Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB)

Paul D Adams¹, Pavel V Afonine¹, Kumaran Baskaran², Helen M Berman³, John Berrisford⁴, Gerard Bricogne⁵, David G Brown⁶, Stephen K Burley³, Minyu Chen⁷, Zukang Feng³, Claus Flensburg⁵, Aleksandras Gutmanas⁴, Jeffrey C Hoch⁸, Yasuyo Ikegawa⁷, Yumiko Kengaku⁷, Eugene Krissinel⁹, Genji Kurisu⁷, Yuhe Liang³, Dorothee Liebschner¹, Lora Mak⁴, John L Markley², Nigel W Moriarty¹, Garib N Murshudov¹⁰, Martin Noble¹¹, Ezra Peisach³, Irina Persikova³, Billy K Poon¹, Oleg V Sobolev¹, Eldon L Ulrich², Sameer Velankar⁴, Clemens Vonrhein⁵, John Westbrook³, Marcin Wojdyr⁵, Masashi Yokochi⁷, Jasmine Y Young³

Affiliations

¹ Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
² BioMagResBank (BMRB), University of Wisconsin-Madison, Madison, WI 53706, USA.
³ Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
⁴ Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
⁵ Global Phasing Limited, Sheraton House, Castle Park, Cambridge, CB3 0AX, UK.
⁶ School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK.
⁷ Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan.
⁸ BioMagResBank (BMRB), UConn Health, 263 Farmington Avenue, Farmington, CT 06030, USA.
⁹ CCP4, Research Complex at Harwell (RCaH), Rutherford Appleton Laboratory, Didcot, Oxon OX11 0FA, UK.
¹⁰ MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK.
¹¹ Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 4HH, UK.

PMID: 30988261
PMCID: PMC6465986
DOI: 10.1107/S2059798319004522

Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB)

Paul D Adams et al. Acta Crystallogr D Struct Biol. 2019.

. 2019 Apr 1;75(Pt 4):451-454.

doi: 10.1107/S2059798319004522. Epub 2019 Apr 8.

Authors

Affiliations

¹ Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
² BioMagResBank (BMRB), University of Wisconsin-Madison, Madison, WI 53706, USA.
³ Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
⁴ Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
⁵ Global Phasing Limited, Sheraton House, Castle Park, Cambridge, CB3 0AX, UK.
⁶ School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK.
⁷ Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan.
⁸ BioMagResBank (BMRB), UConn Health, 263 Farmington Avenue, Farmington, CT 06030, USA.
⁹ CCP4, Research Complex at Harwell (RCaH), Rutherford Appleton Laboratory, Didcot, Oxon OX11 0FA, UK.
¹⁰ MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK.
¹¹ Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 4HH, UK.

PMID: 30988261
PMCID: PMC6465986
DOI: 10.1107/S2059798319004522

Abstract

This letter announces that PDBx/mmCIF format files will become mandatory for crystallographic depositions to the Protein Data Bank (PDB).

Keywords: OneDep; PDB; PDBx/mmCIF format; Protein Data Bank; Worldwide Protein Data Bank; biocuration; data archiving; data dictionary; data standards; macromolecular crystallography; mmCIF; validation; wwPDB.

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References

1. Adams, P. D., Afonine, P. V., Bunkóczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. J., Hung, L.-W., Kapral, G. J., Grosse-Kunstleve, R. W., McCoy, A. J., Moriarty, N. W., Oeffner, R., Read, R. J., Richardson, D. C., Richardson, J. S., Terwilliger, T. C. & Zwart, P. H. (2010). Acta Cryst. D66, 213–221. - PMC - PubMed
1. Bekker, G. J., Nakamura, H. & Kinjo, A. R. (2016). J. Cheminform, 8, 42, 1–5. - PMC - PubMed
1. Berman, H. M., Henrick, K. & Nakamura, H. (2003). Nat. Struct. Biol. 10, 980. - PubMed
1. Bernstein, H. J. (2000). Trends Biochem. Sci. 25, 453–455. - PubMed
1. Blanc, E., Roversi, P., Vonrhein, C., Flensburg, C., Lea, S. M. & Bricogne, G. (2004). Acta Cryst. D60, 2210–2221. - PubMed

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Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB)

Affiliations

Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB)

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