conn.ptnr2_label_seq_id	.
_struct_conn.ptnr2_label_atom_id	C3
_struct_conn.pdbx_ptnr2_label_alt_id	?
_struct_conn.pdbx_ptnr2_PDB_ins_code	?
_struct_conn.ptnr1_auth_asym_id	A
_struct_conn.ptnr1_auth_comp_id	CYS
_struct_conn.ptnr1_auth_seq_id	145
_struct_conn.ptnr2_auth_asym_id	A
_struct_conn.ptnr2_auth_comp_id	4WI
_struct_conn.ptnr2_auth_seq_id	401
_struct_conn.ptnr2_symmetry	1_555
_struct_conn.pdbx_ptnr3_label_atom_id	?
_struct_conn.pdbx_ptnr3_label_seq_id	?
_struct_conn.pdbx_ptnr3_label_comp_id	?
_struct_conn.pdbx_ptnr3_label_asym_id	?
_struct_conn.pdbx_ptnr3_label_alt_id	?
_struct_conn.pdbx_ptnr3_PDB_ins_code	?
_struct_conn.details	?
_struct_conn.pdbx_dist_value	1.804
_struct_conn.pdbx_value_order	?
_struct_conn.pdbx_role	?

PDBx/mmCIF category	Legacy PDB format records	Description
_chem_comp_bond	N/A	Details about the bonds and bond orders between atoms in a chemical component.

Example:

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
4WI	O1	C8	doub	N	N	1
4WI	C8	N2	sing	N	N	2
4WI	C8	C5	sing	N	N	3
4WI	N2	C7	sing	N	N	4
4WI	C4	C5	sing	N	N	5
4WI	C4	C2	sing	N	N	6
4WI	C5	C6	sing	N	N	7
4WI	N5	C3	doub	N	N	8
4WI	C3	C2	sing	N	N	9
4WI	C7	C6	sing	N	N	10
4WI	C2	N1	sing	N	N	11
4WI	N2	H9	sing	N	N	69
... (truncated for brevity)

PDBx/mmCIF category	Legacy PDB format records	Description
_chem_comp_atom	N/A	Details about the atoms in a chemical component.

Example:

loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.pdbx_ordinal
4WI	C8	C	N	N	1
4WI	C3	C	N	N	2
4WI	C1	C	N	N	3
4WI	C13	C	N	N	4
4WI	C21	C	N	N	5
4WI	C6	C	N	N	6
4WI	C7	C	N	N	7
4WI	C10	C	N	N	8
4WI	C5	C	N	S	9
4WI	C9	C	N	S	10
4WI	C11	C	N	S	11
... (truncated for brevity)

Sample preparation

PDBx/mmCIF category	Legacy PDB format records	Description
_exptl_crystal_grow	REMARK 280	Details about the conditions and methods used to grow the crystal.

Example:

_exptl_crystal_grow.apparatus	?
_exptl_crystal_grow.crystal_id	1
_exptl_crystal_grow.method	'VAPOR DIFFUSION, SITTING DROP'
_exptl_crystal_grow.pH	5.5
_exptl_crystal_grow.pdbx_details	'0.4uL protein, 0.4 uL 100mM Bis-Tri pH 5.5, 25% PEG 3350, 0.2M NaCl equilibrated against a well of 0.5M LiCl'
_exptl_crystal_grow.temp	298

PDBx/mmCIF category	Legacy PDB format records	Description
_exptl_crystal	REMARK 280	Results of experimental measurements on the crystal or crystals used, such as shape, size or density.

Example:

_exptl_crystal.density_Matthews	2.16
_exptl_crystal.density_percent_sol	43.08
_exptl_crystal.id	1

---

Data collection

PDBx/mmCIF category	Legacy PDB format records	Description
_diffrn	REMARK 200	Details about the diffraction experiment ambient conditions.

Example:

_diffrn.id	1
_diffrn.ambient_temp	100
_diffrn.crystal_id	1
_diffrn.details	?
_diffrn.pdbx_serial_crystal_experiment	N

PDBx/mmCIF category	Legacy PDB format records	Description
_diffrn_detector	REMARK 200	Details about the detector used to measure the scattered radiation, including any analyser and post-sample collimation.

Example:

_diffrn_detector.diffrn_id	1
_diffrn_detector.details	mirrors
_diffrn_detector.detector	PIXEL
_diffrn_detector.type	'DECTRIS EIGER X 16M'
_diffrn_detector.pdbx_collection_date	2022-10-07

PDBx/mmCIF category	Legacy PDB format records	Description
_diffrn_radiation	REMARK 200	Details about the radiation used in measuring the diffraction intensities, its collimation and monochromatization before the sample.

Example:

_diffrn_radiation.diffrn_id	1
_diffrn_radiation.monochromomator	'Si (111)'
_diffrn_radiation.wavelength_id	1
_diffrn_radiation.pdbx_monochromatic_or_laue_m_l	M
_diffrn_radiation.pdbx_diffrn_protocol	'SINGLE WAVELENGTH'
_diffrn_radiation.pdbx_scattering_type	x-ray

PDBx/mmCIF category	Legacy PDB format records	Description
_diffrn_radiation_wavelength	REMARK 200	Details about the wavelength of the radiation used to measure the diffraction intensities. Several wavelengths can be provided here to describe for example multi-wavelength experiments, such as MAD.

Example:

loop_
_diffrn_radiation_wavelength.id
_diffrn_radiation_wavelength.wavelength
_diffrn_radiation_wavelength.wt
1	1.0	1.0
2	0.9793	1.0

PDBx/mmCIF category	Legacy PDB format records	Description
_diffrn_source	REMARK 200	Details of the source of radiation used in the diffraction experiment.

Example:

_diffrn_source.current	?
_diffrn_source.details	?
_diffrn_source.diffrn_id	1
_diffrn_source.power	?
_diffrn_source.size	?
_diffrn_source.source	SYNCHROTRON
_diffrn_source.target	?
_diffrn_source.type	'NSLS-II BEAMLINE 17-ID-2'
_diffrn_source.voltage	?
_diffrn_source.pdbx_wavelength_list	0.9793
_diffrn_source.pdbx_synchrotron_beamline	17-ID-2
_diffrn_source.pdbx_synchrotron_site	NSLS-II

PDBx/mmCIF category	Legacy PDB format records	Description
_software	REMARK 3 REMARK 200	Details about the software used in the structure analysis, which implies any software used in the generation of any data items associated with the structure determination and structure representation.

Example:

loop_

_software.citation_id

_software.classification

_software.compiler_name

_software.compiler_version

_software.contact_author

_software.contact_author_email

_software.date

_software.description

_software.dependencies

_software.hardware

_software.language

_software.location

_software.mods

_software.name

_software.os

_software.os_version

_software.type

_software.version

_software.pdbx_ordinal

?

refinement

?

?

?

?

?

?

?

?

?

?

?

PHENIX

?

?

?

1.20.1_4487

1

?

'data scaling'

?

?

?

?

?

?

?

?

?

?

?

SCALA

?

?

?

.

2

?

'data reduction'

?

?

?

?

?

?

?

?

?

?

?

XDS

?

?

?

.

3

?

phasing

?

?

?

?

?

?

?

