Re: [ccp4bb] To cryo or not to cryo...
Dear Yuri, I am a big fan of paratone oil (or similar oils) for freezing the holy crystal. The only drawback is that after you have frozen it in the oil its a little bit hard to recover the crystal if you want to seed from it, as its somewhat sticky... Best of luck! Marc Dr. Marc Kvansakul Laboratory Head, NHMRC CDA Fellow Dept. of Biochemistry| La Trobe University | Bundoora Rm 218, Phys Sci Bld 4, Kingsbury Drive, Melbourne, 3086, Australia T: 03 9479 2263 | F: 03 9479 1266 | E: m.kvansa...@latrobe.edu.au | On 1/12/12 8:22 AM, Yuri Pompeu yuri.pom...@ufl.edu wrote: Dear community, I have what seems to be a pretty decent single crystal that grew from a screen set up 2 weeks ago. I am trying to reproduce it but so far I have not succeeded. I am however afraid the crystal that did form will start to deteriorate. So this brings me to dilemma, I feel like I should try and mount this crystal and shoot it. But since I only have 1 sample, I do not want to mess this up... I am inclined to try cryo conditions, but I am afraid the addition of a cryo such as glycerol could destroy the little guy. The crystal formed in 30% PEG 4000, 0.1M NaCitrate pH5.6 and 0.2M NH4AcO, I wonder if this is a cryo condition already? Any suggestions would be appreciated. best,
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Thanks a lot to everyone for their insightful comments I certainly had an interesting day trying to digest all that was said! Although my initial reaction to the request was to turn it down since I had never heard of such a request before, I decided in the end to accede to the request, since not doing so would imply that all reviewers are simply out there to get me. To quote one email that I received Being paranoid is good, but you can't let it interfere with publishingŠ. Whilst on occasion this may be true, I would certainly hope it is not the norm. Without going into detail here there are some unusual topological aspects about the structure that could justify requesting the coordinates, so hopefully whoever is receiving the file will just sit back and enjoy the structure as much as I did, and produce a better review in the end that could not have been produced without the access. Best wishes Marc On 19/04/12 7:25 PM, Francois Berenger beren...@riken.jp wrote: Hi, There is the exact same problem when releasing a software, possibly open source, before the corresponding article is accepted. And I don't know a correct solution to this problem. Regards, F. On 04/19/2012 05:34 PM, Yu Wai Chen wrote: Dear Marc, As a reviewer I find it difficult to ³visualise² a structure based on a static 2D figure. I echo Joel's comments. If the (unreleased) coordinates are not supplied by the authors on request, I would simply refuse to review the paper on that ground. I suppose one can trust a reputable journal on the confidentiality issue. Wai -- Yu Wai Chen, PhDLecturer King's College London, Randall Division +44-207-848-8206 New Hunt's House, Guy's Campus, London SE1 1UL, U.K.
[ccp4bb] Off-topic: Supplying PDB file to reviewers
Dear CCP4BBlers, I was wondering how common it is that reviewers request to have a copy of the PDB coordinate file for the review purpose. I have just been asked to supply this by an editor after several weeks of review, after one of the reviewers requested a copy. Not having ever been asked to do this before I feel just a tad uncomfortable about handing this over… Your opinions would be greatly appreciated. Best wishes Marc Dr. Marc Kvansakul Laboratory Head, NHMRC CDA Fellow Dept. of Biochemistry| La Trobe University | Bundoora Rm 218, Phys Sci Bld 4, Kingsbury Drive, Melbourne, 3086, Australia T: 03 9479 2263 | F: 03 9479 2467 | E: m.kvansa...@latrobe.edu.au |
Re: [ccp4bb] Good way to check ion sites on Coot
Hi Andre, Majorie Harding wrote a few nice papers on metal ion binding sites and their associated coordination geometry, examples are: Harding MM (2006) Acta D vol. 62 pp. 678-82 or Harding MM (2004) Acta D vol. 60 pp. 849-59 Best Marc Dr. Marc Kvansakul Laboratory Head, NHMRC CDA Fellow Dept. of Biochemistry| La Trobe University | Bundoora Rm 218, Phys Sci Bld 4, Kingsbury Drive, Melbourne, 3086, Australia T: 03 9479 2263 | F: 03 9479 2467 | E: m.kvansa...@latrobe.edu.au | From: Zhijie Li zhijie...@utoronto.camailto:zhijie...@utoronto.ca Reply-To: Zhijie Li zhijie...@utoronto.camailto:zhijie...@utoronto.ca Date: Fri, 13 Apr 2012 16:37:43 -0400 To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Good way to check ion sites on Coot Hi This is what I do: ValidateHighly coordinated waters From: Andre Godoymailto:andre_go...@yahoo.com.br Sent: Friday, April 13, 2012 3:57 PM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Good way to check ion sites on Coot Dear all. can someone tell me what is the best way to check for ion binding sites on my structure? I mean, a text with coordination examples, or maybe a tool on coot for it ... best wishes Andre
