Noncrystallographic symmetry

Fitzgerald, P. M. D.; Westbrook, J. D.; Bourne, P. E.; McMahon, B.; Watenpaugh, K. D.; Berman, H. M.

doi:10.1107/97809553602060000738

International
Tables for
Crystallography
Volume G
Definition and exchange of crystallographic data
Edited by S. R. Hall and B. McMahon

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International Tables for Crystallography (2006). Vol. G. ch. 3.6, pp. 184-186

Section 3.6.7.5.5. Noncrystallographic symmetry

P. M. D. Fitzgerald,^a ^* J. D. Westbrook,^b P. E. Bourne,^c B. McMahon,^d K. D. Watenpaugh^e and H. M. Berman^f

^a Merck Research Laboratories, Rahway, New Jersey, USA,^bProtein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, New Jersey, USA,^cResearch Collaboratory for Structural Bioinformatics, San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0537, USA,^dInternational Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England,^eretired; formerly Structural, Analytical and Medicinal Chemistry, Pharmacia Corporation, Kalamazoo, Michigan, USA, and ^fProtein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, New Jersey, USA
Correspondence e-mail: paula_fitzgerald@merck.com

3.6.7.5.5. Noncrystallographic symmetry

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Data items in these categories are as follows:

(a) STRUCT_NCS_ENS [Scheme scheme158]

(b) STRUCT_NCS_ENS_GEN [Scheme scheme159]

(d) STRUCT_NCS_DOM_LIM [Scheme scheme161]

(e) STRUCT_NCS_OPER [Scheme scheme162]

The bullet ( $[\bullet]$ ) indicates a category key. Where multiple items within a category are marked with a bullet, they must be taken together to form a compound key. The arrow ( $[\rightarrow]$ ) is a reference to a parent data item.

Biological macromolecular complexes may be built from domains related by symmetry transformations other than those arising from the crystal lattice symmetry. These domains are not necessarily discrete molecular entities: they may be composed of one or more segments of a single polypeptide or nucleic acid chain, of segments from more than one chain, or of small-molecule components of the structure. The categories above allow the distinct domains that participate in ensembles of structural elements related by noncrystallographic symmetry to be listed and described in detail. The relationships between categories used to describe noncrystallographic symmetry are shown in Fig. 3.6.7.12.

Figure 3.6.7.12 | top | pdf |

The family of categories used to describe noncrystallographic symmetry. Boxes surround categories of related data items. Data items that serve as category keys are preceded by a bullet ( $[\bullet]$ ). Lines show relationships between linked data items in different categories with arrows pointing at the parent data items.

In the mmCIF model of noncrystallographic symmetry, the highest level of organization is the ensemble, which corresponds to the complete symmetry-related aggregate (e.g. tetramer, icosahedron). An identifier is given to the ensemble using the data item _struct_ncs_ens.id.

The symmetry-related elements within the ensemble are referred to as domains. The elements of structure that are to be considered part of the domain are specified using the data items in the STRUCT_NCS_DOM and STRUCT_NCS_DOM_LIM categories. By using the STRUCT_NCS_DOM_LIM data items appropriately, domains can be defined to include ranges of polypeptide chain or nucleic acid strand, bound ligands or cofactors, or even bound solvent molecules. Note that the category keys for STRUCT_NCS_DOM_LIM include the domain ID and the range specifiers. Thus a single domain may be composed of any number of ranges of elements.

Finally, the ensemble is generated from the domains using the rotation matrix and translation vector specified by data items in the STRUCT_NCS_OPER category, which are referenced by the data items in the STRUCT_NCS_ENS_GEN category. There are data items appropriate for two common methods of describing noncrystallographic symmetry:

(1) In the first method, the coordinate list includes all copies of domains related by noncrystallographic symmetry and the aim is to describe the relationships between domains in the ensemble; in this case the data items in STRUCT_NCS_ENS_GEN specify a pair of domains and reference the appropriate operator in STRUCT_NCS_OPER. This method is indicated by giving the data item _struct_ncs_oper.code the value given.

(2) In the second method, the coordinate list contains only one copy of the domain and the aim is to generate the entire ensemble; in this case the data items in STRUCT_NCS_ENS_GEN specify a pair of domains and reference the appropriate operator in STRUCT_NCS_OPER, but now the data item _struct_ncs_oper.code is given the value generate.

Noncrystallographic symmetry in a trimeric molecule is shown in Fig. 3.6.7.13 and described in Example 3.6.7.12.

Figure 3.6.7.13 | top | pdf |

Noncrystallographic symmetry in the structure of trimeric haemerythrin (PDB 1HR3) to be described with data items in the STRUCT_NCS_ENS, STRUCT_NCS_ENS_GEN, STRUCT_NCS_DOM and STRUCT_NCS_DOM_LIM categories.

Example 3.6.7.12. Noncrystallographic symmetry in the structure of trimeric haemerythrin (PDB 1HR3) described with data items in the STRUCT_NCS_ENS, STRUCT_NCS_ENS_GEN, STRUCT_NCS_DOM and STRUCT_NCS_DOM_LIM categories. For brevity, the data items in the STRUCT_NCS_OPER category are not shown.

[Scheme scheme163]

References

International Tables for Crystallography (2006). Vol. G. ch. 3.6, pp. 184-186