?

?

?

?

PHASER

?

?

?

.

4

---

Data collection and processing statistics

PDBx/mmCIF category	Legacy PDB format records	Description
_reflns	REMARK 200	Overall data collection statistics for the X-ray diffraction experiment.

Example:

_reflns.d_resolution_high	1.660
_reflns.d_resolution_low	62.942
_reflns.pdbx_number_measured_all	560202
_reflns.number_obs	112977
_reflns.pdbx_Rmerge_I_obs	0.040
_reflns.pdbx_netI_over_sigmaI	17.990
_reflns.pdbx_chi_squared	1.115
_reflns.percent_possible_obs	99.400
_reflns.observed_criterion_sigma_I	-3.000
_reflns.pdbx_Rrim_I_all	0.045
_reflns.pdbx_CC_half	0.999
_reflns.B_iso_Wilson_estimate	38.223
_reflns.pdbx_diffrn_id	1
_reflns.pdbx_ordinal	1
_reflns.entry_id	7GT6
_reflns.observed_criterion_sigma_F	?
_reflns.number_all	?
_reflns.pdbx_Rsym_value	?
_reflns.pdbx_redundancy	?

PDBx/mmCIF category	Legacy PDB format records	Description
_reflns_shell	REMARK 200	Data collection statistics for the X-ray diffraction experiment broken into resolution shells.

Example:

loop_
_reflns_shell.pdbx_diffrn_id
_reflns_shell.pdbx_ordinal
_reflns_shell.d_res_high
_reflns_shell.d_res_low
_reflns_shell.number_measured_obs
_reflns_shell.number_measured_all
_reflns_shell.number_unique_obs
_reflns_shell.pdbx_rejects
_reflns_shell.Rmerge_I_obs
_reflns_shell.meanI_over_sigI_obs
_reflns_shell.pdbx_Rsym_value
_reflns_shell.pdbx_chi_squared
_reflns_shell.pdbx_redundancy
_reflns_shell.percent_possible_obs
_reflns_shell.pdbx_netI_over_sigmaI_obs
_reflns_shell.number_possible
_reflns_shell.number_unique_all
_reflns_shell.Rmerge_F_all
_reflns_shell.Rmerge_F_obs
_reflns_shell.Rmerge_I_all
_reflns_shell.meanI_over_sigI_all
_reflns_shell.percent_possible_all
_reflns_shell.pdbx_Rrim_I_all
_reflns_shell.pdbx_Rpim_I_all
_reflns_shell.pdbx_CC_half
1	1	1.660	1.760	73562	?	18124	0	0.896	1.320	?	?	?	?	?	18441	?	?	?	?	?	98.300	1.035	?	0.529
1	2	1.760	1.890	73368	?	17113	0	0.473	2.780	?	?	?	?	?	17267	?	?	?	?	?	99.100	0.538	?	0.845
1	3	1.890	2.040	83887	?	15933	0	0.253	5.910	?	?	?	?	?	16040	?	?	?	?	?	99.300	0.282	?	0.968
1	4	2.040	2.230	77815	?	14753	0	0.130	11.180	?	?	?	?	?	14824	?	?	?	?	?	99.500	0.144	?	0.990
1	5	2.230	2.490	69475	?	13360	0	0.079	17.740	?	?	?	?	?	13398	?	?	?	?	?	99.700	0.088	?	0.996
1	6	2.490	2.880	62385	?	11722	0	0.050	27.680	?	?	?	?	?	11738	?	?	?	?	?	99.900	0.056	?	0.998
1	7	2.880	3.520	52823	?	9992	0	0.032	42.650	?	?	?	?	?	9997	?	?	?	?	?	99.900	0.036	?	0.999
1	8	3.520	4.970	40142	?	7731	0	0.024	57.810	?	?	?	?	?	7734	?	?	?	?	?	100.000	0.027	?	0.999
1	9	4.920	62.942	22745	?	4249	0	0.023	62.870	?	?	?	?	?	4252	?	?	?	?	?	99.900	0.025	?	0.999

---

Refinement

PDBx/mmCIF category	Legacy PDB format records	Description
_refine	REMARK 3	Details about the structure-refinement statistics.

Example:

_refine.entry_id	7GT6
_refine.pdbx_refine_id	'X-RAY DIFFRACTION'
_refine.ls_d_res_high	1.6600
_refine.ls_d_res_low	62.9400
_refine.pdbx_ls_sigma_F	0.000
_refine.ls_percent_reflns_obs	99.3700
_refine.ls_number_reflns_obs	56491
_refine.pdbx_ls_cross_valid_method	THROUGHOUT
_refine.pdbx_R_Free_selection_details	RANDOM
_refine.details	'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY'
_refine.ls_R_factor_all	?
_refine.ls_R_factor_obs	0.2007
_refine.ls_R_factor_R_word	0.1996
_refine.ls_R_factor_R_free	0.2276
_refine.ls_percent_reflns_R_free	3.9000
_refine.ls_number_reflns_R_free	2321
_refine.B_iso_mean	37.3880
_refine.aniso_B[1][1]	0.5500
_refine.aniso_B[2][2]	0.5500
_refine.aniso_B[3][3]	-1.7900
_refine.aniso_B[1][2]	0.2800
_refine.aniso_B[1][3]	0.0000
_refine.aniso_B[2][3]	0.0000
_refine.correlation_coeff_Fo_to_Fc	0.9620
_refine.correlation_coeff_Fo_to_Fc_free	0.9530
_refine.pdbx_overall_ESU_R	0.0890
_refine.pdbx_overall_ESU_R_Free	0.0900
_refine.overall_SU_ML	0.0740
_refine.overall_SU_B	2.3210
_refine.solvent_model_details	MASK
_refine.pdbx_solvent_vdw_probe_radii	1.2000
_refine.pdbx_solvent_ion_probe_radii	0.8000
_refine.pdbx_solvent_shrinkage_radii	0.8000
_refine.pdbx_method_to_determine_struct	'MOLECULAR REPLACEMENT'
_refine.pdbx_stereochemistry_target_values	'MAXIMUM LIKELIHOOD'
_refine.B_iso_max	135.070
_refine.B_iso_min	19.500
_refine.pdbx_diffrn_id	1

PDBx/mmCIF category	Legacy PDB format records	Description
_refine_ls_shell	REMARK 3	Details about the results of the least-squares refinement broken down into shells of resolution.

