[ccp4bb] X-ray equipment available
We would like to offer a Rigaku diffraction system free of charge consisting of the following components: -Rigaku RU-H3R generator (1997) (currently non-operational due to vacuum problems, maybe worth repairing or good for spare parts) -motorized R-Axis IV++ imaging plate detector (2001) (good working condition) -spare parts for R-Axis IV imaging plate detector (controler, read out unit, etc.) -spare parts (filaments, lamps, tools, Rietschle pump, colimators) Interested parties should provide shipping and handling. Furthermore we would like to sell (due to residual value since these components are not written off yet), prize negotiable: -Osmic blue mirrors CMF 12-38Cu6 -Xenocs Fox2D mirrors TOM 465/14 12/38Cu Please contact Andreas Heine (hei...@mailer.uni-marburg.de) for more details if you are interested in the system or individual components. Best wishes, Andreas
[ccp4bb] Postdoctoral position - ESRF, Grenoble
*Postdoctoral position in /in-crystallo/ spectroscopy at the European Synchrotron Radiation Facility (Grenoble)* The interpretation of electron density maps resulting from Macromolecular Crystallography (MX) X-ray diffraction experiments can often benefit from the use of complementary techniques including optical spectroscopy (UV-visible absorption, fluorescence, Raman). You will play a major role in the operation and development of the ESRF Cryobench Facility (ID29S) dedicated to the application of optical spectroscopy in the context of MX. In particular, you will be responsible for developing new instruments suitable for various on-line spectroscopies on the MX beamline ID30A currently under construction. The successful candidate will also be responsible for the support of Raman spectroscopy and X-ray diffraction experiments on both the ID29S facility and the MX beamline ID29. Additionally he/she will carry out research aimed at studying the effect of radiation damage on DNA molecules using a combination of X-ray crystallography and Raman spectroscopy. For more information about ID29S please consult: http://www.esrf.eu/UsersAndScience/Experiments/MX/Cryobench/ You should hold a Ph.D. in physics, protein crystallography or a related subject. Experience in the use of optical spectroscopy as applied in Structural Biology is highly desirable as is knowledge of the operation of synchrotron radiation beamlines. You should be capable of integrating into a multidisciplinary and international research team. Further information on the post can be obtained from Gordon Leonard (tel.: +33 (0)4 76 88 23 94, email: leon...@esrf.fr mailto:x...@esrf.fr) or Antoine Royant (tel.: +33 (0)4 76 88 17 46, email: roy...@esrf.fr mailto:x...@esrf.fr). For further information on employment terms and conditions, please refer to http://www.esrf.fr/Jobs/Conditions. The ESRF is an equal opportunity employer and encourages applications from disabled persons. The contract is for 18 months, renewable for a further 6 to 18 month-period. Only candidates holding a Ph.D. obtained less than 3 years ago are eligible for Post-doctoral positions. If you are interested in this position, please apply on-line at this address: http://www.esrf.fr/Jobs.// Ref. PDID29-1 *Deadline for returning application forms: 19/11/2012*
Re: [ccp4bb] Structure example request for large domain movement in crystallo soaking
How about DNA synthesis within crystals? 1: Kiefer JR, Mao C, Braman JC, Beese LS. Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal. Nature. 1998 Jan 15;391(6664):304-7. PubMed PMID: 9440698. 2: Johnson SJ, Taylor JS, Beese LS. Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations. Proc Natl Acad Sci U S A. 2003 Apr 1;100(7):3895-900. Epub 2003 Mar 20. PubMed PMID: 12649320; PubMed Central PMCID: PMC153019. Meindert On 10/9/12 2:33 PM, WENHE ZHONG wrote: Dear CCP4 members, Recently, I got a ligand soaking structure to clearly show a large domain (~100 amino acids) movement compared to the no soaking structure. Although there are some reported examples of this enzyme to suggest the flexibility of this large domain which is relevant to substrate binding. _But it is the first time I can see it happen in crystal soaking procedure._ In this case, I am pleased by this result. My question is, do you have any other example like mine, where domain (or loop) movement is observed _*in crystal*_ during ligand _*soaking*_ procedure? It would be very helpful for me to relate my result to other similar examples. Thank you very much. King regards, Wenhe -- ** Meindert H. Lamers Medical Research Council Laboratory of Molecular Biology Hills Road, Cambridge, CB2 0QH United Kingdom tel +44 (0)1223 402401 fax +44 (0)1223 213556 web: http://www2.mrc-lmb.cam.ac.uk/groups/mlamers/ **
[ccp4bb] Nobel Prize 2012
Congratulations to Robert Lefkowitz and Brian Kobilka: Nobel Prize in Chemistry, 2012! Congrats to the protein structure community. toufic el arnaout
Re: [ccp4bb] Nobel Prize 2012
many congratulations to protein structure community ... On Wed, Oct 10, 2012 at 6:20 AM, Toufic El Arnaout tou...@inmesolabs.netwrote: Congratulations to Robert Lefkowitz and Brian Kobilka: Nobel Prize in Chemistry, 2012! Congrats to the protein structure community. toufic el arnaout -- Vandana kukshal
Re: [ccp4bb] Nobel Prize 2012
