[ccp4bb] Indexing problem
Dear All, A protein with SG P212121 co-crystallized with Benzamidine, cell dimension a=52.8, b=54.6, c= 82.90(reported). when I am going to reproduce the crystal with reported condition I am getting crystals. I am trying to index the frame (DENZO), it is showing P222 /P1 space group but the cell parameters are a=67.9, b=82.4, c=91.7. Should I continue with this parameter? What are the other possibilities for indexing? Thanks for your suggestions in advance. Regards, Dipankar Manna This e-mail and any files transmitted with it are for the sole use of the intended recipient(s) and may contain confidential and privileged information.If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.Any unauthorized review, use, disclosure, dissemination, forwarding,printing or copying of this email or any action taken in reliance on this e-mail is strictly prohibited and may be unlawful. Visit us at http://www.aurigene.com
Re: [ccp4bb] Indexing problem
Dear Dipankar, it happens quite frequently that using the same conditions, on still gets a different crystal form. Just process the data with the space group proposed by DENZO and run a molecular replacement program (e.g. Phaser) to solve the structure. You need to switch on the SGALTERNATIVE ALL option, to find out whether your true space group is P222, P212121, P2221 etc., since the determination of screw axes at the data processing stage is not very reliable. Best regards, Herman From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dipankar Manna Sent: Friday, June 29, 2012 8:15 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Indexing problem Dear All, A protein with SG P212121 co-crystallized with Benzamidine, cell dimension a=52.8, b=54.6, c= 82.90(reported). when I am going to reproduce the crystal with reported condition I am getting crystals. I am trying to index the frame (DENZO), it is showing P222 /P1 space group but the cell parameters are a=67.9, b=82.4, c=91.7. Should I continue with this parameter? What are the other possibilities for indexing? Thanks for your suggestions in advance. Regards, Dipankar Manna This e-mail and any files transmitted with it are for the sole use of the intended recipient(s) and may contain confidential and privileged information.If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.Any unauthorized review, use, disclosure, dissemination, forwarding,printing or copying of this email or any action taken in reliance on this e-mail is strictly prohibited and may be unlawful. Visit us at http://www.aurigene.com
[ccp4bb] Post-doc position - Umea University, Sweden
A two year post-doctoral fellowship is available in the group of Elisabeth Sauer-Eriksson and Tobias Hainzl at Umea University, Sweden. The project will involve structural characterizations of RNA and RNA-protein complexes based on X-ray crystallographic methods. Ideally, the applicant should have experience in macromolecular crystallography, protein and RNA molecular biology, biochemistry, crystallization and structure determination. Closing date is August 9, 2012. We are looking forward to receiving your application! /Liz Sauer-Eriksson and Tobias Hainzl For detailed information and application instructions, please visit http://www.umu.se/english/about-umu/news-events/grants/223-1440-12 For informal enquiries please contact elisabeth.sauer-eriks...@chem.umu.se or tobias.hai...@chem.umu.se
[ccp4bb] Layer Groups: B2 recognized?
Hello Everyone and especially symmetry experts, I found at http://img.chem.ucl.ac.uk/sgp/medium/003dy1.htm that B2 (SG #2) is a recognized space group that has a basis rotated from P2 (and as a result has two new positions). I'm wondering whether a similar B2 for P2 (LG #3) is recognized for the layer groups? I checked wikipedia (http://en.wikipedia.org/wiki/Layer_group) and the Bilbao server (http://www.cryst.ehu.es/subperiodic/get_sub_gen.html) and could find no evidence of a B2 layer group being recognized, but I can also come up with no logical reason why it shouldn't be recognized. Thank you for any input, James -- James Stroud http://www.jamesstroud.com
[ccp4bb] NCS on multiple conformations
Dear all, ok, never mind. I defined either peptide conformation as part of the protein it binds to and applied NCS to that. Should have thought of that before sending out the question. Andreas -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
[ccp4bb] Postdoc position
One postdoctoral position funded by NIH is available immediately at the Center for Membrane Biology, Department of Biochemistry and Molecular Biology, The University of Texas Houston Medical School (http://www.uth.tmc.edu/cmb/). The fellow will focus on structural determination of important membrane proteins involved in lipid metabolism and signaling. The fellow will also work with other lipid experts in the center for structural and functional characterization. The ideal candidate should be a self-motivated individual and have a recent PhD degree in structural biology or biochemistry. Decent experiences with standard molecular biology technique, protein crystallization and structural determination approaches are expected. The laboratory locates in the Texas Medical Center campus which provides an excellent environment for academia and research. The lab is fully equipped for protein x-ray crystallographic study, including a Graphon LCP crystallization robot, a Rigaku rotating anode X-ray home source and immediate access to the Berkeley ALS beamline 4.2.2 in the framework of the molecular biology consortium. To apply or request further information, please contact: Dr. Lei Zheng (E-mail: lei.zh...@uth.tmc.edu). The application should include a current resume and the names and addresses of three referees.