Example:

loop_
_refine_ls_shell.d_res_high
_refine_ls_shell.d_res_low
_refine_ls_shell.pdbx_total_number_of_bins_used
_refine_ls_shell.percent_reflns_obs
_refine_ls_shell.number_reflns_R_work
_refine_ls_shell.R_factor_all
_refine_ls_shell.R_factor_R_work
_refine_ls_shell.R_factor_R_free
_refine_ls_shell.percent_reflns_R_free
_refine_ls_shell.number_reflns_R_free
_refine_ls_shell.R_factor_R_free_error
_refine_ls_shell.number_reflns_all
_refine_ls_shell.number_reflns_obs
_refine_ls_shell.redundancy_reflns_obs
_refine_ls_shell.pdbx_refine_id
2.500	2.6316	7	97.0	4166	.	0.4102	0.4078	.	135	.	4301	4301	.	'X-RAY DIFFRACTION'
2.6316	2.7964	7	100.0	4242	.	0.3417	0.3548	.	156	.	4398	4398	.	'X-RAY DIFFRACTION'
2.7964	3.0123	7	100.0	4332	.	0.2683	0.3923	.	113	.	4445	4445	.	'X-RAY DIFFRACTION'
3.0123	3.3153	7	100.0	4285	.	0.2135	0.2780	.	158	.	4443	4443	.	'X-RAY DIFFRACTION'
3.3153	3.7947	7	98.0	4266	.	0.2193	0.2524	.	137	.	4403	4403	.	'X-RAY DIFFRACTION'
3.7947	4.7796	7	99.0	4312	.	0.1696	0.2265	.	156	.	4468	4468	.	'X-RAY DIFFRACTION'
4.7796	39.7236	7	100.0	4512	.	0.1794	0.1675	.	160	.	4672	4672	.	'X-RAY DIFFRACTION'

PDBx/mmCIF category	Legacy PDB format records	Description
_refine_ls_restr	REMARK 3	Details about the restraints applied to various classes of parameters during the least-squares refinement.

Notes:

• The following PDB to PDB/mmCIF Data Item Correspondences provide description of the restraint types: http://mmcif.wwpdb.org/docs/pdb_to_pdbx_correspondences.html

Example:

loop_
_refine_ls_restr.pdbx_refine_id
_refine_ls_restr.type
_refine_ls_restr.number
_refine_ls_restr.dev_ideal
_refine_ls_restr.dev_ideal_target
_refine_ls_restr.weight
_refine_ls_restr.pdbx_restraint_function
'X-RAY DIFFRACTION'	r_bond_refined_d	3714	0.048	0.025	?	?
'X-RAY DIFFRACTION'	r_bond_other_d	2730	0.001	0.015	?	?
'X-RAY DIFFRACTION'	r_angle_refined_deg	3919	1.717	1.662	?	?
'X-RAY DIFFRACTION'	r_angle_other_deg	6334	1.410	1.601	?	?
'X-RAY DIFFRACTION'	r_dihedral_angle_1_deg	355	6.689	5.000	?	?
'X-RAY DIFFRACTION'	r_dihedral_angle_2_deg	169	29.721	21.361	?	?
'X-RAY DIFFRACTION'	r_dihedral_angle_3_deg	545	14.366	15.000	?	?
'X-RAY DIFFRACTION'	r_dihedral_angle_4_deg	26	24.117	15.000	?	?
'X-RAY DIFFRACTION'	r_chiral_restr	357	0.088	0.200	?	?
'X-RAY DIFFRACTION'	r_gen_planes_refined	3323	0.009	0.020	?	?
'X-RAY DIFFRACTION'	r_gen_planes_other	705	0.001	0.020	?	?
'X-RAY DIFFRACTION'	r_mcbond_it	1792	3.161	3.442	?	?
'X-RAY DIFFRACTION'	r_mcbond_other	1753	3.149	3.416	?	?
'X-RAY DIFFRACTION'	r_mcangle_it	1735	4.416	5.214	?	?

PDBx/mmCIF category	Legacy PDB format records	Description
_pdbx_initial_refinement_model	N/A	The starting model(s) used in structure determination.

Example:

_pdbx_initial_refinement_model.id	1
_pdbx_initial_refinement_model.entity_id_list	1
_pdbx_initial_refinement_model.type	'experimental model'
_pdbx_initial_refinement_model.source_name	PDB
_pdbx_initial_refinement_model.accession_code	6HA3
_pdbx_initial_refinement_model.details	?

---

Crystallographic and Coordinate Transformation Section

PDBx/mmCIF category	Legacy PDB format records	Description
_symmetry	CRYST1	Details about the space group symmetry.

Example:

_symmetry.entry_id	8VCW
_symmeetry.cell_setting	?
_symmetry.Int_Tables_number	19
_symmetry.space_group_name_Hall	?
_symmetry.space_group_name_H-M	'P 21 21 21'
_symmeetry.pdbx_full_space_group_name_H-M	?

PDBx/mmCIF category	Legacy PDB format records	Description
_cell	CRYST1	Details about the crystallographic cell parameters.

Example:

_cell.angle_alpha	90.00
_cell.angle_beta	90.00
_cell.angle_gamma	90.00
_cell.entry_id	8VCW
_cell.length_a	38.209
_cell.length_b	50.7776
_cell.length_c	161.878
_cell.Z_PDB	4

PDBx/mmCIF category	Legacy PDB format records	Description
_atom_sites	SCALE	Details about the matrix used to transform fractional coordinates to Cartesian coordinates.

Example:

_atom_sites.entry_id	8VCW
_atom_sites.Cartn_transf_matrix[1][1]	?
_atom_sites.Cartn_transf_matrix[1][2]	?
_atom_sites.Cartn_transf_matrix[1][3]	?
_atom_sites.Cartn_transf_matrix[2][1]	?
_atom_sites.Cartn_transf_matrix[2][2]	?
_atom_sites.Cartn_transf_matrix[2][3]	?
_atom_sites.Cartn_transf_matrix[3][1]	?
_atom_sites.Cartn_transf_matrix[3][2]	?
_atom_sites.Cartn_transf_matrix[3][3]	?
_atom_sites.Cartn_transf_vector[1]	?
_atom_sites.Cartn_transf_vector[2]	?
_atom_sites.Cartn_transf_vector[3]	?
_atom_sites.Cart_transform_axes	?
_atom_sites.fract_transf_matrix[1][1]	0.026172
_atom_sites.fract_transf_matrix[1][2]	0.000000
_atom_sites.fract_transf_matrix[1][3]	0.000000
_atom_sites.fract_transf_matrix[2][1]	0.000000
_atom_sites.fract_transf_matrix[2][2]	0.019694
_atom_sites.fract_transf_matrix[2][3]	0.000000
_atom_sites.fract_transf_matrix[3][1]	0.000000
_atom_sites.fract_transf_matrix[3][2]	0.000000
_atom_sites.fract_transf_matrix[3][3]	0.006177
_atom_sites.fract_transf_vector[1]	0.00000
_atom_sites.fract_transf_vector[2]	0.00000
_atom_sites.fract_transf_vector[3]	0.00000

Sample Description

PDBx/mmCIF category	Legacy PDB format records	Description
_em_entity_assembly	REMARK 245	Details about each component of the complex.

Notes:

• An isolated protein would be classified in _em_entity_assembly.type as "COMPLEX". The other categories refer to large-scale samples, such as "CELL", "VIRUS", etc.

Example:

_em_entity_assembly.id	1
_em_entity_assembly.parent_id	0
_em_entity_assembly.source	RECOMBINANT
_em_entity_assembly.type	COMPLEX
_em_entity_assembly.name	'Core tetramer assembly (p2) of the phiPA3 bacteriophage PhuN protein'
_em_entity_assembly.details	?
_em_entity_assembly.synonym	?
_em_entity_assembly.oligomeric_details	?
_em_entity_assembly.entity_id_list	1

PDBx/mmCIF category	Legacy PDB format records	Description
_em_entity_assembly_molwt	N/A	Details about the molecular weight of an assembly component of the sample.

