Recommended PDB -> mmCIF Data Item Correspondences

Recommended PDB -> mmCIF Data Item Correspondences

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Last Update: 31-Oct-2000

This document tabulates the correspondences between data items in the structured records of the PDB file format and data items defined in the mmCIF dictionary. The PDB records in the following list are linked to tables which provide the mmCIF data item correspondences. The mmCIF data items are linked to their corresponding dictionary definitions.

PDB Data Records

Title Records and Experimental Description

HEADER
OBSLTE
TITLE
CAVEAT
COMPND
SOURCE
KEYWDS
EXPDTA
AUTHOR
REVDAT
SPRSDE
JRNL
REMARK 3 - Refinement
REMARK 200 - Data Collection
REMARK 280 - Crystallization
Other REMARKs

Polymer Sequence Records

DBREF
SEQADV
SEQRES
MODRES

Heterogen Records

HET
HETNAM
HETSYN
FORMUL

Secondary Structure Records

HELIX
SHEET
TURN

Linkage Records

SSBOND
LINK
HYDBND
SLTBRG
CISPEP

Site Records

SITE

Crystallographic and Coordinate Transformation Records

CRYST1
ORIGX
SCALE
MTRIX
TVECT

Coordinate Records

MODEL
Records ATOM/HETATM/SIGATM
Records ANISOU/SIGUIJ
FTNOTE

Connectivity Records

CONECT

PDB record HEADER

Field Name	mmCIF Data Item
Section	n.a.
Classification	_struct_keywords.pdbx_keywords
Initial_Deposition_Date	_database_pdb_rev.date_original
ID CODE	_entry.id

PDB record OBSLTE

Field Name	mmCIF Data Item
Section	_pdbx_database_pdb_obs_spr.id
Continuation	n.a.
Date	_pdbx_database_pdb_obs_spr.date
ID_old	_pdbx_database_pdb_obs_spr.replace_pdb_id
ID_new	_pdbx_database_pdb_obs_spr.pdb_id

PDB record TITLE

Field Name	mmCIF Data Item
Section	n.a.
Continuation	n.a.
Title	_struct.title

PDB record CAVEAT

Field Name	mmCIF Data Item
Section	n.a.
Continuation	n.a.
PDB_ID	_database_pdb_caveat.id
Comment	_database_pdb_caveat.text

PDB record COMPND

Field Name	mmCIF Data Item
Section	n.a.
PDB_Continuation	n.a.
MOLECULE	_entity.pdbx_description
FRAGMENT	_entity_keywords.pdbx_fragment
EC	_entity_keywords.pdbx_ec
MUTATION	_entity_keywords.pdbx_mutation

PDB record SOURCE

Keyword Name	mmCIF Data Item
FRAGMENT	_entity_src_nat.pdbx_fragment
	_entity_src_gen.pdbx_gene_src_fragment	- or -
ORGANISM_SCIENTIFIC	_entity_src_nat.pdbx_organism_scientific
	_entity_src_gen.pdbx_gene_src_scientific_name	- or -
ORGANISM_COMMON	_entity_src_nat.common_name
	_entity_src_gen.gene_src_common_name	- or -
GENUS	_entity_src_nat.genus
	_entity_src_gen.gene_src_genus	- or -
SPECIES	_entity_src_nat.species
	_entity_src_gen.gene_src_species	- or -
STRAIN	_entity_src_nat.strain
	_entity_src_gen.gene_src_strain	- or -
VARIANT	_entity_src_nat.pdbx_variant
	_entity_src_gen.pdbx_gene_src_variant	- or -
CELL_LINE	_entity_src_nat.pdbx_cell_line
	_entity_src_gen.pdbx_gene_src_cell_line	- or -
ATCC	_entity_src_nat.pdbx_atcc
	_entity_src_gen.pdbx_gene_src_atcc	- or -
ORGAN	_entity_src_nat.pdbx_organ
	_entity_src_gen.pdbx_gene_src_organ	- or -
TISSUE	_entity_src_nat.tissue
	_entity_src_gen.gene_src_tissue	- or -
CELL	_entity_src_nat.pdbx_cell
	_entity_src_gen.pdbx_gene_src_cell	- or -
ORGANELLE	_entity_src_nat.pdbx_organelle
	_entity_src_gen.pdbx_gene_src_organelle	- or -
SECRETION	_entity_src_nat.pdbx_secretion
CELLULAR_LOCATION	_entity_src_nat.pdbx_cellular_location
	_entity_src_gen.pdbx_gene_src_cellular_location	- or -
PLASMID	_entity_src_nat.pdbx_plasmid_name
GENE	_entity_src_gen.pdbx_gene_src_gene
EXPRESSION_SYSTEM	_entity_src_gen.pdbx_host_org_scientific_name
EXPRESSION_SYSTEM_COMMON	_entity_src_gen.host_org_common_name
EXPRESSION_SYSTEM_GENUS	_entity_src_gen.host_org_genus
EXPRESSION_SYSTEM_SPECIES	_entity_src_gen.host_org_species
EXPRESSION_SYSTEM_STRAIN	_entity_src_gen.pdbx_host_org_strain
EXPRESSION_SYSTEM_VARIANT	_entity_src_gen.pdbx_host_org_variant
EXPRESSION_SYSTEM_CELL_LINE	_entity_src_gen.pdbx_host_org_cell_line
EXPRESSION_SYSTEM_ATCC_NUMBER	_entity_src_gen.pdbx_host_org_atcc
EXPRESSION_SYSTEM_ORGAN	_entity_src_gen.pdbx_host_org_organ
EXPRESSION_SYSTEM_TISSUE	_entity_src_gen.pdbx_host_org_tissue
EXPRESSION_SYSTEM_CELL	_entity_src_gen.pdbx_host_org_cell
EXPRESSION_SYSTEM_ORGANELLE	_entity_src_gen.pdbx_host_org_organelle
EXPRESSION_SYSTEM_CELLULAR_LOCATION	_entity_src_gen.pdbx_host_org_cellular_location
EXPRESSION_SYSTEM_VECTOR_TYPE	_entity_src_gen.pdbx_host_org_vector_type
EXPRESSION_SYSTEM_VECTOR	_entity_src_gen.pdbx_host_org_vector
EXPRESSION_SYSTEM_PLASMID	_entity_src_gen.plasmid_name
EXPRESSION_SYSTEM_GENE	_entity_src_gen.pdbx_host_org_gene
OTHER_DETAILS	_entity_src_nat.details	- or -
	_entity_src_gen.pdbx_description

