[ccp4bb] postdoc position available in antibiotics uptake, Newcastle University (UK)
An immediate position is available for up to 5 years for an enthusiastic and highly motivated postdoctoral Research Associate in the area of Outer Membrane Uptake of Antibiotics. You will participate in a European consortium (TRANSLOCATION) consisting of academic labs, small biotech firms and big pharma. The overall goal of the consortium is to understand antibiotics translocation across the outer membrane of pathogenic Gram-negative bacteria, as part of the Innovative Medicines Initiative (IMI) project “New Drugs for Bad Bugs”. The project at Newcastle University (UK) focuses on determining crystal structures of outer membrane channels with and without bound antibiotics, and on determining the specificity of antibiotics uptake by developing and performing in vivo and in vitro transport assays. Relevant experience in these techniques is expected from the applicant. The successful candidate will have a PhD or previous post-doctoral experience in X-ray crystallography and biochemistry or biophysics and should have published at least one first author paper in a leading journal. Further information regarding this post can be obtained by contacting Prof Bert van den Berg (bert.van-den-b...@ncl.ac.ukmailto:bert.van-den-b...@ncl.ac.uk). mailto:CCP4BB@JISCMAIL.AC.UK
Re: [ccp4bb] Build DNA to fit density
Hi Wei, If you have an interpretable density, the efficientest way in my opinion, is to construct manually (only 6bp). You can use coot and the button add residue. Coot can add nucleotide directly at the extremity of your existing nucleic acid model. Hope to help you. Nicolas Le 18/03/13 03:43, Wei Shi a écrit : Hi all, I am refining a structure of protein-DNA complex with coot. The DNA in my search model is shorter than the DNA in the crystal, and now I could see the density for extra DNA(6 base pairs) on either end of the search model DNA. But, I don't know how to build the extra DNA back to fit the density or whether I should build the whole DNA manually to fit the density. I used calculate- other model tools- ideal DNA/RNA to generate a 6 base pairs (B form) and then, I use calculate- model/fit/refine-rotate/Translate molecule to move the 6 bp long stretch of double strand DNA to fit the density, but it's hard for me to fit the DNA into the density and it seems that the B form DNA I generate doesn't fit the density well. I am wondering how to fit the DNA into the density and whether we could fit the DNA into density like we add amino acid to fit the density. Thank you so much! Best, Wei
Re: [ccp4bb] space group determination problem
Dear All, Firstly, thanks Ian and Michael's efforts on this issue and everyone's. We pointed the space group to P43212, then it works okay. Best Wishes, Gengxiang On Fri, Mar 15, 2013 at 1:26 PM, Ian Tickle ianj...@gmail.com wrote: Michael, yes sorry I had (temporarily) forgotten about LABELIT. In the pseudo-precession image in the article (Fig. 3a) one can clearly see the TDS streaks along the axes which could easily fool you into misassigning the space group if all you have are the integrated intensities. Very nice! Cheers -- Ian On 15 March 2013 17:10, Michael Thompson mi...@chem.ucla.edu wrote: As a follow up to Ian's suggestion, the LABELIT software (sorry for a non-CCP4 suggestion) will create artificial precession images from your raw oscillation images. Documentation can be found here: http://adder.lbl.gov/labelit/ And an article describing the functionality can be found here: http://cci.lbl.gov/publications/download/CCN_2011_p15.pdf Hope it helps, Mike - Original Message - From: Ian Tickle ianj...