data for structural and crystallization communications - example

Example: missing and partial residues in the refined model

Example 1: A human growth factor is a single chain of 360 residues. In the refined model, coordinates for the first four residues in from the N-terminus (Ala-Ser-Glu-Gly) are not included because no model could be constructed for them due to lack of electron density. About sixty residues in from the N-terminus, a seven-residue loop between beta strands is partially disordered so that models for residues 62 and 63 (Ser and Val, respectively) lack coordinates for side chains.

Note that _pdbx_feature_monomer.feature_name should take the value 'missing' to indicate residues that have not been refined at all, or 'partial' for incomplete refinements. The item _pdbx_feature_monomer.feature may be used to provide more detail on individual residues.

The items in gray (_pdbx_feature_monomer.id and _pdbx_feature_monomer.feature_type) are identifiers and qualifiers needed to preserve the mmCIF data structure, and are auto-generated during the deposition procedure.

loop_
    _pdbx_feature_monomer.id
    _pdbx_feature_monomer.label_alt_id
    _pdbx_feature_monomer.label_asym_id
    _pdbx_feature_monomer.label_comp_id
    _pdbx_feature_monomer.label_seq_id
    _pdbx_feature_monomer.feature_name
    _pdbx_feature_monomer.feature
    _pdbx_feature_monomer.feature_assigned_by
    _pdbx_feature_monomer.feature_citation_id
    _pdbx_feature_monomer.feature_type
       1 . A Ala  1 'not refined' . CNS cns value
       2 . A Ser  2 'not refined' . CNS cns value
       3 . A Glu  3 'not refined' . CNS cns value
       4 . A Gly  4 'not refined' . CNS cns value
       5 . A Ser 62 'partially refined' 'side chain missing because of partial disorder' CNS cns value
       6 . A Val 63 'partially refined' 'side chain missing because of partial disorder' CNS cns value

How this example will appear in the journal

Omitted residues 4 missing, 2 partially refined  


Example 2: A novel ion channel includes a membrane pore that is assembled of six beta strands twelve residues long from six monomers of identical sequence. To crystallize this pore, short native sequences were required at both ends of the strands to permit assembly and increase stability in solution. The N-terminus included four 'non-pore' residues with sequence SAEG and the C-terminus five AKGET, making each strand 23 residues long. Not all of the extra residues were imaged in the final refined structure. In all, four were missing entirely and another six lacked side chains. The following array presents the data on missing and partial residues as outlined above. In this example, for some reason the three-letter codes for the residues of interest are not available, and are indicated by query marks ? for 'unknown'.
loop_
    _pdbx_feature_monomer.id   
    _pdbx_feature_monomer.label_alt_id
    _pdbx_feature_monomer.label_asym_id
    _pdbx_feature_monomer.label_comp_id
    _pdbx_feature_monomer.label_seq_id
    _pdbx_feature_monomer.feature_name
    _pdbx_feature_monomer.feature
    _pdbx_feature_monomer.feature_assigned_by
    _pdbx_feature_monomer.feature_citation_id
    _pdbx_feature_monomer.feature_type
       1  . 1  ?  1 'not refined.  . CNS cns value
       2  . 3  ?  1 'not refined.  . CNS cns value
       3  . 5  ? 23 'not refined.  . CNS cns value
       4  . 5  ? 22 'not refined.  . CNS cns value
       5  . 2  ?  1 'partially refined'  . CNS cns value
       6  . 4  ?  1 'partially refined'  . CNS cns value
       7  . 4  ? 23 'partially refined'  . CNS cns value
       8  . 5  ?  1 'partially refined'  . CNS cns value
       9  . 6  ?  1 'partially refined'  . CNS cns value
       10 . 6  ? 23 'partially refined'  . CNS cns value

How this example will appear in the journal

Omitted residues 4 missing, 6 partially refined  



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