PDB record KEYWDS

Field Name	mmCIF Data Item
Section	n.a.
Continuation	n.a.
Keywords_PDB	_struct_keywords.text

PDB record AUTHOR

Field Name	mmCIF Data Item
Section	n.a.
Continuation	n.a.
Author1	_audit_author.name

PDB record EXPDTA

Field Name	mmCIF Data Item
Section	n.a.
Continuation	n.a.
Experimental_Technique	_exptl.method

PDB record REVDAT

Field Name	mmCIF Data Item
Section	n.a.
Revision_Number	_database_pdb_rev.num
Continuation	n.a.
Revision_Date	_database_pdb_rev.date
Revision_ID	_database_pdb_rev.replaces
Revision_Type	_database_pdb_rev.mod_type
Revision_Records	_database_pdb_rev_record.type

PDB record SPRSDE

Field Name	mmCIF Data Item
Section	_pdbx_database_pdb_obs_spr.id
Continuation	n.a.
Date	_pdbx_database_pdb_obs_spr.date
ID_new	_pdbx_database_pdb_obs_spr.pdb_id
ID_old	_pdbx_database_pdb_obs_spr.replace_pdb_id

PDB record JRNL AND REMARK 1

Field Name	mmCIF Data Item
Section	_citation.id
AUTH	_citation_author.name
EDIT	_citation_editor.name
TITL	_citation.title
REF	_citation.journal_abbrev
REF VOLUME	_citation.journal_volume
REF PAGE	_citation.page_first
	_citation.page_last
YEAR	_citation.year
REFN ASTM	_citation.journal_id_ASTM
REFN ISSN	_citation.journal_id_ISSN
REFN ISBN	_citation.book_id_ISBN
REFN COUNTRY	_citation.country

PDB record REMARK 3

Remark Field Name	mmCIF Data Item
PROGRAM :	_computing.structure_refinement	- or -
	_software.name
AUTHOR :	_software.contact_author
DATA USED IN REFINEMENT.
RESOLUTION RANGE HIGH (ANGSTROMS) :	_refine.ls_d_res_high
RESOLUTION RANGE LOW (ANGSTROMS) :	_refine.ls_d_res_low
DATA CUTOFF (SIGMA(F)) :	_refine.pdbx_ls_sigma_F
DATA CUTOFF HIGH (ABS(F)) :	_refine.pdbx_data_cutoff_high_absF
DATA CUTOFF LOW (ABS(F)) :	_refine.pdbx_data_cutoff_low_absF
COMPLETENESS (WORKING+TEST) (%) :	_refine.ls_percent_reflns_obs
NUMBER OF REFLECTIONS :	_refine.ls_number_reflns_obs

FIT TO DATA USED IN REFINEMENT.
CROSS-VALIDATION METHOD :	_refine.pdbx_ls_cross_valid_method
FREE R VALUE TEST SET SELECTION :	_refine.pdbx_R_free_selection_details
R VALUE (WORKING SET) :	_refine.ls_R_factor_R_work
FREE R VALUE :	_refine.ls_R_factor_R_free
FREE R VALUE TEST SET SIZE (%) :	_refine.ls_percent_reflns_R_free
FREE R VALUE TEST SET COUNT :	_refine.ls_number_reflns_R_free
ESTIMATED ERROR OF FREE R VALUE :	_refine.ls_R_factor_R_free_error

