Re: [ccp4bb] A question on the diffrentiattion of the salt crystal and salt diffraction in the protein metal complex
*** This message has been scanned by the InterScan for CSC SSM by IICT security policy and found to be free of known security risks. *** This link probably may help you with this and other related questions. http://www2.mrc-lmb.cam.ac.uk/groups/JYL/WWWrobots/newsletters/Newsletter_july_2011.pdf Anthony - Dr. Anthony Addlagatta Center for Chemical Biology Indian Institute of Chemical Technology [IICT] Tarnaka, Hyderabad AP-500 607, INDIA Tel:91-40-27191812 Web: https://sites.google.com/site/chembioliict/home/dr-anthony-addlagatta-1 -- Original Message --- From: Acoot Brett acootbr...@yahoo.com To: CCP4BB@JISCMAIL.AC.UK Sent: Sun, 1 Dec 2013 19:16:06 -0800 Subject: [ccp4bb] A question on the diffrentiattion of the salt crystal and salt diffraction in the protein metal complex *** This message has been scanned by the InterScan for CSC SSM at IICT and found to be free of known security risks. *** Dear All, Suppose I have a crystal hit from the protein-metal complex, with the possibility of that the hit is a salt crystal. When I diffract it by X-ray, I got some metal (or salt) diffraction without the protein diffraction (maybe due to too low protein resolution). Will you please tell me how to know whether my diffraction was from a salt crystal or from the diffraction of the metal in my protein-metal complex? I am looking forward to getting your reply. Cheers, Acoot --- End of Original Message --- - Note: The information contained in the e-Mail message and/or attachments to it may contain confidential or privileged information. If you are not the intended recipient, any dissemination, use, review, distribute, prinitng or copying of the information contianed in this e-Mail message and/or attachments to it are strictly prohibited. If you have received this communication in error. Please notify us by reply e-Mail or telephone and immediately and permanently delete the message and any attachment. Thank you.
Re: [ccp4bb] How it could be possible?
Hi, If there is a hinge motion between the two domains, then allowing for this will give you a much better starting model. As Klaus suggested, you may just be able to do rigid body refinement of the two domains. However, it is also possible to place the two domains separately in Phaser, by putting the two domains in separate PDB files, defining an ENSEMBLE with each of these PDB files, then searching for both of them in the same job. In the ccp4i GUI, you can specify an additional ensemble by clicking the Add ensemble button, and you can add another component to search for in the same job by clicking the Add another search button. I hope that answers the question you were asking! Best wishes, Randy Read On 2 Dec 2013, at 04:11, Prem Prakash prem...@gmail.com wrote: Dear All, The density obtained after molecular replacement using phaser at 2.5 Angstrom and then used buccneer for autobuilding of the model. I am not getting reasonable R value (it is 38.5 %) but the figure of merit is 0.629. As My protein has two domains. So is it possible to fragment the individual domain and then again perform the molecular replacement. How it will improve my phase more and how R-factor will be reduced ? Please help and direct me in proceeding in a right way, and if possible provide a protocol for doing that. Thank you With kind regards -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
Re: [ccp4bb] Proper format for buccaneer heavy atom file?
Hi! Just a list of atoms with type or element set to SE should do it. (Note that your heavy atom program may not have allocated the atom type). Having said that, the heavy atom info biases the sequencing to try and get MET/MSE in the right place, but if the sequence doesn't want to fit it won't force it. That can be a result of tracing errors. Kevin On 1 December 2013 19:00, Francis Reyes francis.re...@colorado.edu wrote: Hi all, Is there a special format (residue naming, atom naming, etc) for the heavy atom file to assist buccaneer with sequence assignment? The one I have now seems to be returning structures that do not have SeMet at these locations. Thanks F - Francis E. Reyes PhD 215 UCB University of Colorado at Boulder -- EMAIL DISCLAIMER: http://www.york.ac.uk/docs/disclaimer/email.htm
[ccp4bb] PhD positions at Imperial College, UK
Dear all, Imperial college currently has some PhD studentships available through a BBSRC DTP. http://www3.imperial.ac.uk/bbsrcdoctoraltrainingpartnership/phdprojects The mode of action of the cereal mildew RNAse-like effectors Structural Basis of Calvin Cycle Regulation Pesticide effects on bee foraging performance and crop yields Using novel machine-learning approaches to understand the structure and function of complex interaction networks in agricultural systems Structure based inhibitor design for multi-drug resistance ABC exporters A toolkit for new biosynthetic protein materials from chaperone-usher pili Unraveling the metabolic basis of microbial responses to environmental temperature Understanding Ribosome Stabilisation in Mycobacteria Several of these are mainly structural or have a structural biology component. I would appreciate it if this information could be brought to the attention of suitable candidates. best wishes James -- Dr. James W. Murray Lecturer in Biotechnology Dept. Life Sciences Imperial College, London Tel: +44 (0)20 759 48895
[ccp4bb] Stand-alone wwPDB X-ray validation server
Dear colleagues, The wwPDB partners are pleased to announce that X-ray structure validation reports can now be generated on demand by macromolecular crystallographers by using the new stand-alone wwPDB validation server. For the full scoop, see: http://wwpdb.org/news/news_2013.html#27-November-2013 If you want to skip the propaganda, go to http://wwpdb.org/validation-servers.html to read the technical notes and from there follow the link to the server. This version of the validation server is still in beta testing. We appreciate your feedback and suggestions for improvement - please mail these to: validat...@mail.wwpdb.org (not to me or the list). Thanks! Best wishes, --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
Re: [ccp4bb] How it could be possible?
