data for structural and crystallization communications - example

Example: sample information

Example 4: mutation and modification

Based in part on Davies, G. J., Ducros, V., Lewis, R. J., Borchert, T. V. & Schulein, M. (1997). Oligosaccharide specificity of a family 7 endoglucanase: insertion of potential sugar-binding subsites. J. Biotechnol. 57, 91 [1A39].

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.

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                                 1A39

_struct.title  'Humicola insolens endocellulase EGI (S37W, P39W double-mutant)'

loop_
    _entity.id
    _entity.type
    _entity.src_method 
    _entity.pdbx_description
    _entity.formula_weight
    _entity.details
    _entity.pdbx_mutation
    _entity.pdbx_number_of_molecules
    _entity.pdbx_fragment
    _entity.pdbx_ec
    1 polymer     man 'endoglucanase I'                44821.914
; pyroglutamate post-translational modification at residue 1 N-linked
  N-acetylglucosamine on residue ASN 247
;
                                                       'S37W, P39W'  1 ? 3.2.1.4
    2 non-polymer man 'sugar (N-acetyl-D-glucosamine)' 221.210 ? ?   1 ? ?
    3 water       nat water                            18.015  ? ? 327 ? ?

_struct_biol.details
;       Enzyme is a monomer of 402 residues. Residues Ser 37 and Pro 39 have
        been mutated to Trp residues for purposes of this study. Residue
        Glu 1 is post-translationally modified to pyroglutamate. Enzyme is 
        glycosylated at residue Asn 247 by N-linkage of an N-acetylglucosamine.
;

_struct_biol.pdbx_formula_weight    44822
_struct_biol.pdbx_formula_weight_method
       'calculated from sequence with mutations, modification and glycosylation'

_entity_poly.entity_id                      1
_entity_poly.type                           polypeptide(L)
_entity_poly.pdbx_seq_one_letter_code       
;(5HP)KPGETKEVHPQLTTFRCTKRGGCKPATNFIVLDSLWHWIHRAEGLGPGGCGDWGNPPPKDVCPDVESCAKNCIME
GIPDYSQYGVTTNGTSLRLQHILPDGRVPSPRVYLLDKTKRRYEMLHLTGFEFTFDVDATKLPCGMNSALYLSEMHPTGA
KSKYNPGGAYYGTGYCDAQCFVTPFINGLGNIEGKGSCCNEMDIWEANSRASHVAPHTCNKKGLYLCEGEECAFEGVCDK
NGCGWNNYRVNVTDYYGRGEEFKVNTLKPFTVVTQFLANRRGKLEKIHRFYVQDGKVIESFYTNKEGVPYTNMIDDEFCE
ATGSRKYMELGATQGMGEALTRGMVLAMSIWWDQGGNMEWLDHGEAGPCAKGEGAPSNIVQVEPFPEVTYTNLRWGEIGS
TYQELQ
;
_entity_poly.pdbx_seq_one_letter_code_can   
;EKPGETKEVHPQLTTFRCTKRGGCKPATNFIVLDSLWHWIHRAEGLGPGGCGDWGNPPPKDVCPDVESCAKNCIMEGIPD
YSQYGVTTNGTSLRLQHILPDGRVPSPRVYLLDKTKRRYEMLHLTGFEFTFDVDATKLPCGMNSALYLSEMHPTGAKSKY
NPGGAYYGTGYCDAQCFVTPFINGLGNIEGKGSCCNEMDIWEANSRASHVAPHTCNKKGLYLCEGEECAFEGVCDKNGCG
WNNYRVNVTDYYGRGEEFKVNTLKPFTVVTQFLANRRGKLEKIHRFYVQDGKVIESFYTNKEGVPYTNMIDDEFCEATGS
RKYMELGATQGMGEALTRGMVLAMSIWWDQGGNMEWLDHGEAGPCAKGEGAPSNIVQVEPFPEVTYTNLRWGEIGSTYQE
LQ
;

loop_
    _pdbx_entity_nonpoly.entity_id
    _pdbx_entity_nonpoly.name 
    _pdbx_entity_nonpoly.comp_id
        2 'sugar (N-acetyl-D-glucosamine)' NAG
        3 water                            HOH

_struct_ref.id                            1
_struct_ref.db_name                       SWS
_struct_ref.db_code                       GUN1_HUMIN
_struct_ref.entity_id                     1

_entity_src_gen.entity_id                        1
_entity_src_gen.pdbx_gene_src_scientific_name    'Humicola insolens'
_entity_src_gen.pdbx_gene_src_strain             ?
_entity_src_gen.pdbx_gene_src_details            ?

How this example will appear in the journal