Acta Crystallographica Section D

Biological Crystallography

Volume 64, Part 8 (August 2008)

research papers

Acta Cryst. (2008). D64, 874-882 [ doi:10.1107/S0907444908017393 ]

Representation of viruses in the remediated PDB archive

C. L. Lawson, S. Dutta, J. D. Westbrook, K. Henrick and H. M. Berman

Abstract: A new scheme has been devised to represent viruses and other biological assemblies with regular noncrystallographic symmetry in the Protein Data Bank (PDB). The scheme describes existing and anticipated PDB entries of this type using generalized descriptions of deposited and experimental coordinate frames, symmetry and frame transformations. A simplified notation has been adopted to express the symmetry generation of assemblies from deposited coordinates and matrix operations describing the required point, helical or crystallographic symmetry. Complete correct information for building full assemblies, subassemblies and crystal asymmetric units of all virus entries is now available in the remediated PDB archive.

Keywords: virus structures; Protein Data Bank; database integration; uniform curation; point symmetry; helical symmetry; biological assemblies.