ContaMiner and ContaBase: a webserver and database for early identification of unwantedly crystallized protein contaminants
KAUST DepartmentBiological and Environmental Sciences and Engineering (BESE) Division
Computational Bioscience Research Center (CBRC)
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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.
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.
SponsorsWe 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.