Many thanks to all of you for useful links and suggestions. Best regards... Hena
On Wed, Jul 24, 2013 at 7:51 PM, Bostjan Kobe <b.k...@uq.edu.au> wrote: > 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> > Reply-To: "Segelke, Brent W." <segel...@llnl.gov> > Date: Wed, 24 Jul 2013 16:52:35 +0000 > > To: <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**** > > ** ** > > ** ** > > ** ** > > *From:* CCP4 bulletin board > [mailto:CCP4BB@JISCMAIL.AC.UK<CCP4BB@JISCMAIL.AC.UK>] > *On Behalf Of *Janet Newman > *Sent:* Wednesday, July 24, 2013 9:23 AM > *To:* 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**** > ------------------------------ > > *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Hena > Dutta [hdutt...@gmail.com] > *Sent:* 25 July 2013 00:36 > *To:* 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**** > >