FIT IN THE HIGHEST RESOLUTION BIN.
TOTAL NUMBER OF BINS USED :	_refine_ls_shell.pdbx_total_number_of_bins_used
BIN RESOLUTION RANGE HIGH (A) :	_refine_ls_shell.d_res_high
BIN RESOLUTION RANGE LOW (A) :	_refine_ls_shell.d_res_low
BIN COMPLETENESS (WORKING+TEST) (%) :	_refine_ls_shell.percent_reflns_obs
REFLECTIONS IN BIN (WORKING SET) :	_refine_ls_shell.number_reflns_R_work
BIN R VALUE (WORKING SET) :	_refine_ls_shell.R_factor_R_work
BIN FREE R VALUE :	_refine_ls_shell.R_factor_R_free
BIN FREE R VALUE TEST SET SIZE (%) :	_refine_ls_shell.percent_reflns_R_free
BIN FREE R VALUE TEST SET COUNT :	_refine_ls_shell.number_reflns_R_free
ESTIMATED ERROR OF BIN FREE R VALUE :	_refine_ls_shell.R_factor_R_free_error
NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
PROTEIN ATOMS :	_refine_hist.pdbx_number_atoms_protein
NUCLEIC ACID ATOMS :	_refine_hist.pdbx_number_atoms_nucleic_acid
HETEROGEN ATOMS :	_refine_hist.pdbx_number_atoms_ligand
SOLVENT ATOMS :	_refine_hist.number_atoms_solvent
B VALUES.
FROM WILSON PLOT (A**2) :	_reflns.B_iso_Wilson_estimate
MEAN B VALUE (OVERALL, A**2) :	_refine.B_iso_mean
OVERALL ANISOTROPIC B VALUE.
B11 (A**2) :	_refine.aniso_B[1][1]
B22 (A**2) :	_refine.aniso_B[2][2]
B33 (A**2) :	_refine.aniso_B[3][3]
B12 (A**2) :	_refine.aniso_B[1][2]
B13 (A**2) :	_refine.aniso_B[1][3]
B23 (A**2) :	_refine.aniso_B[2][3]

ESTIMATED COORDINATE ERROR.
ESD FROM LUZZATI PLOT (A) :	_refine_analyze.Luzzati_coordinate_error_obs
ESD FROM SIGMAA (A) :	_refine_analyze.Luzzati_sigma_a_obs
LOW RESOLUTION CUTOFF (A) :	_refine_analyze.Luzzati_d_res_low_obs
CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
ESD FROM C-V LUZZATI PLOT (A) :	_refine_analyze.Luzzati_coordinate_error_free
ESD FROM C-V SIGMAA (A) :	_refine_analyze.Luzzati_sigma_a_free

RMS DEVIATIONS FROM IDEAL VALUES.
BOND LENGTHS (A) :	_refine_ls_restr.dev_ideal
BOND ANGLES (DEGREES) :	_refine_ls_restr.dev_ideal
DIHEDRAL ANGLES (DEGREES) :	_refine_ls_restr.dev_ideal
IMPROPER ANGLES (DEGREES) :	_refine_ls_restr.dev_ideal

ISOTROPIC THERMAL MODEL :	_refine.pdbx_isotropic_thermal_model

ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
MAIN-CHAIN BOND (A**2) :	an instance of refine_ls_restr
MAIN-CHAIN ANGLE (A**2) :	an instance of refine_ls_restr
SIDE-CHAIN BOND (A**2) :	an instance of refine_ls_restr
SIDE-CHAIN ANGLE (A**2) :	an instance of refine_ls_restr

NCS MODEL :	_refine_ls_restr_ncs.ncs_model_details
NCS RESTRAINTS. RMS SIGMA/WEIGHT
GROUP POSITIONAL (A) :	an instance of refine_ls_restr_ncs
GROUP B-FACTOR (A**2) :	an instance of refine_ls_restr_ncs
OTHER REFINEMENT REMARKS:	_refine.details

PDB record REMARK 200

Remark Field Name	mmCIF Data Item
EXPERIMENTAL DETAILS
EXPERIMENT TYPE :	_exptl.method
DATE OF DATA COLLECTION :	_diffrn_detector.pdbx_collection_date
TEMPERATURE (KELVIN) :	_diffrn.ambient_temp
PH :	_exptl_crystal_grow.ph
NUMBER OF CRYSTALS USED :	_exptl.crystals_number

