Hena I agree with the responses so far, but I think It may not be a complete waste of time looking at the crystallization conditions for similar proteins, you may find a common additive for example and there may be a functional reason for this being required in crystallization.
Bostjan --- Bostjan Kobe NHMRC Research Fellow Professor of Structural Biology School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience (Division of Chemistry and Structural Biology) and Centre for Infectious Disease Research Cooper Road University of Queensland Brisbane, Queensland 4072 Australia Phone: +61 7 3365 2132 Fax: +61 7 3365 4699 E-mail: b.k...@uq.edu.au URL: http://www.scmb.uq.edu.au/staff/bostjan-kobe Office: Building 76 Room 329 Notice: If you receive this e-mail by mistake, please notify me, and do not make any use of its contents. I do not waive any privilege, confidentiality or copyright associated with it. Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland. From: "Segelke, Brent W." <segel...@llnl.gov<mailto:segel...@llnl.gov>> Reply-To: "Segelke, Brent W." <segel...@llnl.gov<mailto:segel...@llnl.gov>> Date: Wed, 24 Jul 2013 16:52:35 +0000 To: <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> Subject: Re: [ccp4bb] database of crystallization condition Hena, I think this notion of fold families having similar crystallization conditions has been kicking around since the 80’s at least. I seem to recall Gary Gilliland presenting a fairly comprehensive and well controlled study for myoglobins and showing some correlation of crystallization conditions. However, I believe this example is an exception. Just to add to what Janet and Enrico have said: Taking the HIV integrase example from David Davies; or any of the Derewenda surface entropy reduction, protein engineering, examples; it is clear that small changes (even single point mutations) can dramatically alter the bulk properties (and crystallization behavior) of a protein. One last point, it is very hard to control for investigator preference when probing a database of successes. It may be that a review of the BMCD will reveal a correlation between crystallization conditions and fold families, but that could be due to a preference for particular crystallization conditions used in crystallization screens rather than properties of the protein family. Brent Brent W. Segelke Senior Biomedical Scientist Lawrence Livermore National Laboratory 7000 East Avenue, Livermore CA, 94550 USA segek...@llnl.gov<mailto:segek...@llnl.gov> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Janet Newman Sent: Wednesday, July 24, 2013 9:23 AM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] database of crystallization condition Dear Hena, The BMCD might be a resource worth investigating: http://xpdb.nist.gov:8060/BMCD4/index.faces Although there are claims that structurally similar proteins may crystallise under similar conditions (the existence of directed screens -such as the Jena Biosciences 'Kinase' screen, you have to wonder (as Enrico points out) how these can work, as the bits that change the most in any protein family are the outside bits (ie, away from the active site) and thus are generally the parts going to affect crystallisation the most. Janet Janet Newman Principal Scientist / Director, Collaborative Crystallisation Centre CSIRO Material Science and Engineering 343 Royal Parade Parkville. VIC. 3052 Australia Tel +613 9662 7326 Email janet.new...@csiro.au<mailto:janet.new...@csiro.au> ________________________________ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>] on behalf of Hena Dutta [hdutt...@gmail.com<mailto:hdutt...@gmail.com>] Sent: 25 July 2013 00:36 To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] database of crystallization condition Hi, Can anyone tell, if there is any database containing the crystallization conditions of published structures? I want to see the conditions people have used for those proteins having some structural similarity. Any suggestion would be appreciated. Regards... Hena
