New Features on the PDB Web Site and FTP Archives

During this past quarter, several new developments that were previously in beta test have been incorporated into the primary PDB web site, its mirrors, and on the PDB FTP site:

Remediated mmCIF Files

The primary PDB Web site and its mirrors now offer the remediated mmCIF files, previously referred to as the "beta" mmCIF files. These files have replaced the set of automatically translated mmCIF files that were created with pdb2cif.pl. The remediated files can be accessed from the Download/Display File section of the Structure Explorer page for any entry, or for a set of query results.

The remediated mmCIF files are also available from the PDB FTP site at ftp://ftp.rcsb.org/pub/pdb/data/structures/all/mmCIF/. The translated files have been removed from the FTP site, and will be made available upon individual request.

For every experimentally-solved structure, both current and obsolete, there is now a remediated mmCIF file in the corresponding directory of the FTP archive in Unix compressed (.Z) format. mmCIF files are not provided for theoretical models. However, the translation software (pdb2cif.pl) is provided at www.bernstein-plus-sons.com/software/pdb2cif for users who wish to generate the translated mmCIF files.

Biological Unit Images and Coordinate Files The View Structure section of the Structure Explorer now offers still ribbon images of the assumed biological unit(s) for structures, where relevant, in addition to static images of the asymmetric unit. Links to the coordinate files that are used to generate the biological unit images are also accessible here, as well as from the Download/Display File section of the Structure Explorer.

Biological unit coordinate files are also available from the FTP archive at ftp://ftp.rcsb.org/pub/pdb/data/biounit. These files are accessible in gzipped (.gz) format. Links to a variety of free uncompression tools can be found at www.rcsb.org/pdb/help-general.html#format_structure_compressed.

Enzyme Names and EC Number Query The Summary Information section of the Structure Explorer page for enzymes in the PDB now displays the enzyme name for entries with complete EC numbers. This section also supports queries for all other PDB entries with the same EC number by clicking on the number shown for that entry.

Questions about these new features may be sent to info@rcsb.org.

The assumed biologically active unit of the Myc-Max heterodimer bound to its DNA target.

PDB ID: 1nkp

Nair, S. K., Burley, S. K. (2003): X-ray structures of Myc-Max and Mad-Max recognizing DNA. Molecular bases of regulation by proto-oncogenic transcription factors. Cell 112, pp. 193-205.