RADIATION SOURCE :	_diffrn_source.source
BEAMLINE :	_diffrn_source.pdbx_synchrotron_beamline
X-RAY GENERATOR MODEL :	_diffrn_source.type
WAVELENGTH OR RANGE (A) :	_diffrn_radiation.pdbx_wavelength_list
MONOCHROMATOR :	_diffrn_radiation.monochromator
OPTICS :	_diffrn_detector.details

DETECTOR TYPE :	_diffrn_detector.detector
DETECTOR MANUFACTURER :	_diffrn_detector.type
INTENSITY-INTEGRATION SOFTWARE :	_computing.data_collection
DATA SCALING SOFTWARE :	_computing.data_reduction

NUMBER OF UNIQUE REFLECTIONS :	_reflns.number_obs
RESOLUTION RANGE HIGH (A) :	_reflns.d_resolution_high
RESOLUTION RANGE LOW (A) :	_reflns.d_resolution_low
REJECTION CRITERIA (SIGMA(I)) :	_reflns.observed_criterion_sigma_I

OVERALL.
COMPLETENESS FOR RANGE (%) :	_reflns.percent_possible_obs
DATA REDUNDANCY :	_reflns.pdbx_redundancy
R MERGE (I) :	_reflns.pdbx_merge_I_obs
R SYM (I) :	_reflns.pdbx_Rsym_value
FOR THE DATA SET :	_reflns.pdbx_netI_over_av_sigmaI

IN THE HIGHEST RESOLUTION SHELL.
HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :	_reflns_shell.d_res_high
HIGHEST RESOLUTION SHELL, RANGE LOW (A) :	_reflns_shell.d_res_low
COMPLETENESS FOR SHELL (%) :	_reflns_shell.percent_possible_all
DATA REDUNDANCY IN SHELL :	_reflns_shell.pdbx_redundancy
R MERGE FOR SHELL (I) :	_reflns_shell.rmerge_I_obs
R SYM FOR SHELL (I) :	_reflns_shell.pdbx_Rsym_value
FOR SHELL :	_reflns_shell.meanI_over_sigI_obs

DIFFRACTION PROTOCOL:	_diffrn_radiation.pdbx_diffrn_protocol
METHOD USED TO DETERMINE THE STRUCTURE:	_refine.pdbx_method_to_determine_struct
SOFTWARE USED:	_computing.structure_solution	- or -
	_software.name
STARTING MODEL:	_refine.pdbx_starting_model

REMARK:	_exptl_crystal.description

PDB record REMARK 280

Remark Field Name	mmCIF Data Item
CRYSTAL
SOLVENT CONTENT, VS (%):	_exptl_crystal.density_percent_sol
MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA):	_exptl_crystal.density_matthews

CRYSTALLIZATION CONDITIONS:	Category EXPTL_CRYSTAL_GROW

Other PDB REMARKs

Field Name	mmCIF Data Item
Section	n.a.
Number	_database_PDB_remark.id
Comment	_database_PDB_remark.text

PDB record HET

The list of non-standard groups present in the entry is easily derived from information in category CHEM_COMP and by searching the coordinate records for the label information of each non-standard group.

PDB record HETNAM

Field Name	mmCIF Data Item
Section	n.a.
Continuation	n.a.
Het_Group_ID	_chem_comp.id
Chemical_Name	_chem_comp.name

PDB record HETSYN

Field Name	mmCIF Data Item
Section	n.a.
Continuation	n.a.
Het_Group_ID	_chem_comp.id
Synonyms	_chem_comp.pdbx_synonyms

PDB record FORMUL

Field Name	mmCIF Data Item
Section	n.a.
Formula_Component_No	_chem_comp.pdbx_component_no
Het_Group_ID	_chem_comp.id
Continuation	n.a.
Formula_MW	_chem_comp.formula_weight
Formula	_chem_comp.formula

PDB record DBREF

Field Name	mmCIF Data Item
Section	n.a.
PDB_ID_Code	_struct_ref_seq.pdbx_PDB_id_code
Strand_ID	_struct_ref_seq.pdbx_strand_id
Begin_Residue_Number	_struct_ref_seq.pdbx_auth_seq_align_beg
Begin_Ins_Code	_struct_ref_seq.pdbx_seq_align_beg_ins_code
End_Residue_Number	_struct_ref_seq.pdbx_auth_seq_align_end
End_Ins_Code	_struct_ref_seq.pdbx_seq_align_end_ins_code
Database	_struct_ref.db_name
Database_Accession_No	_struct_ref_seq.pdbx_db_accession
Database_ID_Code	_struct_ref.db_code
Database_Begin_Residue_Number	_struct_ref_seq.db_align_beg
Databaes_Begin_Ins_Code	_struct_ref_seq.pdbx_db_align_beg_ins_code
Database_End_Residue_Number	_struct_ref_seq.db_align_end
Databaes_End_Ins_Code	_struct_ref_seq.pdbx_db_align_end_ins_code