[ccp4bb] NCS on multiple conformations
Dear all, I have solved the structure of a protein with twofold NCS. On the axis relating the protein molecules sits a peptide ligand in two (mutually exclusive, partially occupied) conformations, effectively interacting with either protein molecule half of the time. Sorting out the side chain conformations of the ligand proves difficult. I would like to impose twofold NCS on the two conformations of the ligand. In Refmac, I can relate residue n of chain A to residue n of chain B. Can I also relate residue An of chain C to residue Bn of chain C? Or is there some other clever way of dealing with this situation? Thanks. Andreas -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
[ccp4bb] PhD position available at Umea University, Sweden
Dear All, A full time PhD student position is available in the laboratory of Uwe Sauer at the Chemical Biology Center at Umea University, Sweden. The project focuses on proteins involved in oxygenic photosynthesis. The successful candidate will determine 3D structures by X-ray Crystallography and study interactions and stabilities by applying Biochemical and Bioinformatics methods. The highly motivated applicant should have previous experience in macromolecular crystallography such as crystallization and structure determination and should be proficient in cloning techniques, protein molecular biology, and biochemistry methods. Enthusiasm, the ability to integrate into a team, and a fluent command of English, both spoken and written, are important. Knowledge of the Swedish language is an additional merit. The applicant should have completed a MSc (or equivalent) degree in Biophysics, Biochemistry or Molecular Biology. The complete application, marked with reference number 313-632-12, should be sent by e-mail to j...@umu.se (state the reference number in the subject field) or send by regular mail to the “Registrar, Umeå University, SE-901 87 Umeå, Sweden”. Closing date for the applications is August 15, 2012. More detailed application instructions are available at : http://www8.umu.se/umu/aktuellt/arkiv/lediga_tjanster/313-632-633-12.html For further information about the project and the PhD position, please have a look at: http://www.chemistry.umu.se/english/research/group-leaders/uwe-sauer/?languageId=1 For informal enquiries please contact uwe.sa...@chem.umu.se I am looking forward to your application! /Uwe Sauer -- Dr. Uwe H. Sauer, Associate Professor BioCrystallography BioInformatics Group Computational Life Science Cluster, CLiC Umea Centre for Molecular Research, UCMR Centre for Chemical Biology, KBC Deptartment of Chemistry Umea University, Linnaeus vag 6, SE-901 87 Umea, Sweden Tel: +46-(0)90-786-5930 FAX: +46-(0)90-786-7655 e-mail: uwe.sa...@chem.umu.se URL: http://soul.ucmp.umu.se/~ucmp/uhs/
[ccp4bb] Off-topic: 96-well plate PCR/plasmid purification
Dear All, I am looking for a bit of advice, and am interested to hear about experiences people have had with various commercially-available 96- well plate-based PCR, plasmid, and protein purification appliances and plates. Forgive me for comparing commercial vendors. We have a 96-well plate-compatible vacuum manifold (Qiavac). However, the plasmid-purification kits from this vendor do seem comparatively pricey to me. So, I am looking for a more cost-efficient system. How compatible are 96-well PCR purification plates/plasmid-binding and filter plates from different vendors with this type of vacuum manifold? From what I can see, it becomes difficult to avoid cross- contamination between wells, when using e.g. Whatman-type 96-well microplates with Qiavac, because the distance between the drip director of the DNA-binding/filter plate and a receiver plate (e.g. PCR plate) in the manifold is relatively long, and the alignment isn't great (drops end up on the rim). The alternative would be centrifugation directly on top of a receiver plate, but I am concerned about cross-contamination. Which type of membranes/filter plates were people most pleased with for (bacterial) lysate-clearing, avoiding clogging with lysates from ~ 5 ml bacterial cultures; and which DNA/plasmid-binding plates have most binding capacity and result in highest purity? Again cost- efficient vendors would be preferred. Regards, Florian
[ccp4bb] Protein thermostability
Dear all I have two homologues structures, from a mesophilic bacterium and a thermophilic bacterium. Is there any software or server that can calculate the differences that contribute to thermostability, e.g. proportion of amino acids that form Hydrogen bonds and number of prolines? Thank you.
Re: [ccp4bb] Protein thermostability
Hi Hsu, You can check my paper. We have done a similar analysis of several factors responsible for thermal stability, analysis done using various mesophiles and thermophiles, Crystal structure of the *Bacillus anthracis* nucleoside diphosphate kinase and its characterization reveals an enzyme adapted to perform under stress conditions. Gauri Misra et al. Proteins: Structure, Function, and Bioinformatics Volume 76, Issue 2, http://onlinelibrary.wiley.com/doi/10.1002/prot.v76:2/issuetoc pages 496–506, 1 August 2009 Hope it gives you some help. Best wishes, Gauri On Sat, Jun 30, 2012 at 7:45 AM, Theresa Hsu theresah...@live.com wrote: Dear all I have two homologues structures, from a mesophilic bacterium and a thermophilic bacterium. Is there any software or server that can calculate the differences that contribute to thermostability, e.g. proportion of amino acids that form Hydrogen bonds and number of prolines? Thank you.