Thank you very much for kind suggestions and comment. With kind regards Prem On Mon, Dec 2, 2013 at 5:41 PM, Randy Read rj...@cam.ac.uk wrote: Hi, If there is a hinge motion between the two domains, then allowing for this will give you a much better starting model. As Klaus suggested, you may just be able to do rigid body refinement of the two domains. However, it is also possible to place the two domains separately in Phaser, by putting the two domains in separate PDB files, defining an ENSEMBLE with each of these PDB files, then searching for both of them in the same job. In the ccp4i GUI, you can specify an additional ensemble by clicking the Add ensemble button, and you can add another component to search for in the same job by clicking the Add another search button. I hope that answers the question you were asking! Best wishes, Randy Read On 2 Dec 2013, at 04:11, Prem Prakash prem...@gmail.com wrote: Dear All, The density obtained after molecular replacement using phaser at 2.5 Angstrom and then used buccneer for autobuilding of the model. I am not getting reasonable R value (it is 38.5 %) but the figure of merit is 0.629. As My protein has two domains. So is it possible to fragment the individual domain and then again perform the molecular replacement. How it will improve my phase more and how R-factor will be reduced ? Please help and direct me in proceeding in a right way, and if possible provide a protocol for doing that. Thank you With kind regards -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
Re: [ccp4bb] A question on the diffrentiattion of the salt crystal and salt diffraction in the protein metal complex
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Acoot, the positions of the reflections on the detector depend on the unit cell dimensions, but not at all on the content of the unit cell. Therefore a protein crystal with a rather large cell produces a large number of reflections per image. A salt crystal has a very small unit cell and you will only observe very few spots. These, however, will be a very high intensity. Best, Tim On 12/02/2013 04:16 AM, Acoot Brett wrote: Dear All, Suppose I have a crystal hit from the protein-metal complex, with the possibility of that the hit is a salt crystal. When I diffract it by X-ray, I got some metal (or salt) diffraction without the protein diffraction (maybe due to too low protein resolution). Will you please tell me how to know whether my diffraction was from a salt crystal or from the diffraction of the metal in my protein-metal complex? I am looking forward to getting your reply. Cheers, Acoot - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFSnKPiUxlJ7aRr7hoRAnLqAJ9TkMhashPG7KMtcFhSGQDGvLfNVgCgxLjQ U/qUNkJS9k6U9VkhiLYKXIY= =jrjW -END PGP SIGNATURE-
[ccp4bb] FINAL CALL: Jalview course + workshop at Oxford, Dec 12-13
There are only two days left to register for the two day training course and workshop on Jalview that takes place in Oxford next week. This workshop is an ideal opportunity for students, educators and researchers of all abilities who want to get to know Jalview better, and for bioinformaticians to get started with the JalviewLite applet and Jalview's source. The event is heavily subsidised and registration for both days including a workshop dinner is just £35, with a very limited number of rooms available for £10 per night. Register by 4th December via http://bit.ly/jalviewOx2014 Link for more information: http://www.jalview.org/training/training-courses/4th-Jalview-and-JABA-Residential-Workshop PDF Poster at :http://www.jalview.org/file/152 Thanks - and please forward this to people in your institute who might be interested! Jim Procter and Geoff Barton -- Geoff Barton Professor of Bioinformatics Head of Division of Computational Biology College of Life Sciences University of Dundee, Scotland, UK. g.j.bar...@dundee.ac.uk Tel:+44 1382 385860 www.compbio.dundee.ac.uk The University of Dundee is registered Scottish charity: No.SC015096
[ccp4bb] Postdoc position in membrane protein crystallography and pharmacology
Dear All, The laboratory of Hiro Furukawa at Cold Spring Harbor Laboratory (CSHL) is seeking a postdoc with dynamic interests in solving problems in neurological disorders and diseases using biochemical and biophysical techniques. We conduct x-ray crystallography on transmembrane proteins to understand basic mechanisms of ion and substrate transport across the membrane and on fragments of water soluble domains to answer specific pharmacological questions. We validate structure-based functional hypotheses by a combination of techniques such as electrophysiology and calcium imaging. We have excellent setups to conduct membrane protein biochemistry and crystallography such as Mosquito LCP and have frequent accesses to synchrotron light sources including NSLS and APS. CSHL offers a unique scientific environment to interact with scientists within the institute as well as from outside at courses and meetings. A qualified candidate should hold or soon expected to hold (within ~1yr) Ph.D. in the area of crystallography and biochemistry and have experiences in basic molecular biology, biochemistry, and protein expression. Experience in x-ray crystallography or electron microscopy is desired but not necessary. Please see the lab website (http://www.cshl.edu/public/SCIENCE/furukawa.html) for further information and send CV with a brief research statement as well as 2-3 contacts for references to furuk...@cshl.edu Best wishes, Tomas Dr. Tomas Malinauskas Cold Spring Harbor Laboratory One Bungtown Road Cold Spring Harbor New York 11724 United States of America Email: tmalinaus...@cshl.edu tomas.malinaus...@gmail.com Tel: (516) 367-6824