PDB record SEQADV

Field Name	mmCIF Data Item
Section	n.a.
PDB_ID_Code	_struct_ref_seq_dif.pdbx_pdb_id_code
PDB_Res_Name_In_Conflict	_struct_ref_seq_dif.mon_id
PDB_Strand_ID	_struct_ref_seq_dif.pdbx_pdb_strand_id
PDB_Residue_Number	_struct_ref_seq_dif.pdbx_auth_seq_num
PDB_Ins_Code	_struct_ref_seq_dif.pdbx_pdb_ins_code
Sequence_Database	_struct_ref_seq_dif.pdbx_seq_db_name
Seq_Database_Accession_No	_struct_ref_seq_dif.pdbx_seq_db_accession_code
Seq_Res_Name	_struct_ref_seq_dif.db_mon_id
Seq_Residue_Number	_struct_ref_seq_dif.pdbx_seq_db_seq_num
Conflict_Comment	_struct_ref_seq_dif.details

PDB record SEQRES

Field Name	mmCIF Data Item
Section	n.a.
Serial_No	n.a.
Strand_ID	PDB strand ID corresponding to _entity_poly_seq.entity_id	**
Strand_Length	derived
Residue_Names	_entity_poly_seq.mon_id
** Chemically distinct polymer strands are mapped to mmCIF entities. Two instances or the same polymer molecule in the PDB data file are mapped to a single mmCIF entity (eg. a homodimer). For convenience a table of monomer label correspondences is stored in category PDBX_POLY_SEQ_SCHEME

PDB record MODRES

The list of non-standard residues present in the entry is easily derived from information in category CHEM_COMP and by searching the coordinate records for the label information of each non-standard residue. If a residue is covalently modified and the modified residue is not labeled in the PDB file entry as with a non-standard 3-letter code, then the modification may be found by searching category STRUCT_CONN for the covalent linkage.

PDB record HELIX

Field Name	mmCIF Data Item
Section	_struct_conf.conf_type_id
Serial_No	_struct_conf.id
Helix_id	_struct_conf.pdbx_PDB_helix_id
Beg_res_name	_struct_conf.beg_auth_comp_id
Beg_Strand_ID	_struct_conf.beg_auth_asym_id
Beg_res_num	_struct_conf.beg_auth_seq_id
Beg_ins_code	_struct_conf.pdbx_beg_PDB_ins_code
End_res_name	_struct_conf.end_auth_comp_id
End_Strand_ID	_struct_conf.end_auth_asym_id
End_res_num	_struct_conf.end_auth_seq_id
End_ins_code	_struct_conf.pdbx_end_PDB_ins_code
Helix_class	_struct_conf.pdbx_PDB_helix_class
Details	_struct_conf.details
Length	_struct_conf.pdbx_PDB_helix_length

PDB record SHEET

Field Name	mmCIF Data Item
Section	n.a.
Range_id	_struct_sheet_range.id	**
Sheet_id	_struct_sheet.id
Number_of_strands	_struct_sheet.number_strands
Beg_res_name	_struct_sheet_range.beg_auth_comp_id
Beg_Strand_ID	_struct_sheet_range.beg_auth_asym_id
Beg_res_num	_struct_sheet_range.beg_auth_seq_id
Beg_ins_code	_struct_sheet_range.pdbx_beg_PDB_ins_code
End_res_name	_struct_sheet_range.end_auth_comp_id
End_Strand_ID	_struct_sheet_range.end_auth_asym_id
End_res_num	_struct_sheet_range.end_auth_seq_id
End_ins_code	_struct_sheet_range.pdbx_end_PDB_ins_code
Sense	_struct_sheet_order.sense
H_bond_cur_str_atom_id	_pdbx_struct_sheet_hbond.range_1_auth_atom_id
H_bond_cur_str_res_name	_pdbx_struct_sheet_hbond.range_1_auth_comp_id
H_bond_cur_str_Strand_ID	_pdbx_struct_sheet_hbond.range_1_auth_asym_id
H_bond_cur_str_res_num	_pdbx_struct_sheet_hbond.range_1_auth_seq_id
H_bond_cur_str_ins_code	_pdbx_struct_sheet_hbond.range_1_PDB_ins_code
H_bond_prev_str_atom_id	_pdbx_struct_sheet_hbond.range_2_auth_atom_id
H_bond_prev_str_res_name	_pdbx_struct_sheet_hbond.range_2_auth_comp_id
H_bond_prev_str_Strand_ID	_pdbx_struct_sheet_hbond.range_2_auth_asym_id
H_bond_prev_str_res_num	_pdbx_struct_sheet_hbond.range_2_auth_seq_id
H_bond_prev_str_ins_code	_pdbx_struct_sheet_hbond.range_2_PDB_ins_code
** Each sheet is mapped to mmCIF category STRUCT_SHEET and the range of residues within each contributing strand are enumerated in category STRUCT_SHEET_RANGE The PDB SHEET records specify a single hydrogen bond to register the strands within the sheet. mmCIF provides for the specification of the initial and terminal hydrogen bonds between a pair of strands. Because the registration hydrogen bond is often neither the initial nor terminal hydrogen bond, this information is stored in a separate exchange category PDBX_STRUCT_SHEET_HBOND . The standard mmCIF category STRUCT_SHEET_HBOND should be used when complete hydrogen bonding is availible.

