ContaMiner and ContaBase: a webserver and database for early identification of unwantedly crystallized protein contaminants

Handle URI:
http://hdl.handle.net/10754/622056
Title:
ContaMiner and ContaBase: a webserver and database for early identification of unwantedly crystallized protein contaminants
Authors:
Hungler, Arnaud; Momin, Afaque Ahmad Imtiyaz; Diederichs, Kay; Arold, Stefan T. ( 0000-0001-5278-0668 )
Abstract:
Solving the phase problem in protein X-ray crystallography relies heavily on the identity of the crystallized protein, especially when molecular replacement (MR) methods are used. Yet, it is not uncommon that a contaminant crystallizes instead of the protein of interest. Such contaminants may be proteins from the expression host organism, protein fusion tags or proteins added during the purification steps. Many contaminants co-purify easily, crystallize and give good diffraction data. Identification of contaminant crystals may take time, since the presence of the contaminant is unexpected and its identity unknown. A webserver (ContaMiner) and a contaminant database (ContaBase) have been established, to allow fast MR-based screening of crystallographic data against currently 62 known contaminants. The web-based ContaMiner (available at http://strube.cbrc.kaust.edu.sa/contaminer/) currently produces results in 5 min to 4 h. The program is also available in a github repository and can be installed locally. ContaMiner enables screening of novel crystals at synchrotron beamlines, and it would be valuable as a routine safety check for 'crystallization and preliminary X-ray analysis' publications. Thus, in addition to potentially saving X-ray crystallographers much time and effort, ContaMiner might considerably lower the risk of publishing erroneous data. A web server, titled ContaMiner, has been established, which allows fast molecular-replacement-based screening of crystallographic data against a database (ContaBase) of currently 62 potential contaminants. ContaMiner enables systematic screening of novel crystals at synchrotron beamlines, and it would be valuable as a routine safety check for 'crystallization and preliminary X-ray analysis' publications. © Arnaud Hungler et al. 2016.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; Computational Bioscience Research Center (CBRC)
Citation:
Hungler A, Momin A, Diederichs K, Arold S T (2016) ContaMiner and ContaBase: a webserver and database for early identification of unwantedly crystallized protein contaminants. Journal of Applied Crystallography 49: 2252–2258. Available: http://dx.doi.org/10.1107/S1600576716014965.
Publisher:
International Union of Crystallography (IUCr)
Journal:
Journal of Applied Crystallography
KAUST Grant Number:
URF/1/1976-04; URF/1/2602-01-01
Issue Date:
2-Nov-2016
DOI:
10.1107/S1600576716014965
Type:
Article
ISSN:
1600-5767
Sponsors:
We thank Dr Alexey Vagin for help with the MoRDa program, Sarah Sahli for editorial help, and all colleagues who helped test the ContaMiner web page. We also thank all colleagues who have made their own compiled contaminant databases accessible to the community, including Dr Marcin Wojdyr and Dr James Murray. We thank ContaMiner users for communicating several contaminants and Dr Albane le Maire, Dr Manfred Weiss, Dr Ronan Keegan and the reviewers for interesting suggestions and discussions. The research reported in this publication was supported by the King Abdullah University of Science and Technology (KAUST) through the baseline fund and the Office of Sponsored Research (OSR) under award Nos. URF/1/1976-04 and URF/1/2602-01-01.
Additional Links:
http://scripts.iucr.org/cgi-bin/paper?S1600576716014965
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC); Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorHungler, Arnauden
dc.contributor.authorMomin, Afaque Ahmad Imtiyazen
dc.contributor.authorDiederichs, Kayen
dc.contributor.authorArold, Stefan T.en
dc.date.accessioned2016-12-22T13:34:55Z-
dc.date.available2016-12-22T13:34:55Z-
dc.date.issued2016-11-02en
dc.identifier.citationHungler A, Momin A, Diederichs K, Arold S T (2016) ContaMiner and ContaBase: a webserver and database for early identification of unwantedly crystallized protein contaminants. Journal of Applied Crystallography 49: 2252–2258. Available: http://dx.doi.org/10.1107/S1600576716014965.en
dc.identifier.issn1600-5767en
dc.identifier.doi10.1107/S1600576716014965en
dc.identifier.urihttp://hdl.handle.net/10754/622056-
dc.description.abstractSolving the phase problem in protein X-ray crystallography relies heavily on the identity of the crystallized protein, especially when molecular replacement (MR) methods are used. Yet, it is not uncommon that a contaminant crystallizes instead of the protein of interest. Such contaminants may be proteins from the expression host organism, protein fusion tags or proteins added during the purification steps. Many contaminants co-purify easily, crystallize and give good diffraction data. Identification of contaminant crystals may take time, since the presence of the contaminant is unexpected and its identity unknown. A webserver (ContaMiner) and a contaminant database (ContaBase) have been established, to allow fast MR-based screening of crystallographic data against currently 62 known contaminants. The web-based ContaMiner (available at http://strube.cbrc.kaust.edu.sa/contaminer/) currently produces results in 5 min to 4 h. The program is also available in a github repository and can be installed locally. ContaMiner enables screening of novel crystals at synchrotron beamlines, and it would be valuable as a routine safety check for 'crystallization and preliminary X-ray analysis' publications. Thus, in addition to potentially saving X-ray crystallographers much time and effort, ContaMiner might considerably lower the risk of publishing erroneous data. A web server, titled ContaMiner, has been established, which allows fast molecular-replacement-based screening of crystallographic data against a database (ContaBase) of currently 62 potential contaminants. ContaMiner enables systematic screening of novel crystals at synchrotron beamlines, and it would be valuable as a routine safety check for 'crystallization and preliminary X-ray analysis' publications. © Arnaud Hungler et al. 2016.en
dc.description.sponsorshipWe thank Dr Alexey Vagin for help with the MoRDa program, Sarah Sahli for editorial help, and all colleagues who helped test the ContaMiner web page. We also thank all colleagues who have made their own compiled contaminant databases accessible to the community, including Dr Marcin Wojdyr and Dr James Murray. We thank ContaMiner users for communicating several contaminants and Dr Albane le Maire, Dr Manfred Weiss, Dr Ronan Keegan and the reviewers for interesting suggestions and discussions. The research reported in this publication was supported by the King Abdullah University of Science and Technology (KAUST) through the baseline fund and the Office of Sponsored Research (OSR) under award Nos. URF/1/1976-04 and URF/1/2602-01-01.en
dc.publisherInternational Union of Crystallography (IUCr)en
dc.relation.urlhttp://scripts.iucr.org/cgi-bin/paper?S1600576716014965en
dc.rightsArchived with thanks to Journal of Applied Crystallographyen
dc.subjectcomputer programsen
dc.subjectcontaminant crystalsen
dc.subjectdiffractionen
dc.subjectmolecular replacementen
dc.titleContaMiner and ContaBase: a webserver and database for early identification of unwantedly crystallized protein contaminantsen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalJournal of Applied Crystallographyen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionFachbereich Biologie, Universität Konstanz, M647, Konstanz, Germanyen
kaust.authorHungler, Arnauden
kaust.authorMomin, Afaque Ahmad Imtiyazen
kaust.authorArold, Stefan T.en
kaust.grant.numberURF/1/1976-04en
kaust.grant.numberURF/1/2602-01-01en
All Items in KAUST are protected by copyright, with all rights reserved, unless otherwise indicated.