Re: [ccp4bb] A question on the diffrentiattion of the salt crystal and salt diffraction in the protein metal complex
Dear Acoot, Just to add to other good ideas, you could also try to index your frames, find the cell parameters, check them against one of the relevant databases (CSD, ICSD; see http://www.iucr.org/resources/data or COD, http://www.crystallography.net/index.php, which unfortunately is still not listed at that IUCr page) or have a friend run them for you, if you don't have access. Chances are you might even find out what your salt is from the cell dimensions, which might give you some directions at reducing relevant concentrations or changing some other parameter of technique. (And, by the way, if the cell parameters are novel, you might even have a new compound--e.g. a new set of ligands around the metal center. In that case, just measure your data out to 1.2 A or better, preferably at least 0.83 A--doable on an ordinary home Cu source meant for protein crystallography--solve, refine and publish it.) Best regards, Navdeep --- On Sun, Dec 01, 2013 at 07:16:06PM -0800, Acoot Brett wrote: Dear All, Suppose I have a crystal hit from the protein-metal complex, with the possibility of that the hit is a salt crystal. When I diffract it by X-ray, I got some metal (or salt) diffraction without the protein diffraction (maybe due to too low protein resolution). Will you please tell me how to know whether my diffraction was from a salt crystal or from the diffraction of the metal in my protein-metal complex? I am looking forward to getting your reply. Cheers, Acoot --- Navdeep Sidhu University of Goettingen ---
[ccp4bb] Job Posting Request
*Merck* is a global health care leader with a diversified portfolio of prescription medicines, vaccines and consumer health products, as well as animal health products. Today, we are building a new kind of healthcare company - one that is ready to help create a healthier future for all of us. Our ability to excel depends on the integrity, knowledge, imagination, skill, diversity and teamwork of people like you. To this end, we strive to create an environment of mutual respect, encouragement and teamwork. As part of our global team, you'll have the opportunity to collaborate with talented and dedicated colleagues while developing and expanding your career. This exciting position within Merck's Structural Chemistry group will support drug lead discovery and optimization through the determination of the X-ray structures of therapeutically important proteins. The successful candidate will perform crystallization, crystal optimization, and structure determination of protein-ligand complexes and will work in collaboration with medicinal and computational chemists. The successful candidate will also work closely with molecular biologists and protein biochemists and will have access to automated cloning, expression, and crystallization technologies. *Sr. Scientist, Chemistry West Point, PA Job # CHE003955* Productive and collaborative interactions with other members of the global, cross-functional department are a must. Cooperative and collaborative use of internal expertise will be essential to success. The position requires active interaction with the scientific community to continually improve scientific understanding, including presentations at national or international meetings. *Qualifications:* - PhD degree with 2- 3 years postdoctoral training in membrane protein crystallography. - Demonstrated capability to design and execute X-ray crystallographic structure determination using all modern techniques, including molecular replacement and experimental phasing. - Demonstrated potential to develop project management skills and identify/develop new areas of scientific expertise in protein crystallography. - Excellent communication skills (written, presentation, and oral) that enhance team-based progress is required. Application of those skills both within and outside the department to ensure the maximum understanding of program status for therapeutic area project teams and management is required. - Ability to work effectively within timelines. - Ability to prepare peer-reviewed publications. PREFERRED SKILLS: - State-of-the-art knowledge of GPCR structural biology techniques including all aspects of GPCR construct design, expression, solubilization, purification, crystallization screening/optimization (including LCP and LCP-FRAP), and structure determination/analysis a significant plus. - Experience in the application of biophysical and functional characterization methods (e.g., protein NMR, Biacore, Thermofluor, ligand binding and receptor modality) to guide protein construct optimization for crystallography is a plus. Our employees are the key to our company's success. We demonstrate our commitment to our employees by offering a competitive and valuable rewards program. Merck's benefits are designed to support the wide range of goals, needs and lifestyles of our employees, and many of the people that matter the most in their lives. To be considered for this position, please visit: http://jobs.merck.com/job/West-Point-Sr_-Scientist%2C-GSC%2C-Chemistry-Job-PA-19486/29518900/ Merck is an equal opportunity employer, M/F/D/V - proudly embracing diversity in all of its manifestations. Former Military, Transitioning Service Members, National Guard Reserves - We value your past and present service.
