data for structural and crystallization communications - example

Example: sample information

Example 2: heterodimer of two calcium-free isoforms of phospholipase A₂

Based in part on Jabeen, T., Sharma, S., Singh, N., Singh, R. K., Verma, A. K. Paramasivam, M., Srinivasana, A. & Singh, T. P. (2005). Structure of the zinc-induced heterodimer of two calcium-free isoforms of phospholipase A₂ from Naja naja sagittifera at 2.7 Å resolution. Acta Cryst. D61, 302-308 [1XXW].

In the example below, the items in gray are identifiers and qualifiers needed to preserve the mmCIF data structure (and auto-generated during the deposition procedure), or other data items stored in the same category in a PDB deposition, but not normally published in the journal. Note how the individual isoforms are tracked through the file by use of the _entity.id and related labels (e.g. _entity_poly_seq.entity_id).

Wherever possible, one should distinguish within a CIF between items that are unknown, denoted by a query character (?), and those that are not applicable, denoted by a full stop character (.). The example below tries to preserve this distinction, but PDB depositions may not always be able to provide this discrimination.

_entry.id                                 1XXW

_struct.title	'Heterodimer of isoforms of phospholipase A2 (PLA2) from cobra'

loop_
    _entity.id
    _entity.type
    _entity.src_method
    _entity.pdbx_description
    _entity.pdbx_formula_weight_exptl
    _entity.pdbx_formula_weight_exptl_meth
    _entity.pdbx_mutation
    _entity.pdbx_modification
    _entity.pdbx_number_of_molecules
    _entity.pdbx_ec
    1 polymer     nat 'phospholipase A2 isoform 1' 13224.76 ? . . 1   3.1.1.4
    2 polymer     nat 'phospholipase A2 isoform 2' 13292.76 ? . . 1   3.1.1.4
    3 non-polymer syn 'zinc ion'                   65.38    ? . . 1   ?
    4 non-polymer syn 'acetic acid'                60.05    ? . . 2   ?
    5 water       nat water                        18.025   ? . . 194 ?

_struct_biol.details
;       Protein is a heterodimer of the two PLA2 isoforms.  Isoforms are
	calcium-free.  One dimer in the asymmetric unit.  One of the
	monomers, isoform 1 or molecule A, binds two acetate ions, one
	on the surface and one in the active site.  The zinc ion bridges the
	two molecules of the heterodimer.
;

_struct_biol.pdbx_formula_weight	26703.1
_struct_biol.pdbx_formula_weight_method
                'calculated from sequences with both acetate and the zinc ions'


loop_
    _entity_poly.entity_id
    _entity_poly.type
    _entity_poly.pdbx_seq_one_letter_code
    _entity_poly.pdbx_seq_one_letter_code_can
1 polypeptide(L)
;
NTYQFKNMIQCTVPKRSWWDFADYGCYCGRGGSGTPIDDLDRCCQVHDNCYNSAREQGGCRPKQKTYSYECKAGTLSCSG
SNNSCAATVCDCDRLAAICFAGAPYNDNNYNIDLKARCQ
;
;
NTYQFKNMIQCTVPKRSWWDFADYGCYCGRGGSGTPIDDLDRCCQVHDNCYNSAREQGGCRPKQKTYSYECKAGTLSCSG
SNNSCAATVCDCDRLAAICFAGAPYNDNNYNIDLKARCQ
;

2 polypeptide(L)
;
NRWQFKNMISCTVPSRSWWDFADYGCYCGRGGSGTPVDDLDRCCQVHDNCYNEAEKISGCNPRFRTYSYECTAGTLTCTG
RNNACAASVCDCDRLAAICFAGAPYNDNNYNIDLQARCN
;
;
NRWQFKNMISCTVPSRSWWDFADYGCYCGRGGSGTPVDDLDRCCQVHDNCYNEAEKISGCNPRFRTYSYECTAGTLTCTG
RNNACAASVCDCDRLAAICFAGAPYNDNNYNIDLQARCN
;

loop_
    _entity_poly_seq.entity_id
    _entity_poly_seq.num
    _entity_poly_seq.mon_id
1 1  ASN 1 2   THR 1 3   TYR 1 4   GLN 1 5   PHE 1 6   LYS 1 7   ASN
1 8   MET 1 9   ILE 1 10  GLN 1 11  CYS 1 12  THR 1 13  VAL 1 14  PRO
1 15  LYS 1 16  ARG 1 17  SER 1 18  TRP 1 19  TRP 1 20  ASP 1 21  PHE
1 22  ALA 1 23  ASP 1 24  TYR 1 25  GLY 1 26  CYS 1 27  TYR 1 28  CYS
1 29  GLY 1 30  ARG 1 31  GLY 1 32  GLY 1 33  SER 1 34  GLY 1 35  THR
1 36  PRO 1 37  ILE 1 38  ASP 1 39  ASP 1 40  LEU 1 41  ASP 1 42  ARG
1 43  CYS 1 44  CYS 1 45  GLN 1 46  VAL 1 47  HIS 1 48  ASP 1 49  ASN
1 50  CYS 1 51  TYR 1 52  ASN 1 53  SER 1 54  ALA 1 55  ARG 1 56  GLU
1 57  GLN 1 58  GLY 1 59  GLY 1 60  CYS 1 61  ARG 1 62  PRO 1 63  LYS
1 64  GLN 1 65  LYS 1 66  THR 1 67  TYR 1 68  SER 1 69  TYR 1 70  GLU
1 71  CYS 1 72  LYS 1 73  ALA 1 74  GLY 1 75  THR 1 76  LEU 1 77  SER
1 78  CYS 1 79  SER 1 80  GLY 1 81  SER 1 82  ASN 1 83  ASN 1 84  SER
1 85  CYS 1 86  ALA 1 87  ALA 1 88  THR 1 89  VAL 1 90  CYS 1 91  ASP
1 92  CYS 1 93  ASP 1 94  ARG 1 95  LEU 1 96  ALA 1 97  ALA 1 98  ILE
1 99  CYS 1 100 PHE 1 101 ALA 1 102 GLY 1 103 ALA 1 104 PRO 1 105 TYR
1 106 ASN 1 107 ASP 1 108 ASN 1 109 ASN 1 110 TYR 1 111 ASN 1 112 ILE
1 113 ASP 1 114 LEU 1 115 LYS 1 116 ALA 1 117 ARG 1 118 CYS 1 119 GLN

