3.6. Classification and use of macromolecular data

P. M. D. Fitzgerald, J. D. Westbrook, P. E. Bourne, B. McMahon, K. D. Watenpaugh and H. M. Berman, with Appendix 3.6.2 by J. D. Westbrook, K. Henrick, E. L. Ulrich and H. M. Berman

Abstract

The macromolecular CIF (mmCIF) dictionary is a major extension of the core CIF dictionary designed to provide data names to be used in a machine-readable description of a macromolecular structure determination experiment and the derived structural model. To allow a complete and self-consistent account of a macromolecular structure at various levels of detail, the dictionary has been implemented in the relational dictionary definition language DDL2. It includes the data items defined in the core CIF dictionary.

mmCIF supersedes an older file format of the Protein Data Bank (PDB), and therefore includes a representation of all the information historically archived at the PDB. In addition, it provides data items suitable for use in: a journal 'materials and methods' article; descriptions of biologically active molecules and any important sub-components; descriptions of crystallographic and noncrystallographic symmetry; information about the chemistry and geometry of monomomer components of macromolecules, and of any ligands or small-molecule complexes; and descriptions of functional and structural aspects of macromolecules.

Links

Figures

The printed figures in this chapter were reduced to fit the physical page dimensions. The links below display the figures at full size or in colour.

	Fig. 3.6.3.1. A representation of crambin (PDB 3CNR) with a co-crystallized ethanol molecule.
	Fig. 3.6.6.1. The family of categories used to describe MAD phasing. Boxes surround categories of related data items. Data items that serve as category keys are preceded by a bullet. Lines show relationships between linked data items in different categories with arrows pointing at the parent data items.
	Fig. 3.6.6.2. The family of categories used to describe MIR phasing. Boxes surround categories of related data items. Data items that serve as category keys are preceded by a bullet. Lines show relationships between linked data items in different categories with arrows pointing at the parent data items.
	Fig. 3.6.7.1. The family of categories used to describe atom sites. Boxes surround categories of related data items. Data items that serve as category keys are preceded by a bullet. Lines show relationships between linked data items in different categories with arrows pointing at the parent data items.
	Fig. 3.6.7.2. Alternative conformations in an HIV-1 protease structure (PDB 5HVP) to be described with data items in the ATOM_SITES_ALT, ATOM_SITES_ALT_ENS and ATOM_SITES_ALT_GEN categories. (a) Complete structure, (b) ensemble 1, (c) ensemble 2.
	Fig. 3.6.7.3. The family of categories used to describe the chemical and structural features of the monomers and small molecules used to build a model of a structure. Boxes surround categories of related data items. Data items that serve as category keys are preceded by a bullet. Lines show relationships between linked data items in different categories with arrows pointing at the parent data items.
	Fig. 3.6.7.4. The family of categories used to describe the links between chemical components. Boxes surround categories of related data items. Data items that serve as category keys are preceded by a bullet. Lines show relationships between linked data items in different categories with arrows pointing at the parent data items.
	Fig. 3.6.7.5. The family of categories used to describe chemical entities. Boxes surround categories of related data items. Data items that serve as category keys are preceded by a bullet. Lines show relationships between linked data items in different categories with arrows pointing at the parent data item.
	Fig. 3.6.7.6. The family of categories used to describe polymer chemical entities. Boxes surround categories of related data items. Data items that serve as category keys are preceded by a bullet. Lines show relationships between linked data items in different categories with arrows pointing at the parent data items.
	Fig. 3.6.7.7. The family of categories used to describe the higher-level macromolecular structure. Boxes surround categories of related data items. Data items that serve as category keys are preceded by a bullet. Lines show relationships between linked data items in different categories with arrows pointing at the parent data items.
	Fig. 3.6.7.8. The higher-level structure of the complex of HIV-1 protease with an inhibitor (PDB 5HVP) to be described with data items in the STRUCT_ASYM, STRUCT_BIOL, STRUCT_BIOL_KEYWORDS and STRUCT_BIOL_GEN categories. (a) Complete structure; (b), (c), (d) three different biological units.
	Fig. 3.6.7.9. The family of categories used to describe secondary structure. Boxes surround categories of related data items. Data items that serve as category keys are preceded by a bullet. Lines show relationships between linked data items in different categories with arrows pointing at the parent data items.
	Fig. 3.6.7.10. The family of categories used to describe structural interactions such as hydrogen bonding, salt bridges and disulfide bridges. Boxes surround categories of related data items. Data items that serve as category keys are preceded by a bullet. Lines show relationships between linked data items in different categories with arrows pointing at the parent data items.
	Fig. 3.6.7.11. The family of categories used to describe the structural features of monomers. Boxes surround categories of related data items. Data items that serve as category keys are preceded by a bullet. Lines show relationships between linked data items in different categories with arrows pointing at the parent data items.
	Fig. 3.6.7.12. 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. Lines show relationships between linked data items in different categories with arrows pointing at the parent data items.
	Fig. 3.6.7.13. 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.
	Fig. 3.6.7.14. The family of categories used to describe -sheets. Boxes surround categories of related data items. Data items that serve as category keys are preceded by a bullet. Lines show relationships between linked data items in different categories with arrows pointing at the parent data items.
	Fig. 3.6.7.15. A hypothetical -sheet to be described with data items in the STRUCT_SHEET, STRUCT_SHEET_ORDER, STRUCT_SHEET_RANGE and STRUCT_SHEET_HBOND categories. Note that the strands come from two different polypeptides, labelled A and B.
	Fig. 3.6.7.16. The family of categories used to describe molecular sites. Boxes surround categories of related data items. Data items that serve as category keys are preceded by a bullet. Lines show relationships between linked data items in different categories with arrows pointing at the parent data items.

Dictionaries

The following CIF dictionaries are referenced in this chapter:

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