@gmail.com To: CCP4BB@JISCMAIL.AC.UK Sent: Friday, March 15, 2013 8:51:47 AM GMT -08:00 US/Canada Pacific Subject: Re: [ccp4bb] space group determination problem Hi Gengxiang, Personally I find it impossible to reliably assign a space group from integrated reflections because you just don't know if the apparent systematic absence violations are due to a TDS streak or overlapping neighbouring strong spots. In the old days (i.e. when we had precession cameras) we would never do this: we would look at the images and see if there was actually a spot at the Bragg position. Now technology has advanced and with rotation images it's much harder to do this. Maybe it's possible to make pseudo-precession images? What I would do is assume the worst and assign it temporarily as P422; then let the HA or MR program sort out the space group by trying all the possibilities; it's only CPU time after all! My 2p's worth. -- Ian On 15 March 2013 15:09, gengxiang zhao gzh...@gmail.com wrote: Dear CCP4s, I am looking for more experienced concerns to determine which space group my crystal is. At present, we take it as P42212 (#94). HKL is below: Intensities of systematic absences h k l Intensity Sigma I/Sigma 0 0 9 -58.6 40.8 -1.4 0 0 11 -204.4 53.9 -3.8 0 0 13 -57.1 62.8 -0.9 0 0 15 -470.6 92.7 -5.1 0 0 17 -626.1 105.1 -6.0 0 0 19 -64.7 62.4 -1.0 0 0 21 266.6 75.9 3.5 0 0 23 1372.4 116.4 11.8 0 0 25 -543.9 84.8 -6.4 0 0 27 -396.8 93.1 -4.3 0 0 29 -598.8 102.1 -5.9 0 0 31 617.4 116.2 5.3 0 0 33 445.4 93.8 4.7 0 0 35 -64.5 89.5 -0.7 7 0 0 -241.4 134.7 -1.8 9 0 0 -375.8 55.5 -6.8 11 0 0 -39.1 61.8 -0.6 13 0 0 -356.1 78.1 -4.6 15 0 0 -262.6 65.6 -4.0 17 0 0 -324.7 89.3 -3.6 19 0 0 -178.7 88.5 -2.0 21 0 0 -726.3 115.3 -6.3 23 0 0 -189.4 131.0 -1.4 25 0 0 157.7 157.5 1.0 27 0 0 -591.5 213.4 -2.8 29 0 0 -111.7 198.4 -0.6 31 0 0 -94.2 247.0 -0.4 33 0 0 -169.8 306.5 -0.6 35 0 0 -71.2 347.8 -0.2 39 0 0 -82.8 417.9 -0.2 Thanks a lot. Best Wishes, Gengxiang -- Michael C. Thompson Graduate Student Biochemistry Molecular Biology Division Department of Chemistry Biochemistry University of California, Los Angeles mi...@chem.ucla.edu -- Gengxiang Zhao, Ph.D
[ccp4bb] Most Abundant Eukaryotic Membrane Protein List?
Dear List, Does anyone know of a source of quantification of membrane proteins in garden-variety eukaryotic cell lines, e.g. HEK or HeLa cells (incidentally, it just occurred to me that probably all HeLa cells are XX--seems right, no?) I am looking for the highest-expressed, particularly, and definitely want to include single-pass proteins as well. Jacob -- *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org ***
[ccp4bb] international PhD program at IGBMC, deadline for application 22.3.2013
Dear all, kind reminder for the International PhD program at the IGBMC, notably for integrated structural biology, with a deadline for applications 22nd of march 2013: http://phdprogramme.igbmc.fr/ see also http://www.igbmc.fr/research/department/3/ Best regards, Bruno Klaholz ### Dr. Bruno P. Klaholz Department of Integrated Structural Biology Institute of Genetics and of Molecular and Cellular Biology IGBMC - UMR 7104 - U 964 1, rue Laurent Fries BP 10142 67404 ILLKIRCH CEDEX FRANCE websites: http://www.igbmc.fr/ http://igbmc.fr/Klaholz
Re: [ccp4bb] Most Abundant Eukaryotic Membrane Protein List?
In the mitocondrial inner membrane (which is very protein-dense) I believe the most abundant protein is the adenine nucleotide transporter. (e.g. pdb1OKC). Single chain or homodimer, but apparently its not very easy to crystallize. Jacob Keller wrote: Dear List, Does anyone know of a source of quantification of membrane proteins in garden-variety eukaryotic cell lines, e.g. HEK or HeLa cells (incidentally, it just occurred to me that probably all HeLa cells are XX--seems right, no?) I am looking for the highest-expressed, particularly, and definitely want to include single-pass proteins as well. Jacob -- *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org mailto:kell...@janelia.hhmi.org ***
Re: [ccp4bb] Most Abundant Eukaryotic Membrane Protein List?