2 1   ASN 2 2   ARG 2 3   TRP 2 4   GLN 2 5   PHE 2 6   LYS 2 7   ASN
2 8   MET 2 9   ILE 2 10  SER 2 11  CYS 2 12  THR 2 13  VAL 2 14  PRO
2 15  SER 2 16  ARG 2 17  SER 2 18  TRP 2 19  TRP 2 20  ASP 2 21  PHE
2 22  ALA 2 23  ASP 2 24  TYR 2 25  GLY 2 26  CYS 2 27  TYR 2 28  CYS
2 29  GLY 2 30  ARG 2 31  GLY 2 32  GLY 2 33  SER 2 34  GLY 2 35  THR
2 36  PRO 2 37  VAL 2 38  ASP 2 39  ASP 2 40  LEU 2 41  ASP 2 42  ARG
2 43  CYS 2 44  CYS 2 45  GLN 2 46  VAL 2 47  HIS 2 48  ASP 2 49  ASN
2 50  CYS 2 51  TYR 2 52  ASN 2 53  GLU 2 54  ALA 2 55  GLU 2 56  LYS
2 57  ILE 2 58  SER 2 59  GLY 2 60  CYS 2 61  ASN 2 62  PRO 2 63  ARG
2 64  PHE 2 65  ARG 2 66  THR 2 67  TYR 2 68  SER 2 69  TYR 2 70  GLU
2 71  CYS 2 72  THR 2 73  ALA 2 74  GLY 2 75  THR 2 76  LEU 2 77  THR
2 78  CYS 2 79  THR 2 80  GLY 2 81  ARG 2 82  ASN 2 83  ASN 2 84  ALA
2 85  CYS 2 86  ALA 2 87  ALA 2 88  SER 2 89  VAL 2 90  CYS 2 91  ASP
2 92  CYS 2 93  ASP 2 94  ARG 2 95  LEU 2 96  ALA 2 97  ALA 2 98  ILE
2 99  CYS 2 100 PHE 2 101 ALA 2 102 GLY 2 103 ALA 2 104 PRO 2 105 TYR
2 106 ASN 2 107 ASP 2 108 ASN 2 109 ASN 2 110 TYR 2 111 ASN 2 112 ILE
2 113 ASP 2 114 LEU 2 115 GLN 2 116 ALA 2 117 ARG 2 118 CYS 2 119 ASN

loop_
    _pdbx_entity_nonpoly.entity_id
    _pdbx_entity_nonpoly.name
    _pdbx_entity_nonpoly.comp_id
        3 'zinc ion'    ZN
        4 'acetic acid' ACY
        5 water         HOH

loop_
    _struct_ref.id
    _struct_ref.db_name
    _struct_ref.db_code
    _struct_ref.pdbx_db_accession
    _struct_ref.entity_id
    _struct_ref.pdbx_seq_one_letter_code
    _struct_ref.pdbx_align_begin
    _struct_ref.biol_id
1 SWS PA21_NAJSG P60043 1
;NTYQFKNMIQCTVPKRSWWDFADYGCYCGRGGSGTPIDDLDRCCQVHDNCYNSAREQGGCRPKQKTYSYECKAGTLSC
SGSNNSCAATVCDCDRLAAICFAGAPYNDNNYNIDLKARCQ
;
8 .
2 SWS PA22_NAJSG P60044 2
;NRWQFKNMISCTVPSRSWWDFADYGCYCGRGGSGTPVDDLDRCCQVHDNCYNEAEKISGCNPRFRTYSYECTAGTLTC
TGRNNACAASVCDCDRLAAICFAGAPYNDNNYNIDLQARCN
;
8 .
3 GenBank  AY422775 .  1  .  .  .
4 GenBank  AY422776 .  2  .  .  .

loop_
    _entity_src_nat.entity_id
    _entity_src_nat.common_name
    _entity_src_nat.pdbx_organism_scientific
    _entity_src_nat.details
        1 'Andaman cobra' 'Naja sagittifera'
                                         'isolated from lyophilized cobra venom'
        2 'Andaman cobra' 'Naja sagittifera'
                                         'isolated from lyophilized cobra venom'

_entity_src_gen.pdbx_gene_src_scientific_name	.
_entity_src_gen.pdbx_gene_src_organ	        .
_entity_src_gen.pdbx_gene_src_atcc        	.
_entity_src_gen.pdbx_gene_src_cellular_location	.

How this example will appear in the journal