Structure deposition

The coordinates of the final structure are deposited in the Protein Data Bank (PDB). This databank is maintained by three consortiums, being PDBe (in Europe), RCSB (in USA) and PDBj (in Japan).

These consortiums also provide tools for validation and deposition of coordinate sets. Whatever consortium is chosen for the deposition, the coordinates will subsequently become available at each of the three portals.

Before deposition the coordinate sets can be validated, by uploading the coordinates to the validation server.

It is highly recommended to test the quality of your coordinate set via this recently made available tool before starting the deposition protocol.

Normally we deposit through PDBe or RCSB.

In the protein crystallography community it is stressed that also the raw data, associated with the coordinate set that is deposited, should be archived. At FBMM we have setup a special folder (/structures) for this. In this folder the raw data (the images) are copied. In addition also the relevant metadata (key logfiles on scaling, refinement, the relevant libraries used in this refinement, as well the crystallization and crystal handling information) is provided.

For data archiving of the raw data and important meta-data, together with the final PDB-coordinates,  we have implemented a simple protocol.

Further information can be provided by Tiila Kiema and Rik Wierenga.

Contact persons:

Rik Wierenga, professor
Faculty of Biochemistry and Molecular Medicine F202B
University of Oulu
PO Box 5400, 90014 University of Oulu, Finland
tel. +358-(0)294 481199
e-mail: rik.wierenga (at)

Tiila-Riikka Kiema, Ph.D.
Faculty of Biochemistry and Molecular Medicine F217
University of Oulu
PO Box 5400, 90014 University of Oulu, Finland
tel. +358-(0)294 481179
e-mail: tiila.kiema (at)

Last updated: 12/9/2016