PDB record TURN

Field Name	mmCIF Data Item
Serial_no	_struct_conf.id
Turn_id	_struct_conf.pdbx_PDB_helix_id
Beg_res_name	_struct_conf.beg_auth_comp_id
Beg_Strand_ID	_struct_conf.beg_auth_asym_id
Beg_res_num	_struct_conf.beg_auth_seq_id
Beg_ins_code	_struct_conf.pdbx_beg_PDB_ins_code
End_residue_name	_struct_conf.end_auth_comp_id
End_Strand_ID	_struct_conf.end_auth_asym_id
End_res_num	_struct_conf.end_auth_seq_id
End_ins_code	_struct_conf.pdbx_end_PDB_ins_code
Comment	_struct_conf.details

PDB record SSBOND

Field Name	mmCIF Data Item
Section	_struct_conn.conn_type_id
Serial_No	_struct_conn.id
NDB_Res_Name_CYS_1	_struct_conn.ptnr1_auth_comp_id
NDB_Strand_ID_CYS_1	_struct_conn.ptnr1_auth_asym_id
NDB_Res_No_CYS_1	_struct_conn.ptnr1_auth_seq_id
NDB_Ins_Code_CYS_1	_struct_conn.pdbx_ptnr1_PDB_ins_code
NDB_Res_Name_CYS_2	_struct_conn.ptnr2_auth_comp_id
NDB_Strand_ID_CYS_2	_struct_conn.ptnr2_auth_asym_id
NDB_Res_No_CYS_2	_struct_conn.ptnr2_auth_seq_id
NDB_Ins_Code_CYS_2	_struct_conn.pdbx_ptnr2_PDB_ins_code
Symmetry_Operator_1	_struct_conn.details
Symmetry_Operator_2	n.a.

PDB record LINK

Field Name	mmCIF Data Item
Section	_struct_conn.conn_type_id
Atom_Name_1	_struct_conn.ptnr1_auth_atom_id
Alt_Loc_1	_struct_conn.pdbx_ptnr1_auth_alt_id
Residue_Name_1	_struct_conn.ptnr1_auth_comp_id
Strand_ID_1	_struct_conn.ptnr1_auth_asym_id
Residue_Number_1	_struct_conn.ptnr1_auth_seq_id
Ins_Code_1	_struct_conn.pdbx_ptnr1_PDB_ins_code
Atom_Name_2	_struct_conn.ptnr2_auth_atom_id
Alt_Loc_2	_struct_conn.pdbx_ptnr2_auth_alt_id
Residue_Name_2	_struct_conn.ptnr2_auth_comp_id
Strand_ID_2	_struct_conn.ptnr2_auth_asym_id
Residue_Number_2	_struct_conn.ptnr2_auth_seq_id
Ins_Code_2	_struct_conn.pdbx_ptnr2_PDB_ins_code
Symmetry_Operator_1	_struct_conn.ptnr1_symmetry
Symmetry_Operator_2	_struct_conn.ptnr2_symmetry

PDB record HYDBND

Field Name	mmCIF Data Item
Section	_struct_conn.conn_type_id
Atom_Name_1	_struct_conn.ptnr1_auth_atom_id
Alt_Loc_1	_struct_conn.pdbx_ptnr1_auth_alt_id
Residue_Name_1	_struct_conn.ptnr1_auth_comp_id
Strand_ID_1	_struct_conn.ptnr1_auth_asym_id
Residue_Number_1	_struct_conn.ptnr1_auth_seq_id
Ins_Code_1	_struct_conn.pdbx_ptnr1_PDB_ins_code
Atom_Name_H	_struct_conn.pdbx_ptnr3_auth_atom_id
Alt_Loc_H	_struct_conn.pdbx_ptnr3_auth_alt_id
Strand_ID_H	_struct_conn.pdbx_ptnr3_auth_asym_id
Residue_Number_H	_struct_conn.pdbx_ptnr3_auth_seq_id
Ins_Code_H	_struct_conn.pdbx_ptnr3_PDB_ins_code
Atom_Name_2	_struct_conn.ptnr2_auth_atom_id
Alt_Loc_2	_struct_conn.pdbx_ptnr2_auth_alt_id
Residue_Name_2	_struct_conn.ptnr2_auth_comp_id
Strand_ID_2	_struct_conn.ptnr2_auth_asym_id
Residue_Number_2	_struct_conn.ptnr2_auth_seq_id
Ins_Code_2	_struct_conn.pdbx_ptnr2_PDB_ins_code
Symmetry_Operator_1	_struct_conn.ptnr1_symmetry
Symmetry_Operator_2	_struct_conn.ptnr2_symmetry