Example:

loop_
_em_entity_assembly_molwt.entity_assembly_id
_em_entity_assembly_molwt.id
_em_entity_assembly_molwt.units
_em_entity_assembly_molwt.value
1	1	MEGADALTONS	30.5

PDBx/mmCIF category	Legacy PDB format records	Description
_em_entity_assembly_naturalsource	N/A	Details about the natural source for EM assemblies and assembly components.

Example:

_em_entity_assembly_naturalsource.cell	?
_em_entity_assembly_naturalsource.cellular_location	?
_em_entity_assembly_naturalsource.entity_assembly_id	1
_em_entity_assembly_naturalsource.id	2
_em_entity_assembly_naturalsource.ncbi_tax_id	998086
_em_entity_assembly_naturalsource.organism	'Pseudomonas phage PhiPA3'
_em_entity_assembly_naturalsource.organelle	?
_em_entity_assembly_naturalsource.organ	?
_em_entity_assembly_naturalsource.strain	?
_em_entity_assembly_naturalsource.tissue	?

PDBx/mmCIF category	Legacy PDB format records	Description
_em_entity_assembly_recombinant	N/A	Details about the recombinant expression of the assembly or assembly component.

Example:

_em_entity_assembly_recombinant.cell	?
_em_entity_assembly_recombinant.entity_assembly_id	1
_em_entity_assembly_recombinant.id	2
_em_entity_assembly_recombinant.ncbi_tax_id	562
_em_entity_assembly_recombinant.organism	'Escherichia coli'
_em_entity_assembly_recombinant.plasmid	?
_em_entity_assembly_recombinant.strain	'BL21 Star (DE3)pLysS'

---

EM Experiment

PDBx/mmCIF category	Legacy PDB format records	Description
_em_experiment	REMARK 245	High-level classification of the EM experiment.

Example:

_em_experiment.entry_id	8FNE
_em_experiment.id	1
_em_experiment.reconstruction_method	'SINGLE PARTICLE'
_em_experiment.aggregation_state	'2D ARRAY'
_em_experiment.entity_assembly_id	1

---

Sample preparation

PDBx/mmCIF category	Legacy PDB format records	Description
_em_specimen	REMARK 245	Details about specimens prepared for imaging by electron microscopy.

Example:

_em_specimen.concentration	?
_em_specimen.details	?
_em_specimen.embedding_applied	NO
_em_specimen.experiment_id	1
_em_specimen.id	1
_em_specimen.shadowing_applied	NO
_em_specimen.staining_applied	NO
_em_specimen.vitrification_applied	YES

PDBx/mmCIF category	Legacy PDB format records	Description
_em_buffer	REMARK 245	Details of the sample buffer.

Example:

_em_buffer.id	1
_em_buffer.specimen_id	1
_em_buffer.name	?
_em_buffer.details	'0.25 complete Protease Inhibitor Tablet also included'
_em_buffer.pH	6.5

PDBx/mmCIF category	Legacy PDB format records	Description
_em_buffer_component	N/A	Details of the sample buffer components.

Example:

loop_
_em_buffer_component.buffer_id
_em_buffer_component.concentration
_em_buffer_component.concentration_units
_em_buffer_component.formula
_em_buffer_component.id
_em_buffer_component.name
1	20	mM	?	1	BisTrisPropane
1	150	mM	?	2	'Sodium Chloride'
1	1	mM	?	3	DTT
1	1	mM	?	4	EDTA
1	2	mM	?	5	'Magnesium Chloride'
1	1	mM	?	6	ATP

PDBx/mmCIF category	Legacy PDB format records	Description
_em_staining	N/A	Details about the staining procedure used in the specimen preparation.

Example:

_em_staining.id	1
_em_staining.specimen_id	1
_em_staining.material	'Uranyl Acetate'
_em_staining.type	NEGATIVE
_em_staining.details	'Negatively stained EM specimens were prepared using a carbon-sandwich technique and uranyl-acetate stain.'

PDBx/mmCIF category	Legacy PDB format records	Description
_em_embedding	N/A	Details about the embedding procedure used in the specimen preparation.

Example:

_em_embedding.details	'3% trehalose'
_em_embedding.id	1
_em_embedding.material	trehalose
_em_embedding.specimen_id	1

PDBx/mmCIF category	Legacy PDB format records	Description
_em_shadowing	N/A	Details about the shadowing of an EM specimen.

Example:

_em_shadowing.id	1
_em_shadowing.specimen_id	1
_em_shadowing.angle	45
_em_shadowing.thickness	3
_em_shadowing.material	Platinum
_em_shadowing.details	'shadowing was used to create a platinum replica'

PDBx/mmCIF category	Legacy PDB format records	Description
_em_sample_support	REMARK 245	Details of the electron microscope grid type, grid support film and pretreatment of the whole before sample is applied.

Example:

_em_sample_support.id	1
_em_sample_support.film_material	'HOLEY CARBON'
_em_sample_support.grid_material	COPPER
_em_sample_support.grid_mesh_size	400
_em_sample_support.details	'GLOW DISCHARGED 120 seconds'

PDBx/mmCIF category	Legacy PDB format records	Description
_em_support_film	N/A	Describes films supporting the specimen.

Example:

_em_support_film.id	1
_em_support_film.material	CARBON

PDBx/mmCIF category	Legacy PDB format records	Description
_em_grid_pretreatment	N/A	Describes glow discharge pretreatment for an EM grid.

Example:

_em_grid_pretreatment.id	1
_em_grid_pretreatment.sample_support_id	1
_em_grid_pretreatment.type	'GLOW DISCHARGE'
_em_grid_pretreatment.time	12

PDBx/mmCIF category	Legacy PDB format records	Description
_em_vitrification	REMARK 245	Details about the method and cryogen used in rapid freezing of the sample on the grid prior to its insertion in the electron microscope.

Example:

_em_vitrification.entry_id	8FNE
_em_vitrification.id	1
_em_vitrification.specimen_id	1
_em_vitrification.cryogen_name	ETHANE
_em_vitrification.humidity	100
_em_vitrification.temp	?
_em_vitrification.chamber_temperature	283.15
_em_vitrification.instrument	'FEI VITROBOT MARK IV'
_em_vitrification.method	?
_em_vitrification.time_resolved_state	?
_em_vitrification.citation_id	?
_em_vitrification.details	?

---

Imaging

PDBx/mmCIF category	Legacy PDB format records	Description
_em_imaging	REMARK 245	Details about the parameters used in imaging the sample in the electron microscope.

Example:

_em_imaging.entry_id	8FNE
_em_imaging.id	1
_em_imaging.microscope_model	'FEI TITAN KRIOS'
_em_imaging.specimen_holder_type	?
_em_imaging.specimen_holder_model	'FEI TITAN KRIOS AUTOGRID HOLDER'
_em_imaging.accelerating_voltage	300
_em_imaging.illumination_mode	'FLOOD BEAM'
_em_imaging.mode	'BRIGHT FIELD'
_em_imaging.nominal_cs	2.7
_em_imaging.nominal_defocus_min	800
_em_imaging.nominal_defocus_max	2500
_em_imaging.nominal_magnification	105000
_em_imaging.electron_source	'FIELD EMISSION GUN'
_em_imaging.specimen_id	1
_em_imaging.cryogen	NITROGEN

PDBx/mmCIF category	Legacy PDB format records	Description
_em_image_scans	REMARK 245	Details of the image scanning device (microdensitometer) and parameters for digitization of the image.

