data for structural and crystallization communications - example

Example: Presentation of Ramachandran plot data

Example 2: A nuclear hormone receptor ligand-binding domain is a heterodimer composed of two chains of homologous, but different sequences. For the A monomer, the Ramachandran plot percentages are, for FA, AA, GA and D regions, 77, 11, 8 and 4%, respectively, while for the X monomer, they are 82, 13, 3 and 2%, respectively.

In this example, the Ramachandran plot is calculated separately over the two monomers, for which the sequence limits (referenced by the labels 'A' and 'X' respectively) will be found elsewhere in the file (in the PDBX_SEQUENCE_RANGE category).

       1  A   'Ramachandran plot'  'Most favored'           77  PROCHECK   pro value
       2  A   'Ramachandran plot'  'Additionally allowed'   11  PROCHECK   pro value
       3  A   'Ramachandran plot'  'Generously allowed'     8   PROCHECK   pro value
       4  A   'Ramachandran plot'  'Disallowed'             4   PROCHECK   pro value
       5  X   'Ramachandran plot'  'Most favored'           82  PROCHECK   pro value
       6  X   'Ramachandran plot'  'Additionally allowed'   13  PROCHECK   pro value
       7  X   'Ramachandran plot'  'Generously allowed'     3   PROCHECK   pro value
       8  X   'Ramachandran plot'  'Disallowed'             2   PROCHECK   pro value

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

How this example will appear in the journal

Ramachandran plot analysis
   Sequence range
   Most favoured regions (%)
   Additionally allowed regions (%)
   Generously allowed regions (%)
   Disallowed regions (%)



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