Introduction of the Protein Data Bank Japan (PDBj)

Institute for Protein Research, Osaka University* Institute for Protein Research, Osaka University, Japan, Japan Science and Technology Agency.**
â—‹Takashi Kosada* Reiko Igarashi** Yumiko Kengaku** Yasuyo Morita** Kanna Matsuura** Masami Kusunoki* Yukiko Shimizu** Reiko Yamashita** Haruki Nakamura*

The Protein Data Bank (PDB) is the sole international public repository for three dimensional structure data of biological macromolecules and serves for supporting essential biological sciences. Macromolecular structures in the PDB help to solve crystallographic structure determination. In 1999, the Protein Data Bank Japan (PDBj) was founded at the Institute for Protein Research, Osaka University, to accept and process PDB entries in Asia and Oceania with collaboration of RCSB. The PDBj enhances the PDB capabilities and has performed the following activities:

1. PDB search web site [1]. 2. PDB deposition site [1]. 3. FTP download site [1].
4. Process and Release of Deposited entries.
5. Exploiting an XML format database[2], a 3D viewer, and secondary databases[3].

The PDBj, RCSB and MSD-EBI have formed the world wide Protein Data Bank (wwPDB) on 2003[4]. The mission of the wwPDB is to maintain a single archive of macromolecular structural data that is freely and publicly available to the global community.
Convenient methods of finding particular entries from such many entries and the deposition method including the above list 1. to 5. will be presented here. Also the stastics of recent refinement information and expresison system will be shown.
The PDBj processed 1586 entries for 2006 in a year. The PDBj would like to solicit you to deposit your entries through the PDBj deposition site.

1. All PDBj sites can access through http://www.pdbj.org/
2. XML-based Protein Structure Search Service (xpss:http://www.pdbj.org/xpsss/).
3. Kinoshita, K., Nakamura, H. (2004) Bioinformatics 20, 1329-1330.
4. Berman, H., Henrick, Kim., and Nakamura, H. (2002) Nat. struct. biol. 12, 979-1024.