Example:

_em_image_scans.entry_id	1DYL
_em_image_scans.id	2
_em_image_scans.number_digital_images	48

PDBx/mmCIF category	Legacy PDB format records	Description
_em_tomography	N/A	Microscopy parameters only relevant for tomography.

Example:

_em_tomography.id	1
_em_tomography.imaging_id	1
_em_tomography.dual_tilt_axis_rotation	90.0
_em_tomography.axis1_angle_increment	2
_em_tomography.axis1_min_angle	-70.00
_em_tomography.axis1_max_angle	70.0
_em_tomography.axis2_angle_increment	2
_em_tomography.axis2_min_angle	-70.0
_em_tomography.axis2_max_angle	70.0

PDBx/mmCIF category	Legacy PDB format records	Description
_em_imaging_optics	N/A	Description of a few specialist optics apparatus.

Example:

_em_imaging_optics.id	1
_em_imaging_optics.imaging_id	1
_em_imaging_optics.chr_aberration_corrector	'CEOS manufactured Cc corrector'
_em_imaging_optics.energyfilter_lower	0
_em_imaging_optics.energyfilter_upper	15
_em_imaging_optics.energyfilter_name	FEI
_em_imaging_optics.phase_plate	?
_em_imaging_optics.sph_aberration_corrector	?

PDBx/mmCIF category	Legacy PDB format records	Description
_em_focused_ion_beam	N/A	Description of sectioning by focused_ion_beam.

Example:

No example available

PDBx/mmCIF category	Legacy PDB format records	Description
_em_image_recording	REMARK 245	Details of the image recording (either film/microdensitometer or electronic densitometer) and parameters for image digitization.

Example:

_em_image_recording.average_exposure_time	?
_em_image_recording.avg_electron_dose_per_subtomogram	?
_em_image_recording.avg_electron_dose_per_image	67
_em_image_recording.details	?
_em_image_recording.detector_mode	?
_em_image_recording.film_or_detector_model	'GATAN K3 BIOQUANTUM (6k x 4k)'
_em_image_recording.id	1
_em_image_recording.imaging_id	1
_em_image_recording.num_diffraction_images	?
_em_image_recording.num_grids_imaged	?
_em_image_recording.num_real_images	?

---

Reconstruction

PDBx/mmCIF category	Legacy PDB format records	Description
_em_3d_reconstruction	REMARK 3 REMARK 245	Details of the 3D reconstruction procedure from 2D projections.

Example:

_em_3d_reconstruction.entry_id	8FNE
_em_3d_reconstruction.id	1
_em_3d_reconstruction.method	?
_em_3d_reconstruction.algorithm	?
_em_3d_reconstruction.citation_id	?
_em_3d_reconstruction.details	?
_em_3d_reconstruction.resolution	3.9
_em_3d_reconstruction.resolution_method	'FSC 0.143 CUT-OFF'
_em_3d_reconstruction.magnification_calibration	?
_em_3d_reconstruction.nominal_pixel_size	?
_em_3d_reconstruction.actual_pixel_size	?
_em_3d_reconstruction.num_particles	29303
_em_3d_reconstruction.euler_angles_details	?
_em_3d_reconstruction.num_class_averages	?
_em_3d_reconstruction.refinement_type	?
_em_3d_reconstruction.image_processing_id	1
_em_3d_reconstruction.symmetry_type	POINT

PDBx/mmCIF category	Legacy PDB format records	Description
_em_particle_selection	N/A	Details of images from scanned micrographs and the number of particles selected from a scanned set of micrographs.

Example:

_em_particle_selection.id	1
_em_particle_selection.image_processing_id	1
_em_particle_selection.num_particles_selected	5267
_em_particle_selection.method	'INTERACTIVE'
_em_particle_selection.details	?

PDBx/mmCIF category	Legacy PDB format records	Description
_em_image_processing	N/A	Details of the EM image processing procedure.

Example:

_em_image_processing.id	1
_em_image_processing.image_recording_id	1
_em_image_processing.details	'The selected images were high-pass filtered and normalized'

PDBx/mmCIF category	Legacy PDB format records	Description
_em_ctf_correction	N/A	Description of the Contrast Transfer Function (CTF) correction.

Example:

_em_ctf_correction.details	?
_em_ctf_correction.id	1
_em_ctf_correction.em_image_processing_id	1
_em_ctf_correction.type	'PHASE FLIPPING ONLY'

---

Symmetry

PDBx/mmCIF category	Legacy PDB format records	Description
_em_helical_entity	N/A	Details for a helical or filament type of assembly component.

Example:

_em_helical_entity.id	1
_em_helical_entity.image_processing_id	1
_em_helical_entity.details	?
_em_helical_entity.axial_symmetry	C2
_em_helical_entity.angular_rotation_per_subunit	-0.782
_em_helical_entity.axial_rise_per_subunit	4.763

PDBx/mmCIF category	Legacy PDB format records	Description
_pdbx_helical_symmetry	N/A	Details about the helical symmetry group associated with this entry.

Example:

_pdbx_helical_symmetry.entry_id	'1ABC'
_pdbx_helical_symmetry.number_of_operations	35
_pdbx_helical_symmetry.rotation_per_n_subunits	131.84
_pdbx_helical_symmetry.rise_per_n_subunits	6.10
_pdbx_helical_symmetry.n_subunits_divisor	1
_pdbx_helical_symmetry.dyad_axis	no
_pdbx_helical_symmetry.circular_symmetry	1

PDBx/mmCIF category	Legacy PDB format records	Description
_em_single_particle_entity	N/A	Details of the enforced symmetry for a single particle entity type.

Example:

_em_single_particle_entity.entry_id	8GA0
_em_single_particle_entity.id	1
_em_single_particle_entity.image_processing_id	1
_em_single_particle_entity.point_symmetry	C1

---

Fitting

PDBx/mmCIF category	Legacy PDB format records	Description
_em_3d_fitting	REMARK 3	Details of the method of fitting atomic coordinates from a coordinate file into a 3d-em volume map file.

Example:

_em_3d_fitting.id	1
_em_3d_fitting.entry_id	8FNE
_em_3d_fitting.method	?
_em_3d_fitting.target_criteria	?
_em_3d_fitting.details	'The initial model was generated using AlphaFold based on sequence alone.'
_em_3d_fitting.overall_b_value	?
_em_3d_fitting.ref_space	?
_em_3d_fitting.ref_protocol	'FLEXIBLE FIT'

PDBx/mmCIF category	Legacy PDB format records	Description
_em_3d_fitting_list	N/A	Details of the initial model used in fitting.

Example:

_em_3d_fitting_list.id	1
_em_3d_fitting_list.3d_fitting_id	1
_em_3d_fitting_list.pdb_entry_id	?
_em_3d_fitting_list.pdb_chain_id	?
_em_3d_fitting_list.pdb_chain_residue_range	?
_em_3d_fitting_list.details	?
_em_3d_fitting_list.chain_id	?
_em_3d_fitting_list.chain_residue_range	?
_em_3d_fitting_list.source_name	AlphaFold
_em_3d_fitting_list.type	'in silico model'
_em_3d_fitting_list.accession_code	?

