data for structural and crystallization communications - example

Example: sample information

Example 3: mutation

Based in part on the hypothetical protein MPN555 [Schulze-Gahmen, U., Aono, S., Chen, S., Yokota, H., Kim, R. & Kim, S.-H. (2005). Structure of the hypothetical Mycoplasma protein MPN555 suggests a chaperone function. Acta Cryst. D61, 1343-1347; 1ZXJ].

The M. pneumoniae product shares features with two bacterial chaperone proteins. The crystallized peptide retains an N-terminal His-tag extension of 25 residues attached to the methionyl first residue. There are four molecules in the asymmetric unit.

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.

In this example, it may be noted that a loop structure is used for the list of non-polymer entities present, even though there is only one (water). Often in mmCIF data structures a list with a single entry is collapsed to a simple tag-value listing, i.e.

    _pdbx_entity_nonpoly.entity_id     2
    _pdbx_entity_nonpoly.name          water
    _pdbx_entity_nonpoly.comp_id       HOH

_entry.id                                        1ZXJ

_struct.title 'Crystal structure of the hypothetical Mycoplasma protein, MPN555'

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 man 'MPN555 hypothetical protein monomer' 25456.152 ?
                                                   'N-terminal His tag' .  4 .
        2 water   nat water                                    18.015 . . 14 .

_struct_biol.details
;        MPN555 is a monomer.  There are four MPN555 
         monomers in the asymmetric unit, each with an N-terminal 
         tag of sequence MGSSHHHHHHDYDIPTTENLYFQGH.
;

_struct_biol.pdbx_formula_weight                 25456
_struct_biol.pdbx_formula_weight_method      'calculated from sequence with tag'

_entity_poly.entity_id                           1
_entity_poly.type                                polypeptide(L)
_entity_poly.pdbx_seq_one_letter_code       
;MGSSHHHHHHDYDIPTTENLYFQGHMATNLKSTAKLVKPIQYDEVIEVERIFADPAFIEQHRQRILASFKDAKESALYHE
LTHIVIKDNLFSCAMNAIVGYFEFNIDEAELKNVMEGLKRDVIQGAEDNTVQAIAEKIIKKALVFNHLQKEWKVEITDEV
VKNVISLYYEKTNQSVREYLDDKQKFEGVRTALLEERMVLETINHFKFHFNLTGQLPN
;
_entity_poly.pdbx_seq_one_letter_code_can        .

loop_
    _pdbx_entity_nonpoly.entity_id 
    _pdbx_entity_nonpoly.name 
    _pdbx_entity_nonpoly.comp_id 
        2    water    HOH

_struct_ref.id                                   1
_struct_ref.db_name                              SWS
_struct_ref.db_code                              Y555_MYCPN

_entity_src_nat.pdbx_organism_scientific         .
_entity_src_nat.strain                           .
_entity_src_nat.details                          .

_entity_src_gen.entity_id                        1
_entity_src_gen.pdbx_gene_src_scientific_name    'Mycoplasma pneumoniae
_entity_src_gen.pdbx_gene_src_strain             ?
_entity_src_gen.pdbx_gene_src_details            ?

How this example will appear in the journal