I don't want to crystallize the protein--I have another reason Jacob On Mon, Mar 18, 2013 at 1:18 PM, Edward A. Berry ber...@upstate.edu wrote: In the mitocondrial inner membrane (which is very protein-dense) I believe the most abundant protein is the adenine nucleotide transporter. (e.g. pdb1OKC). Single chain or homodimer, but apparently its not very easy to crystallize. Jacob Keller wrote: Dear List, Does anyone know of a source of quantification of membrane proteins in garden-variety eukaryotic cell lines, e.g. HEK or HeLa cells (incidentally, it just occurred to me that probably all HeLa cells are XX--seems right, no?) I am looking for the highest-expressed, particularly, and definitely want to include single-pass proteins as well. Jacob -- * Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org mailto:kell...@janelia.hhmi.**orgkell...@janelia.hhmi.org * -- *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org ***
[ccp4bb] Balbes serv
Dear Crystallographers, the Balbes webserver is now hosted at the Research Complex at Harwell, on the Rutherford site. The new URL is http://rcoisin.rc-harwell.ac.uk/BALBESSERV/ The service should still be considered somewhat experimental, due to ongoing work to add another MR pipeline, MrBUMP, to the service. The old server is still available on the YSBL server in York, but it will be discontinued at some point in the near future. Best wishes, Ville -- Scanned by iCritical.
[ccp4bb] Philosophical question
Dear all I have a somewhat philosophical question. Why do all protein sequences start with a methionine (not referring to mature/processed form)? What is so special about methionine and cannot be replaced by other amino acids? Second, how does the ribosome know the first start codon is for methionine when the codon is not AUG? This is about the alternative start codons like GUG. Thank you. Theresa
Re: [ccp4bb] Most Abundant Eukaryotic Membrane Protein List?
BLASPHEMY! haha From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob Keller Sent: Monday, March 18, 2013 1:22 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Most Abundant Eukaryotic Membrane Protein List? I don't want to crystallize the protein--I have another reason Jacob On Mon, Mar 18, 2013 at 1:18 PM, Edward A. Berry ber...@upstate.edumailto:ber...@upstate.edu wrote: In the mitocondrial inner membrane (which is very protein-dense) I believe the most abundant protein is the adenine nucleotide transporter. (e.g. pdb1OKC). Single chain or homodimer, but apparently its not very easy to crystallize. Jacob Keller wrote: Dear List, Does anyone know of a source of quantification of membrane proteins in garden-variety eukaryotic cell lines, e.g. HEK or HeLa cells (incidentally, it just occurred to me that probably all HeLa cells are XX--seems right, no?) I am looking for the highest-expressed, particularly, and definitely want to include single-pass proteins as well. Jacob -- *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.orgmailto:kell...@janelia.hhmi.org mailto:kell...@janelia.hhmi.orgmailto:kell...@janelia.hhmi.org *** -- *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.orgmailto:kell...@janelia.hhmi.org *** Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
[ccp4bb] Structural biology to support anticancer drug discovery at the NICR, Newcastle University
Dear all, As per the attached, we are really pleased to announce up to four positions to join a structural biology team supporting drug discovery in the Northern Institute for Cancer Research and the Chemistry Department, Newcastle University. The structural biology positions, supported by an exciting Alliance Partnership between Newcastle University, CRT, and Astex Pharmaceuticals, will help to complete a highly interdisciplinary team of clinicians, bioscientists, and medicinal and computational chemists working to deliver next generation cancer therapies. We plan to appoint a Senior Research Associate, up to two more junior postdocs, and a technician. If the possibility appeals, then please hunt out and complete the online application on the Newcastle University website (www.ncl.ac.uk/vacancieshttp://www.ncl.ac.uk/vacancies). martin.no...@ncl.ac.ukmailto:martin.no...@ncl.ac.uk or jane.endic...@ncl.ac.ukmailto:jane.endic...@ncl.ac.uk With best wishes, Martin Newcastle University has a strong track-record in cancer research and cancer drug discovery, hosting the Cancer Research UK Newcastle Cancer Drug Discovery Programme. The programme has attracted £17M over the past 5 years in direct funding, and in collaboration with industry partners has generated compounds for clinical trials. Currently, the programme has 5 projects at various stages of small-molecule drug discovery from hit identification to lead optimisation. Astex Pharmaceuticals™ is a dynamic company striving to make an impact in the fight against cancer and other major diseases. The Company has a team of highly qualified and motivated individuals who want to make a difference to patients by playing a key role in the development of novel therapies. Great value is placed on strategic partnerships with leading academic institutes, which is seen as an important means to maximise patient benefit from internationally outstanding science. Newcastle University and Cancer Research Technology have recently established