---

Software

PDBx/mmCIF category	Legacy PDB format records	Description
_em_software	REMARK 3	Details of the software that was used for data collection, data processing, data analysis, structure calculations and refinement.

Example:

loop_
_em_software.category
_em_software.details
_em_software.id
_em_software.image_processing_id
_em_software.fitting_id
_em_software.imaging_id
_em_software.name
_em_software.version
'PARTICLE SELECTION'	?	1	1	?	?	cryoSPARC	v2.15.0
'PARTICLE SELECTION'	?	2	1	?	?	cryoSPARC	v3.3.1
'PARTICLE SELECTION'	?	3	1	?	?	?	?
'IMAGE ACQUISITION'	?	4	?	?	1	SerialEM	v.3.6-v.3.8
MASKING	?	5	?	?	?	?	?
'CTF CORRECTION'	?	6	1	?	?	?	?
'LAYERLINE INDEXING'	?	7	1	?	?	?	?
'DIFFRACTION INDEXING'	?	8	1	?	?	?	?
'MODEL FITTING'	RosettaRelax	9	?	1	?	Rosetta	?
'MODEL FITTING'	?	10	?	1	?	'UCSF ChimeraX'	?
'MODEL FITTING'	?	11	?	1	?	'UCSF Chimera'	?
OTHER	?	12	?	?	?	?	?
'IMAGE ACQUISITION'	?	13	?	?	?	?	?
'MODEL REFINEMENT'	RosettaRefine	14	?	1	?	Rosetta	?
'MODEL REFINEMENT'	?	15	?	1	?	ISOLDE	1.2.1
'INITIAL EULER ASSIGNMENT'	'Ab-Initio Reconstruction'	16	1	?	?	cryoSPARC	v2.15.0
'INITIAL EULER ASSIGNMENT'	?	17	1	?	?	?	?
'FINAL EULER ASSIGNMENT'	?	18	1	?	?	cisTEM	1.0.0-beta
'FINAL EULER ASSIGNMENT'	?	19	1	?	?	?	?
CLASSIFICATION	?	20	1	?	?	cisTEM	1.0.0-beta
CLASSIFICATION	?	21	1	?	?	?	?
RECONSTRUCTION	?	22	1	?	?	?	?

Ensemble Description

PDBx/mmCIF category	Legacy PDB format records	Description
_pdbx_nmr_ensemble	REMARK 210	Describes the ensemble of deposited structures.

Example:

_pdbx_nmr_ensemble.entry_id	8COO
_pdbx_nmr_ensemble.conformers_calculated_total_number	40
_pdbx_nmr_ensemble.conformers_submitted_total_number	20
_pdbx_nmr_ensemble.conformer_selection_criteria	'structures with the lowest energy'
_pdbx_nmr_ensemble.representative_conformer	?
_pdbx_nmr_ensemble.average_constraints_per_residue	?
_pdbx_nmr_ensemble.average_constraint_violations_per_residue	?
_pdbx_nmr_ensemble.maximum_distance_constraint_violation	?
_pdbx_nmr_ensemble.average_distance_constraint_violation	?
_pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation	?
_pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation	?
_pdbx_nmr_ensemble.distance_constraint_violation_method	?
_pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation	?
_pdbx_nmr_ensemble.average_torsion_angle_constraint_violation	?
_pdbx_nmr_ensemble.torsion_angle_constraint_violation_method	?

PDBx/mmCIF category	Legacy PDB format records	Description
_pdbx_nmr_representative	REMARK 210	Describes selection of the representative structure.

Example:

_pdbx_nmr_representative.entry_id	8COO
_pdbx_nmr_representative.conformer_id	1
_pdbx_nmr_representative.selection_criteria	'lowest energy'

---

Sample Preparation

PDBx/mmCIF category	Legacy PDB format records	Description
_pdbx_nmr_sample_details	REMARK 210	Complete description of each NMR sample, including the solvent system used.

Example:

_pdbx_nmr_sample_details.solution_id	1
_pdbx_nme_sample_details.contents	'300 uM [U-100% 13C; U-100% 15N] sample 1, 95% H2O/5% D2O'
_pdbx_nmr_sample_details.solvent_system	'95% H2O/5% D2O'
_pdbx_nmr_sample_details.label	13C15N_sample
_pdbx_nmr_sample_details.type	solution
_pdbx_nmr_sample_details.details	?

PDBx/mmCIF category	Legacy PDB format records	Description
_pdbx_nmr_exptl_sample	N/A	The chemical constituents of each NMR sample. Each sample is identified by a number and each component in the sample is identified by name.

Example:

_pdbx_nmr_exptl_sample.solution_id	1
_pdbx_nmr_exptl_sample.component	'sample 1'
_pdbx_nmr_exptl_sample.concentration	300
_pdbx_nmr_exptl_sample.concentration_range	?
_pdbx_nmr_exptl_sample.concentration_units	uM
_pdbx_nmr_exptl_sample.isotopic_labeling	'[U-100% 13C; U-100% 15N]'

PDBx/mmCIF category	Legacy PDB format records	Description
_pdbx_nmr_exptl_sample_conditions	REMARK 210	The experimental conditions used for each sample. Each set of conditions is identified by a numerical code.

Example:

_pdbx_nmr_exptl_sample_conditions.conditions_id	1
_pdbx_nmr_exptl_sample_conditions.temperature	310
_pdbx_nmr_exptl_sample_conditions.pressure_units	atm
_pdbx_nmr_exptl_sample_conditions.pressure	ambient
_pdbx_nmr_exptl_sample_conditions.pH	6.5
_pdbx_nmr_exptl_sample_conditions.ionic_strength	0.02
_pdbx_nmr_exptl_sample_conditions.details	'0.3 mM [U-100% 13C; U-100% 15N]'
_pdbx_nmr_exptl_sample_conditions.ionic_strength_err	?
_pdbx_nmr_exptl_sample_conditions.ionic_strength_units	'Not defined'
_pdbx_nmr_exptl_sample_conditions.label	13C15N_sample
_pdbx_nmr_exptl_sample_conditions.pH_err	?
_pdbx_nmr_exptl_sample_conditions.pH_units	pH
_pdbx_nmr_exptl_sample_conditions.pressure_err	?
_pdbx_nmr_exptl_sample_conditions.temperature_err	?
_pdbx_nmr_exptl_sample_conditions.temperature_units	K

---

Data Collection

PDBx/mmCIF category	Legacy PDB format records	Description
_pdbx_nmr_spectrometer	REMARK 210	Details about each spectrometer used to collect data for this deposition.

Example:

loop_
_pdbx_nmr_spectrometer.spectrometer_id
_pdbx_nmr_spectrometer.model
_pdbx_nmr_spectrometer.type
_pdbx_nmr_spectrometer.manufacturer
_pdbx_nmr_spectrometer.field_strength
_pdbx_nmr_spectrometer.details
1	'AVANCE III'	?	Bruker	600	?
2	'AVANCE III'	?	Bruker	850	?

