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

Macromolecule details
Component molecules phospholipase A2 isoform 1, phospholipase A2 isoform 2, zinc ion, acetic acid, water
Macromolecular assembly 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.
  Mass (Da) 26703.1 (calculated from sequences with both acetate and the zinc ions)
Source organism Naja sagittifera
  Details Isolated from lyophilized cobra venom



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