a 5-year research alliance with Astex Pharmaceuticals that will provide significant additional resource for the joint exploitation of innovative targets in cancer. To support the expanded Programme and alliance, Newcastle University is seeking to recruit new staff with expertise in medicinal chemistry, structural biology and drug discovery bioscience. Applicants who have experience in the discovery/development of small molecule anticancer therapeutics or validation of therapeutic targets are invited to apply, although high calibre candidates with expertise in other disease areas are also encouraged. Further details of this exciting opportunity to join a large and successful team of researchers at the cutting edge of cancer drug discovery are available at: www.ncl.ac.uk/vacancieshttp://www.ncl.ac.uk/vacancies The positions can be found under the heading “Search for Job Vacancies” and selecting NICR. The closing date for all positions is the 10th of April. Interviews for the posts will be held during the weeks commencing 22nd and 29th of April. Professor Martin Noble Northern Institute for Cancer Research Paul O'Gorman Building Medical School Newcastle University Framlington Place Newcastle Upon Tyne NE2 4HH E-mail: martin.no...@ncl.ac.ukmailto:martin.no...@ncl.ac.uk Direct line: +44 (0) 191 246 4466
[ccp4bb] International Conference on Structural Genomics - Structural Life Science, Sapporo, Japan, July 29-Aug 1, 2013
Dear Colleagues: On behalf of the organizing committee of the International Conference on Structural Genomics 2013 – Structural Life Science – (ICSG2013-SLS), we cordially welcome you to the conference, to be held in Sapporo, Hokkaido, Japan, July 29th – August 1st, 2013. ICSG2013-SLS is intended to provide an overview for the most recent developments in Structural Genomics and its impact on research in biology, medicine and disease, and to foster international collaboration among researchers. You can see all the details of the conference at: http://www.c-linkage.co.jp/ICSG2013 . Registration for the conference is now open. The scientific topics covered in ICSG2013-SLS include the wider life science research fields with particular attention to drug discovery (small molecules and biopharmaceuticals), biotechnology and industrial issues while keeping strength in the high-throughput technologies and integration of hybrid methods. These technologies are now leading to the new field of “Structural Life Science”. ICSG2-13-SLS is partially supported by the Grant-in-Aid for Scientific Research on Innovative Areas; “Structural Cell Biology”, “Intrinsically Disordered Protein” and “Transient Macromolecular Complexes”, from Ministry of Education, Culture, Sports, Science and Technology (MEXT) . In order to widen the opportunity to young and enthusiastic fellows to study more, we have organized several satellite workshops before ICSG2013- SLS. The topics will include “Small molecule screening”, “Automation of X-ray Structure Determination”, “Cell-free Protein Production”, “Automated NMR methods”, Eukaryotic expression, “Interaction analyses and Bioinformatics”. We hope you also find the satellite workshops are informative and productive. The conference will be held in Keio Plaza Hotel Sapporo, in walking distance of Hokkaido University's main campus and Sapporo station. The summer in Sapporo is a great time to stay and enjoy the cool summer night of Japan. We are looking forward to welcoming you to Sapporo in the summer of 2013. Sincerely yours, Katsumi Maenaka, Ph.D. Chair, International Conference on Structural Genomics 2013 -Structural Life Science- (ICSG2013-SLS) Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Japan Soichi Wakatsuki Chair of Program Committee, ICSG2013-SLS Photon Science, SLAC National Accelerator Laboratory Department of Structural Biology School of Medicine Stanford University
Re: [ccp4bb] Most Abundant Eukaryotic Membrane Protein List?
I wouldn't be so sure that HeLa is just XX, or that it should be called garden variety after what I read today. http://www.nature.com/news/most-popular-human-cell-in-science-gets-sequenced-1.12609#/b1 -- David On 18 March 2013 15:08, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Dear List, Does anyone know of a source of quantification of membrane proteins in garden-variety eukaryotic cell lines, e.g. HEK or HeLa cells (incidentally, it just occurred to me that probably all HeLa cells are XX--seems right, no?) I am looking for the highest-expressed, particularly, and definitely want to include single-pass proteins as well. Jacob -- *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org ***
[ccp4bb] How to convert file format from CNS to CCP4
Dear all, I have used CNS to calculate the experimental phase of my structure. After Heavy-atom search, Heavy-atom refinement/SAD phasing and SAD Phasing - Density Modification - Selection of Map. Some files outputted: sad_phase2.hkl sad_phase2.sdb density_modify.hkl density_modify.map density_modify.mask ... I want to use these files to do the model building, but I do not know how to do it in CNS. So I want to convert these files to CCP4 format and do the model building by ARP/Warp, but I do not know which files should be converted and which software can be used to convert the file format from CNS to CCP4. Thank you for your time! Wei