PDBx/mmCIF category	Legacy PDB format records	Description
_pdbx_nmr_exptl	REMARK 210	Information on the experiments that were used to generate constraint data.

Example:

loop_
_pdbx_nmr_exptl.experiment_id
_pdbx_nmr_exptl.conditions_id
_pdbx_nmr_exptl.solution_id
_pdbx_nmr_exptl.type
_pdbx_nmr_exptl.spectrometer_id
_pdbx_nmr_exptl.sample_state
1	1	1	'2D 1H-15N HSQC'	1	isotropic
2	1	1	'2D 1H-13C HSQC'	1	isotropic
3	1	1	'3D 1H-13C NOESY aliphatic'	1	isotropic
4	1	1	'3D 1H-15N NOESY'	1	isotropic
5	1	1	'2D 1H-1H NOESY'	2	isotropic
6	1	1	'2D 1H-1H NOESY'	3	isotropic

---

Refinement

PDBx/mmCIF category	Legacy PDB format records	Description
_pdbx_nmr_refine	REMARK 210	Method and details of the refinement of the deposited structure.

Example:

_pdbx_nmr_refine.entry_id	8COO
_pdbx_nmr_refine.method	'torsion angle dynamics'
_pdbx_nmr_refine.details	?
_pdbx_nmr_refine.software_ordinal	1

---

Software

PDBx/mmCIF category	Legacy PDB format records	Description
_pdbx_nmr_software	REMARK 3 REMARK 210	Description of the software that was used for data collection, data processing, data analysis, structure calculations and refinement.

Example:

loop_
_pdbx_nmr_software.ordinal
_pdbx_nmr_software.classification
_pdbx_nmr_software.name
_pdbx_nmr_software.version
_pdbx_nmr_software.authors
1	refinement	ARIA	?
;Linge, O'Donoghue and Nilges
;
2	'structure calculation'	ARIA	?
;Linge, O'Donoghue and Nilges
;
3	'chemical shift assignment'	XEASY	?	'Bartels et al.'
4	'peak picking'	XEASY	?	'Bartels et al.'

PDBx/mmCIF category	Legacy PDB format records	Description
_pdbx_struct_assembly	REMARK 350	Details about the structural elements that form macromolecular assemblies.

Example:

_pdbx_struct_assembly.id	1
_pdbx_struct_assembly.details	author_and_software_defined_assembly
_pdbx_struct_assembly.method_details	PISA
_pdbx_struct_assembly.oligomeric_details	dimeric
_pdbx_struct_assembly.oligomeric_count	2

PDBx/mmCIF category	Legacy PDB format records	Description
_pdbx_struct_assembly_gen	REMARK 350	Details about the generation of each macromolecular assembly.

Notes:

• _pdbx_struct_assembly_gen.asym_id_list lists the ASYM_IDs (a unique identifier of each molecule in the model) of all components forming the assembly including ligands excluding water molecules.
• Ligands are included in the _pdbx_struct_assembly_gen.asym_id_list.

Example:

_pdbx_struct_assembly_gen.assembly_id	1
_pdbx_struct_assembly_gen.oper_expression	1,2
_pdbx_struct_assembly_gen.asym_id_list	A,B,C,D

PDBx/mmCIF category	Legacy PDB format records	Description
_pdbx_struct_assembly_prop	REMARK 350	Details about the calculated total surface area, buried surface area and free energy gain for an assembly.

Example:

loop_
_pdbx_struct_assembly_prop.biol_id
_pdbx_struct_assembly_prop.type
_pdbx_struct_assembly_prop.value
_pdbx_struct_assembly_prop.details
1	'ABSA (A^2)'	3090	?
1	MORE	-33	?
1	'SSA (A^2)'	25780	?

PDBx/mmCIF category	Legacy PDB format records	Description
_pdbx_struct_oper_list	REMARK 350	Details about the symmetry operations and Cartesian rotation and translation matrices required to transform the coordinates deposited with the entry to generate the biological assembly.

Example:

loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[3]
1	'identity operation'	1_555	x,y,z	1.0000000000	0.0000000000	0.0000000000	0.0000000000	0.0000000000	1.0000000000	0.0000000000	0.0000000000	0.0000000000	0.0000000000	1.0000000000	0.0000000000
2	'crystal symmetry operation'	2_555	-x,-y,-z	-1.0000000000	0.0000000000	0.0000000000	0.0000000000	0.0000000000	1.0000000000	0.0000000000	0.0000000000	0.0000000000	0.0000000000	-1.0000000000	0.0000000000

PDBx/mmCIF category	Legacy PDB format records	Description
_struct_conf_type	HELIX	Type of the conformation of the backbone of the polymer.

Example:

_struct_conf_type.id

HELX_P

PDBx/mmCIF category	Legacy PDB format records	Description
_struct_conf	HELIX	Details about the backbone conformation of a segment of polymer.

Example:

loop_

_struct_conf.conf_type_id

_struct_conf.id

_struct_conf.pdbx_PDB_helix_id

_struct_conf.beg_label_comp_id

_struct_conf.beg_label_asym_id

_struct_conf.beg_label_seq_id

_struct_conf.pdbx_beg_PDB_ins_code

_struct_conf.end_label_comp_id

_struct_conf.end_label_asym_id

_struct_conf.end_label_seq_id

_struct_conf.pdbx_end_PDB_ins_code

_struct_conf.beg_auth_comp_id

_struct_conf.beg_auth_asym_id

_struct_conf.beg_auth_seq_id

_struct_conf.end_auth_comp_id

_struct_conf.end_auth_asym_id

_struct_conf.end_auth_seq_id

_struct_conf.pdbx_PDB_helix_class

_struct_conf.details

_struct_conf.pdbx_PDB_helix_length

HELX_P

HELX_P1

AA1

SER

A

10

?

GLY

A

15

?

SER

A

10

GLY

A

15

1

?

6

HELX_P

HELX_P2

AA2

HIS

A

41

?

CYS

A

44

?

HIS

A

41

CYS

A

44

5

?

4

HELX_P

HELX_P3

AA3

GLU

A

47

?

ASN

A

51

?

GLU

A

47

ASN

A

51

5

?

5

HELX_P

HELX_P4

AA4

ASN

A

53

?

ARG

A

60

?

ASN

A

53

ARG

A

60

1

?

8

HELX_P

HELX_P5

AA5

LYS

A

61

?

HIS

A

64

?

LYS

A

61

HIS

A

64

5

?

4

HELX_P

HELX_P6

AA6

ILE

A

200

?

ASN

A

214

?

ILE

A

200

ASN

A

214

1

?

15

HELX_P

HELX_P7

AA7

THR

A

226

?

TYR

A

237

?

THR

A

226

TYR

A

237

1

?

12

HELX_P

HELX_P8

AA8

THR

A

243

?

LEU

A

250

?

THR

A

243

LEU

A

250

1

?

8

HELX_P

HELX_P9

AA9

LEU

A

250

?

GLY

A

258

?

LEU

A

250

GLY

A

258

1

?

9

HELX_P

HELX_P10

AB1

ALA

A

260

?

GLY

A

275

?

ALA

A

260

GLY

A

275

1

?

