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Category entity
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Category Description
Data items in the ENTITY category record details (such as
chemical composition, name, and source) about the molecular
entities that are present in the crystallographic structure.
Items in the various ENTITY sub-categories provide a full
chemical description of these molecular entities.
Entities are of three types: polymer, non-polymer and water.
Note that the water category includes only water; ordered
solvent such as sulfate ion or acetone would be described as
individual non-polymer entities.
The ENTITY category is specific to macromolecular CIF
applications, and replaces the function of the CHEMICAL category
in the CIF core.
It is important to remember that the ENTITY data are not the
result of the crystallographic experiment; those results are
represented in the ATOM_SITE data items. ENTITY data items
describe the chemistry of the molecules under investigation,
and can most usefully be thought of as the ideal groups to which
the structure is restrained or constrained during refinement.
It is also important to remember that entities do not correspond
directly to the enumeration of the contents of the asymmetric
unit. Entities are described only once, even in those structures
that contain multiple observations of an entity. The
STRUCT_ASYM data items, which reference the entity list,
describe and label the contents of the asymmetric unit.
Category Examples
Example 1:
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
loop_
_entity.id
_entity.type
_entity.formula_weight
_entity.details
1 polymer 10916
; The enzymatically competent form of HIV protease is a
dimer. This entity corresponds to one monomer of an
active dimer.
;
2 non-polymer '762' '.'
3 water 18 '.'
Key Category Items
Items in Category entity
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This HTML dictionary was created using the
CIFLIB C Language Application Program Interface
at the
Resource Collaboratory for Structural Bioinformatics
Rutgers University, Department of Chemistry
New Brunswick, New Jersey
help@rcsb.rutgers.edu