[ccp4bb] Postdoc position available
SUMMARY DESCRIPTION: Structural biology of virus-host interactions The Kvansakul Laboratory is seeking a postdoctoral fellow to investigate the structural basis of inhibition of programmed cell death during viral infection (e.g. Kvansakul et al 2007 Mol. Cell 25: 933 942, Kvansakul et al Cell Death Differ 2008 15: 1564 1571, Kvansakul et al 2010 PLoS Pathogens Dec 23;6(12):e1001236). This position offers the opportunity to work in a highly collaborative and stimulating environment. The Kvansakul Lab is part of the recently established La Trobe Institute for Molecular Sciences (LIMS) at La Trobe University, Melbourne, Australia. LIMS is a multidisciplinary institute that brings together the Departments of Biochemistry, Chemistry, Genetics and Pharmacy. The successful candidate will have the opportunity to: 1.Express and purify viral and host proteins and their complexes 2.Investigate different host binding partners for viral effector proteins and their affinities 3. Crystallize and determine the macromolecular structure of these proteins and their complexes with ligands START DATE: The position is available immediately for 2 years in the first instance. REQUIREMENTS: Ph.D. in biochemistry, biophysics or structural biology. Experience with expression of recombinant proteins in a variety of hosts (bacteria, yeast, insects) and purification of proteins to a high degree of homogeneity are required. Prior experience with protein crystallization and structure determination is strongly desirable. Experience with biochemical assays and analyzing protein-protein interactions is also highly desirable. For more details see http://jobs.latrobe.edu.au/jobDetails.asp?sJobIDs=545338lWorkTypeID=lLoca tionID=lCategoryID=stp=AWsLanguage=en For informal enquiries please email m.kvansa...@latrobe.edu.au or come to the IUCr 2011 in Madrid. APPLICATION: Closing date is September 11th. Please apply online at http://jobs.latrobe.edu.au/jobDetails.asp?sJobIDs=545338lWorkTypeID=lLoca tionID=lCategoryID=stp=AWsLanguage=en
Re: [ccp4bb] Fwd: Regarding Sel-Met containing proteing crystallisation
Dear Atul, Whilst finding Se-Met conditions you could always just phase with mercury if you are lucky enough to have an accessible free Cys residue or try NaI or I3C soaks. Always worth trying if you have readily reproducible crystals… Best of luck Marc From: atul kumar atulsingh21...@gmail.commailto:atulsingh21...@gmail.com Reply-To: atul kumar atulsingh21...@gmail.commailto:atulsingh21...@gmail.com Date: Mon, 13 Jun 2011 15:53:12 +1000 To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Fwd: Regarding Sel-Met containing proteing crystallisation -- Forwarded message -- From: Dilip Kumar dku...@igib.inmailto:dku...@igib.in Date: Mon, Jun 13, 2011 at 11:21 AM Subject: Fwd: Regarding Sel-Met containing proteing crystallisation To: atulsingh21...@gmail.commailto:atulsingh21...@gmail.com -- Forwarded message -- From: Dilip Kumar dku...@igib.inmailto:dku...@igib.in Date: Sat, Jun 11, 2011 at 6:09 PM Subject: Regarding Sel-Met containing proteing crystallisation To: CCP4BB@jiscmail.ac.ukmailto:CCP4BB@jiscmail.ac.uk Dear all I have got protein crystals,crystallisation condition (LiCl, PEG and HEPES) .Crystals of native protein have been successesfully reproduced but when i tried to reproduce these crystals with protein having Met replaced by Sel-Met, i could not get any crystal.I tried crystallisation trials by varying pH and PEG concentration and diffferent drop ratio but i could not get any hit.Please suggest me what could be the possible reasons behind it? And also suggest the other variables that i can try ? thanks With Regards -- Dilip Tiwari Graduate Student Structural Biology Unit Institute of Genomics Integrative Biology Delhi-07 -- Dilip Tiwari Graduate Student Structural Biology Unit Institute of Genomics Integrative Biology Delhi-07
Re: [ccp4bb] PreScission Protease protein sequence
Dear BBlers, Would the kind donor of the prescission protease plasmid be willing to share another round? I would love to make this stuff in the lab... Best wishes Marc On 26/05/11 12:04 PM, Lieh Yoon Low liehy...@gmail.com wrote: Dear All, Thanks to all who replied me so quickly. In case you do not know, like myself until a few hours ago, that this protease is also known as the 3C protease from human rhinovirus. Thanks to Dima, the sequence is here if anyone is interested: gpeheflnal irrnchiitt dkgefnllgi ysncavvpth aepgdvvdid grlvrvlkqq vltdmndvdt evtvlwldqn ekfrdirrfi pehqqdwhni hlatnvtkfp mlnvevghtv pygeinlsgn atcrlykydy ptqpgqcgav lantgniigi hvggngrvgy aaallrkyfa eeq Someone within the bb has already offered to send the expression plasmid to me, and I understand that many labs already has it. You just need to ask around! Thanks again ray