PDB record SLTBRG

Field Name	mmCIF Data Item
Section	_struct_conn.conn_type_id
Atom_Name_1	_struct_conn.ptnr1_auth_atom_id
Alt_Loc_1	_struct_conn.pdbx_ptnr1_auth_alt_id
Residue_Name_1	_struct_conn.ptnr1_auth_comp_id
Strand_ID_1	_struct_conn.ptnr1_auth_asym_id
Residue_Number_1	_struct_conn.ptnr1_auth_seq_id
Ins_Code_1	_struct_conn.pdbx_ptnr1_PDB_ins_code
Atom_Name_2	_struct_conn.ptnr2_auth_atom_id
Alt_Loc_2	_struct_conn.pdbx_ptnr2_auth_alt_id
Residue_Name_2	_struct_conn.ptnr2_auth_comp_id
Strand_ID_2	_struct_conn.ptnr2_auth_asym_id
Residue_Number_2	_struct_conn.ptnr2_auth_seq_id
Ins_Code_2	_struct_conn.pdbx_ptnr2_PDB_ins_code
Symmetry_Operator_1	_struct_conn.ptnr1_symmetry
Symmetry_Operator_2	_struct_conn.ptnr2_symmetry

PDB record CISPEP

Field Name	mmCIF Data Item
Section	n.a.
Serial_No	_struct_mon_prot_cis.pdbx_id
Residue_Name_1	_struct_mon_prot_cis.auth_comp_id
Strand_ID_1	_struct_mon_prot_cis.auth_asym_id
Sequence_Number_1	_struct_mon_prot_cis.auth_seq_id
Ins_Code_1	_struct_mon_prot_cis.pdbx_PDB_ins_code
Residue_Name_2	_struct_mon_prot_cis.pdbx_auth_comp_id_2
Strand_ID_2	_struct_mon_prot_cis.pdbx_auth_asym_id_2
Sequence_Number_2	_struct_mon_prot_cis.pdbx_auth_seq_id_2
Ins_Code_2	_struct_mon_prot_cis.pdbx_PDB_ins_code_2
Model_Num	_struct_mon_prot_cis.pdbx_PDB_model_num
Angle	_struct_mon_prot_cis.pdbx_omega_angle

PDB record SITE

Field Name	mmCIF Data Item
Section	n.a.
Serial_No	_struct_site_gen.id
Site_ID	_struct_site_gen.site_id
Residue_No	_struct_site_gen.pdbx_num_res
Residue_Name	_struct_site_gen.auth_comp_id
Strand_ID	_struct_site_gen.auth_asym_id
Seq_No	_struct_site_gen.auth_seq_id
Ins_Code	_struct_site_gen.pdbx_auth_ins_code

PDB record CRYST1

Field Name	mmCIF Data Item
Section	n.a.
a	_cell.length_a
b	_cell.length_b
c	_cell.length_c
Alpha	_cell.angle_alpha
Beta	_cell.angle_beta
Gamma	_cell.angle_gamma
Space_Group	_symmetry.space_group_name_h-m
Z	_cell.z_pdb

PDB record ORIGX

Field Name	mmCIF Data Item
Section	n.a.
O[N][1]	_database_pdb_matrix.origx[1][1]	- or -
	_database_pdb_matrix.origx[2][1]	- or -
	_database_pdb_matrix.origx[3][1]
O[N][2]	_database_pdb_matrix.origx[1][2]	- or -
	_database_pdb_matrix.origx[2][2]	- or -
	_database_pdb_matrix.origx[3][2]
O[N][3]	_database_pdb_matrix.origx[1][3]	- or -
	_database_pdb_matrix.origx[2][3]	- or -
	_database_pdb_matrix.origx[3][3]
T[N]	_database_pdb_matrix.origx_vector[1]	- or -
	_database_pdb_matrix.origx_vector[2]	- or -
	_database_pdb_matrix.origx_vector[3]

PDB record SCALE

Field Name	mmCIF Data Item
Section	n.a.
S[N][1]	_atom_sites.fract_transf_matrix[1][1]	- or -
	_atom_sites.fract_transf_matrix[2][1]	- or -
	_atom_sites.fract_transf_matrix[3][1]
S[N][2]	_atom_sites.fract_transf_matrix[1][2]	- or -
	_atom_sites.fract_transf_matrix[2][2]	- or -
	_atom_sites.fract_transf_matrix[3][2]
S[N][3]	_atom_sites.fract_transf_matrix[1][3]	- or -
	_atom_sites.fract_transf_matrix[2][3]	- or -
	_atom_sites.fract_transf_matrix[3][3]
U[N]	_atom_sites.fract_transf_vector[1]	- or -
	_atom_sites.fract_transf_vector[2]	- or -
	_atom_sites.fract_transf_vector[3]

