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International
Tables for Crystallography Volume G Definition and exchange of crystallographic data Edited by S. R. Hall and B. McMahon © International Union of Crystallography 2006 |
International Tables for Crystallography (2006). Vol. G. ch. 3.6, p. 197
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The IUCr-sponsored development of data dictionaries has been focused exclusively on crystallographic methods. As the repository for all three-dimensional macromolecular structure data, the PDB accepts structures determined using noncrystallographic techniques such as NMR and cryo-electron microscopy. The description of noncrystallographic methods is beyond the remit of the IUCr, so the PDB has worked with the NMR and cryo-electron microscopy communities to develop data dictionaries that describe these techniques within the mmCIF framework.
The PDB exchange dictionary includes a description of NMR sample preparation, structure solution methodology, refinement and refinement metrics. These extensions were developed in collaboration with the BioMagResBank (BMRB; Ulrich et al., 1989![[link]](/graphics/greenarr.gif)
). The BMRB is the archive for experimental NMR data for biological macromolecules and has played an active role in the development of the mmCIF data dictionary. In selecting a format for archiving NMR data, the BMRB opted to use the STAR syntax (Hall, 1991) rather than the more restrictive CIF syntax. Despite this difference in syntax, the conceptual representation of macromolecular structure in the NMR dictionary (NMRStar) has remained semantically very close to the mmCIF representation. This has facilitated the exchange of data and dictionaries between the BMRB and the PDB, the sharing of software tools, and the development of a common platform for depositing data.
Cryo-electron microscopy (as a technique for the determination of the structure of large molecular assemblies) is also described in the PDB exchange dictionary. The data extensions for cryo-electron microscopy include a description of the sample preparation, raw volume data (Henrick et al., 2003), structure solution and refinement. These extensions have a prefix of em_ (http://mmcif.pdb.org/dictionaries/mmcif_iims.dic/Index/
).
The International Task Force on Deposition, Archiving, and Curation of Primary Information for Structural Genomics (Section A3.6.2.2) has also provided recommendations for the deposition of information about protein production. These recommendations are summarized at http://deposit.pdb.org/mmcif/sg-data/protprod.html
. These data extensions have been used as the foundation for the Protein Expression Purification and Crystallization database (PEPCdb, http://pepcdb.pdb.org/
) and for the protein production process model developed to support the Structural Proteomics in Europe initiative (SPINE; http://www.spineurope.org/
).
References
Hall, S. R. (1991). The STAR file: a new format for electronic data transfer and archiving. J. Chem. Inf. Comput. Sci. 31, 326–333.Google Scholar
Henrick, K., Newman, R., Tagari, M. & Chagoyen, M. (2003). EMDep: a web-based system for the deposition and validation of high-resolution electron microscopy macromolecular structural information. J. Struct. Biol. 144, 228–237.Google Scholar
Ulrich, E. L., Markley, J. L. & Kyogoku, Y. (1989). Creation of a nuclear magnetic resonance data repository and literature database. Protein Seq. Data Anal. 2, 23–37.Google Scholar