16

HELX_P

HELX_P11

AB2

THR

A

292

?

SER

A

301

?

THR

A

292

SER

A

301

1

?

10

PDBx/mmCIF category	Legacy PDB format records	Description
_struct_sheet	SHEET	Details about the beta sheets.

Example:

loop_
_struct_sheet.id
_struct_sheet.type
_struct_sheet.number_strands
_struct_sheet.details
AA1	?	7	?
AA2	?	5	?
AA3	?	3	?

PDBx/mmCIF category	Legacy PDB format records	Description
_struct_sheet_order	SHEET	Details about the order of the residue ranges that form a beta-sheet. All order links are pairwise and the specified pairs are assumed to be adjacent to one another in the sheet.

Example:

loop_
_struct_sheet_order.sheet_id
_struct_sheet_order.range_id_1
_struct_sheet_order.range_id_2
_struct_sheet_order.offset
_struct_sheet_order.sense
AA1	1	2	?	anti-parallel
AA1	2	3	?	anti-parallel
AA1	3	4	?	anti-parallel
AA1	4	5	?	anti-parallel
AA1	5	6	?	anti-parallel
AA1	6	7	?	anti-parallel
AA2	1	2	?	parallel
AA2	2	3	?	anti-parallel
AA2	3	4	?	anti-parallel
AA2	4	5	?	anti-parallel
AA3	1	2	?	parallel
AA3	2	3	?	anti-parallel

PDBx/mmCIF category	Legacy PDB format records	Description
_struct_sheet_range	SHEET	Details about the residue ranges that form a beta-sheet. Residues are included in a range if they make beta-sheet-type hydrogen-bonding interactions with at least one adjacent strand and if there are at least two residues in the range.

Example:

loop_

_struct_sheet_range.sheet_id

_struct_sheet_range.id

_struct_sheet_range.beg_label_comp_id

_struct_sheet_range.beg_label_asym_id

_struct_sheet_range.beg_label_seq_id

_struct_sheet_range.pdbx_beg_PDB_ins_code

_struct_sheet_range.end_label_comp_id

_struct_sheet_range.end_label_asym_id

_struct_sheet_range.end_label_seq_id

_struct_sheet_range.pdbx_end_PDB_ins_code

_struct_sheet_range.beg_auth_comp_id

_struct_sheet_range.beg_auth_asym_id

_struct_sheet_range.beg_auth_seq_id

_struct_sheet_range.end_auth_comp_id

_struct_sheet_range.end_auth_asym_id

_struct_sheet_range.end_auth_seq_id

AA1

1

VAL

A

73

?

LEU

A

75

?

VAL

A

73

LEU

A

75

AA1

2

PHE

A

66

?

ALA

A

70

?

PHE

A

66

ALA

A

70

AA1

3

MET

A

17

?

CYS

A

22

?

MET

A

17

CYS

A

22

AA1

4

THR

A

25

?

LEU

A

32

?

THR

A

25

LEU

A

32

AA1

5

VAL

A

35

?

PRO

A

39

?

VAL

A

35

PRO

A

39

AA1

6

VAL

A

86

?

VAL

A

91

?

VAL

A

86

VAL

A

91

AA1

7

VAL

A

77

?

GLN

A

83

?

VAL

A

77

GLN

A

83

AA2

1

LYS

A

100

?

PHE

A

103

?

LYS

A

100

PHE

A

103

AA2

2

CYS

A

156

?

GLU

A

166

?

CYS

A

156

GLU

A

166

AA2

3

VAL

A

148

?

ASP

A

153

?

VAL

A

148

ASP

A

153

AA2

4

THR

A

111

?

TYR

A

118

?

THR

A

111

TYR

A

118

AA2

5

SER

A

121

?

ALA

A

129

?

SER

A

121

ALA

A

129

AA3

1

LYS

A

100

?

PHE

A

103

?

LYS

A

100

PHE

A

103

AA3

2

CYS

A

156

?

GLU

A

166

?

CYS

A

156

GLU

A

166

AA3

3

HIS

A

172

?

THR

A

175

?

HIS

A

172

THR

A

175

PDBx/mmCIF category	Legacy PDB format records	Description
_pdbx_struct_sheet_hbond	SHEET	Details about the hydrogen bonding between residue ranges in a beta sheet.

Example:

loop_

_pdbx_struct_sheet_hbond.sheet_id

_pdbx_struct_sheet_hbond.range_id_1

_pdbx_struct_sheet_hbond.range_id_2

_pdbx_struct_sheet_hbond.range_1_label_atom_id

_pdbx_struct_sheet_hbond.range_1_label_comp_id

_pdbx_struct_sheet_hbond.range_1_label_asym_id

_pdbx_struct_sheet_hbond.range_1_label_seq_id

_pdbx_struct_sheet_hbond.range_1_PDB_ins_code

_pdbx_struct_sheet_hbond.range_1_auth_atom_id

_pdbx_struct_sheet_hbond.range_1_auth_comp_id

_pdbx_struct_sheet_hbond.range_1_auth_asym_id

_pdbx_struct_sheet_hbond.range_1_auth_seq_id

_pdbx_struct_sheet_hbond.range_2_label_atom_id

_pdbx_struct_sheet_hbond.range_2_label_comp_id

_pdbx_struct_sheet_hbond.range_2_label_asym_id

_pdbx_struct_sheet_hbond.range_2_label_seq_id

_pdbx_struct_sheet_hbond.range_2_PDB_ins_code

_pdbx_struct_sheet_hbond.range_2_auth_atom_id

_pdbx_struct_sheet_hbond.range_2_auth_comp_id

_pdbx_struct_sheet_hbond.range_2_auth_asym_id

_pdbx_struct_sheet_hbond.range_2_auth_seq_id

AA1

1

2

O

LEU

A

75

?

O

LEU

A

75

N

VAL

A

68

?

N

VAL

A

68

AA1

2

3

O

LEU

A

67

?

O

LEU

A

67

N

THR

A

21

?

N

THR

A

21

AA1

3

4

N

VAL

A

20

?

N

VAL

A

20

O

LEU

A

27

?

O

LEU

A

27

AA1

4

5

N

LEU

A

30

?

N

LEU

A

30

O

TYR

A

37

?

O

TYR

A

37

AA1

5

6

N

CYS

A

38

?

N

CYS

A

38

O

LEU

A

87

?

O

LEU

A

87

AA1

6

7

O

LYS

A

90

?

O

LYS

A

90

N

ILE

A

78

?

N

ILE

A

78

AA2

1

2

N

LYS

A

100

?

N

LYS

A

100

O

VAL

A

157

?

O

VAL

A

157

AA2

2

3

O

SER

A

158

?

O

SER

A

158

N

ASN

A

151

?

N

ASN

A

151

AA2

3

4

O

PHE

A

150

?

O

PHE

A

150

N

SER

A

113

?

N

SER

A

113

AA2

4

5

N

ALA

A

116

?

N

ALA

A

116

O

SER

A

123

?

O

SER

A

123

AA3

1

2

N

LYS

A

100

?

N

LYS

A

100

O

VAL

A

157

?

O

VAL

A

157

AA3

2

3

N

MET

A

165

?

N

MET

A

165

O

ALA

A

173

?

O

ALA

A

173