PDB record MTRIX

Field Name	mmCIF Data Item
Section	n.a.
SerialNo	_struct_ncs_oper.id
M[N][1]	_struct_ncs_oper.matrix[1][1]	- or -
	_struct_ncs_oper.matrix[2][1]	- or -
	_struct_ncs_oper.matrix[3][1]
M[N][2]	_struct_ncs_oper.matrix[1][2]	- or -
	_struct_ncs_oper.matrix[2][2]	- or -
	_struct_ncs_oper.matrix[3][2]
M[N][3]	_struct_ncs_oper.matrix[1][3]	- or -
	_struct_ncs_oper.matrix[2][3]	- or -
	_struct_ncs_oper.matrix[3][3]
V[N]	_struct_ncs_oper.vector[1]	- or -
	_struct_ncs_oper.vector[2]	- or -
	_struct_ncs_oper.vector[3]
IGIVEN	_struct_ncs_oper.code

PDB record TVECT

Field Name	mmCIF Data Item
Section	n.a.
Serial_No	_database_pdb_tvect.id
T1	_database_pdb_tvect.vector[1]
T2	_database_pdb_tvect.vector[2]
T3	_database_pdb_tvect.vector[3]
Comment	_database_pdb_tvect.details

PDB record MODEL

Field Name	mmCIF Data Item
Section	n.a.
SerialNo	_atom_site.pdbx_PDB_model_num

PDB records ATOM/HETATM/SIGATM

Field Name	mmCIF Data Item
Section	_atom_site.group_pdb
Serial_No	_atom_site.id
Atom_Name	_atom_site.auth_atom_id
Alt_Loc	_atom_site.auth_alt_id
Residue_Name	_atom_site.auth_comp_id
Strand_ID	_atom_site.auth_asym_id
Residue_No	_atom_site.auth_seq_id	[1]
Ins_Code	_atom_site.pdbx_PDB_ins_code
X	_atom_site.cartn_x
Y	_atom_site.cartn_y
Z	_atom_site.cartn_z
Occupancy	_atom_site.occupancy
T_Factor	_atom_site.b_iso_or_equiv
Sigma_X	_atom_site.cartn_x_esd
Sigma_Y	_atom_site.cartn_y_esd
Sigma_Z	_atom_site.cartn_z_esd
Sigma_Occupancy	_atom_site.occupancy_esd
Sigma_T_Factor	_atom_site.b_iso_or_equiv_esd
[1] As recommended in the mmCIF definition _atom_site.auth_seq_id is the concatenation of the PDB residue number and insertion codes. The insertion code is maintained as separated local data item for convenience.

PDB records ANISOU/SIGUIJ

Field Name	mmCIF Data Item
Section	n.a.
Serial_No	_atom_site_anisotrop.id
Atom_Name	_atom_site_anisotrop.pdbx_auth_atom_id
Alt_Loc	_atom_site_anisotrop.pdbx_auth_alt_id
Residue_Name	_atom_site_anisotrop.pdbx_auth_comp_id
Strand_ID	_atom_site_anisotrop.pdbx_auth_asym_id
Residue_No	_atom_site_anisotrop.pdbx_auth_seq_id	[1]
Ins_Code	_atom_site_anisotrop.pdbx_PDB_ins_code
U11	_atom_site_anisotrop.u[1][1]
U22	_atom_site_anisotrop.u[1][2]
U33	_atom_site_anisotrop.u[1][3]
U12	_atom_site_anisotrop.u[2][2]
U13	_atom_site_anisotrop.u[2][3]
U23	_atom_site_anisotrop.u[3][3]
Sigma_U11	_atom_site_anisotrop.u[1][1]_esd
Sigma_U22	_atom_site_anisotrop.u[1][2]_esd
Sigma_U33	_atom_site_anisotrop.u[1][3]_esd
Sigma_U12	_atom_site_anisotrop.u[2][2]_esd
Sigma_U13	_atom_site_anisotrop.u[2][3]_esd
Sigma_U23	_atom_site_anisotrop.u[3][3]_esd
[1] _atom_site_anisotrop.pdbx_auth_seq_id is the concatenation of the PDB residue number and insertion codes. The insertion code is maintained as separated local data item for convenience.

PDB record FTNOTE

Field Name	mmCIF Data Item
Section	n.a.
Footnote_Number	_atom_sites_footnote.id
Footnote	_atom_sites_footnote.text

PDB record CONECT

Connectivity records are are derived from the mmCIF category CHEM_COMP, CHEM_COMP_ATOM, and CHEM_COMP_BOND.