29] Protein data bank archives of three-dimensional macromolecular structures

Abstract

Publisher Summary This chapter discusses the Protein Data Bank (PDB) archives of three-dimensional (3D) macromolecular structures. Several pieces of information related to an entry are archived by the PDB. In addition to the coordinate entry file, the PDB stores files related to the experiment such as structure factors, nuclear Overhauser effect (NOE) restraints, and lists of chemical shifts. Also archived are auxiliary files used in structure analysis and refinement such as X-PLOR parameter and topology files. Currently, the archives are managed as a set of individual files, and each entry may have several associated files. The PDB is in the process of building a relational database, 3Dbase that will replace the current data management and access system. A description of 3DBase, including an outline of the way users can access its contents is provided in the chapter. Coordinate entries in the PDB are stored in separate files, each of which reports the results of an experiment or analysis that elucidates the structure of proteins, nucleic acids, polysaccharides, and other biological macromolecules. Although most of the data are generated from single crystal X-ray diffraction studies, a growing number of PDB entries are from nuclear magnetic resonance (NMR) studies.