Crystallographic Structure Deposition

Background

Once a crystallographic structure is solved, it is usually deposited in the Worldwide Protein Data Bank (wwPDB). This is necessary for publication as most journals require a PDB ID to be included in any manuscript that describes a new crystallographic structure. The wwPDB is an invaluable resource that contains over 190,000 structures (as of July 2021).

Procedure

The model files (PDB and mmCIF) generated by phenix.refine contain the information required when depositing a structure to the wwPDB. However, the wwPDB currently only accepts the mmCIF (i.e., PDBx/mmCIF) model files for deposition.

To generate a model file suitable for deposition, we recommend a two-stage process:

1. By default, phenix.refine will output model files in mmCIF and PDB format. If you turned off the option for mmCIF output, run a final cycle of phenix.refine that writes mmCIF files for model and data. This can be set in the Output section of the GUI.
2. You can then process the model file (mmCIF) and a sequence file with mmtbx.prepare_pdb_deposition to create a mmCIF file with the sequence. This program requires the full sequence for the macromolecule to be provided. In the GUI, this program is in the "PDB Deposition" section of tools.

How to use *mmtbx.prepare_pdb_deposition*: Click here

Related programs

• phenix.get_pdb_validation_report: This program submits your model and data in CIF format to the PDB OneDep server to get a validation report in PDF and XML formats.
• phenix.table_one: This program generates the table of crystallographic statistics required by most scientific journals.

References

• Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB). P.D. Adams, P.V. Afonine, K. Baskaran, H.M. Berman, J. Berrisford, G. Bricogne, D.G. Brown, S.K. Burley, M. Chen, Z. Feng, C. Flensburg, A. Gutmanas, J.C. Hoch, Y. Ikegawa, Y. Kengaku, E. Krissinel, G. Kurisu, Y. Liang, D. Liebschner, L. Mak, J.L. Markley, N.W. Moriarty, G.N. Murshudov, M. Noble, E. Peisach, I. Persikova, B.K. Poon, O.V. Sobolev, E.L. Ulrich, S. Velankar, C. Vonrhein, J. Westboork, M. Wojdyr, M. Yokochi, and J.Y. Young. Acta Cryst. D75, 451-454 (2019).