[ccp4bb] CCP4-6.4.0 Update 005
Dear CCP4 Users, An update for the CCP4-6.4.0 series has just been released, consisting of the following changes: - Documentation (all): new documentation for othercell and updated documentation for pointless and aimless - cprodrg (Mac): fix for segfault on OSX - ctruncate (all): better handling of resolution limits for tests - crank (all): fixes for use of ARP/wARP 7.4 - aimless (all): inclusion of history in MTZ - pointless (all): fix axial reflection bug Note that auto-updates work only with CCP4 6.4.0 series, therefore please upgrade if necessary. The Update Manager is now included in the package so you do not need to install it separately. In addition, all available updates will be installed automatically if you are using Setup Manager for CCP4 installation. Please report any bugs to c...@stfc.ac.uk. Many thanks for using CCP4. -- David
[ccp4bb] PhD positions at AgResearch New Zealand
Dear all, AgResearch currently has some PhD positions available. Please contact Dr Ron Ronimus if you are interested (Details below). cheers Vince We are seeking two outstanding PhD candidates to undertake research thesis projects within the overall program: “The writing is on the wall: elucidating the deep evolutionary links between cell wall synthesis in bacteria and methanogenic archaea”. Applicants are invited to apply for a three year PhD full scholarship that is funded by a prestigious Royal Society of New Zealand Marsden fund grant. The research would be undertaken at AgResearch in Palmerston North, New Zealand and the Institute of Fundamental Sciences at Massey University, Palmerston North, New Zealand (www.ifs.massey.ac.nz). PhD enrolment will be at Massey University. These two projects will investigate the early evolution of cell walls in methanogenic archaea. Bacterial cell walls are predominantly comprised of murein (peptidoglycan) which contains a glycan backbone with beta (1-4) bonds composed of alternating N-acetylglucosamine (NAG) and muramic acid (NAM) residues, the latter of which is bonded to a pentapeptide. Interestingly, archaea are not known to possess murein, but instead they contain a diverse range of cell wall types composed of sulphated-heteropolysaccharides, methanochondroitin, glutaminylglycan, protein, glycoprotein surface layers or pseudomurein, the latter being a structural analogue of murein. These projects will investigate whether there are deep evolutionary connections between the biosynthesis of cell walls in methanogenic archaea and murein in bacteria using thermophilic methanogens as model organisms. The intended start date for these projects is March 1st, 2013, or as soon as possible, after this date. The closing date for applications is January 9th, 2014. Candidates are encouraged to apply as soon as possible. The candidates will have strong supervisory support in all aspects of the research and would be in a good position to acquire a wide range of research skills, with emphasis on structural biology and biochemical characterisation. There will be opportunities to attend conferences both in New Zealand and abroad. The stipend is 30,000$ NZ (tax free) per year for three years. Tuition fees will be paid for separately by the Marsden fund grant. The primary supervisors include Dr Andrew Sutherland-Smith (Massey University, specialising in crystal structure determinations and in vitro mutagenesis), and Dr Ron Ronimus (AgResearch, specialising in cloning, protein purification, phylogenetics and biochemical characterisation). The Marsden project also includes collaboration with Professor William F. Martin based at the University of Dusseldorf, Germany. Interested persons can contact principle investigator Dr Ron Ronimus by email (ron.roni...@agresearch.co.nz, phone (+64-6-351-8036) or Fax (+64-6-351-8003)). Alternatively, interested persons can contact Dr Andrew Sutherland-Smith (phone: +64-6-356-9099 Ext 84701; Fax: +64-6-350-5688; a.j.sutherland-sm...@massey.ac.nz).