Dear all, You can learn more about this important family of receptors by exploring their structures within the PDB archive. http://pdbe.org/nobel2012 The crystal structures of the beta2 adrenergic receptor were determined using X-ray diffraction by Kobilka's group. The structures http://pdbe.org/2rh1, http://pdbe.org/2r4r and http://pdbe.org/2r4s were published and released in 2007. Subsequently, the structure of a G protein (Gs) bound to the beta2 adrenergic receptor http://pdbe.org/3sn6 was determined using X-ray diffraction by the same group at a resolution of 3.2 Å and published in 2011, providing important insights into how GPCRs activate G proteins. On 10/10/2012 15:17, Vandna Kukshal wrote: many congratulations to protein structure community ... On Wed, Oct 10, 2012 at 6:20 AM, Toufic El Arnaout tou...@inmesolabs.net mailto:tou...@inmesolabs.net wrote: Congratulations to Robert Lefkowitz and Brian Kobilka: Nobel Prize in Chemistry, 2012! Congrats to the protein structure community. toufic el arnaout -- Vandana kukshal -- Gary Battle Outreach Coordinator Protein Data Bank in Europe (PDBe) EMBL-EBI Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD Tel: 01223 49-4654 email: bat...@ebi.ac.uk http://www.facebook.com/proteindatabank http://twitter.com/PDBeurope
Re: [ccp4bb] Nobel Prize 2012
Your nice historic chart of Nobel prizes missed Hauptman and Karle in 1985. Frances Bernstein = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339FAX: 1-631-286-1999 = On Wed, 10 Oct 2012, Gary Battle wrote: Dear all, You can learn more about this important family of receptors by exploring their structures within the PDB archive. http://pdbe.org/nobel2012 The crystal structures of the beta2 adrenergic receptor were determined using X-ray diffraction by Kobilka's group. The structures http://pdbe.org/2rh1, http://pdbe.org/2r4r and http://pdbe.org/2r4s were published and released in 2007. Subsequently, the structure of a G protein (Gs) bound to the beta2 adrenergic receptor http://pdbe.org/3sn6 was determined using X-ray diffraction by the same group at a resolution of 3.2 A and published in 2011, providing important insights into how GPCRs activate G proteins. On 10/10/2012 15:17, Vandna Kukshal wrote: many congratulations to protein structure community ... On Wed, Oct 10, 2012 at 6:20 AM, Toufic El Arnaout tou...@inmesolabs.net wrote: Congratulations to Robert Lefkowitz and Brian Kobilka: Nobel Prize in Chemistry, 2012! Congrats to the protein structure community. toufic el arnaout -- Vandana kukshal -- Gary Battle Outreach Coordinator Protein Data Bank in Europe (PDBe) EMBL-EBI Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD Tel: 01223 49-4654 email: bat...@ebi.ac.uk http://www.facebook.com/proteindatabank http://twitter.com/PDBeurope
Re: [ccp4bb] residues forming the surface of a cavity
Dear All, Sorry for the late reply. I wish to compare binding pockets of some homologous proteins, a couple of which have a ligand bound, while the rest don't. I wish to check if there is any difference in the nature of the cavity in the homologous proteins, e.g. properties like hydrophobicity, electrostatics, etc. But I also wish to determine exactly which residues are surfacing/lining the cavity. Thanks and regards, sreetama From: Francois Berenger beren...@riken.jp To: CCP4BB@JISCMAIL.AC.UK Sent: Thursday, 4 October 2012 12:56 PM Subject: Re: [ccp4bb] residues forming the surface of a cavity On 10/04/2012 04:09 PM, sreetama das wrote: Dear all, Is there any CCP4 module/ other software/ web server which can determine which particular residues form the surface of a pocket/ binding-site in a protein? Do you mean residues not far from any ligand atom? And you know where is the ligand. Or do you mean residues surfacing a pocket or cavity? Regards, F.
Re: [ccp4bb] Nobel Prize 2012
Thanks, Frances. The chart has been updated. Gary. On 10/10/2012 16:36, Frances C. Bernstein wrote: Your nice historic chart of Nobel prizes missed Hauptman and Karle in 1985. Frances Bernstein = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339FAX: 1-631-286-1999 = On Wed, 10 Oct 2012, Gary Battle wrote: Dear all, You can learn more about this important family of receptors by exploring their structures within the PDB archive. http://pdbe.org/nobel2012 The crystal structures of the beta2 adrenergic receptor were determined using X-ray diffraction by Kobilka's group. The structures http://pdbe.org/2rh1, http://pdbe.org/2r4r and http://pdbe.org/2r4s were published and released in 2007. Subsequently, the structure of a G protein (Gs) bound to the beta2 adrenergic receptor http://pdbe.org/3sn6 was determined using X-ray diffraction by the same group at a resolution of 3.2 A and published in 2011, providing important insights into how GPCRs activate G proteins. On 10/10/2012 15:17, Vandna Kukshal wrote: many congratulations to protein structure community ... On Wed, Oct 10, 2012 at 6:20 AM, Toufic El Arnaout tou...@inmesolabs.net wrote: Congratulations to Robert Lefkowitz and Brian Kobilka: Nobel Prize in Chemistry, 2012! Congrats to the protein structure community. toufic el arnaout -- Vandana kukshal -- Gary Battle Outreach Coordinator Protein Data Bank in Europe (PDBe) EMBL-EBI Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD Tel: 01223 49-4654 email: bat...@ebi.ac.uk http://www.facebook.com/proteindatabank http://twitter.com/PDBeurope -- Gary Battle Outreach Coordinator Protein Data Bank in Europe (PDBe) EMBL-EBI Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD Tel: 01223 49-4654 email: bat...@ebi.ac.uk http://www.facebook.com/proteindatabank http://twitter.com/PDBeurope
Re: [ccp4bb] Nobel Prize 2012
Yes agreed great work - more of that please. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://lupo.jhsph.edu On Oct 10, 2012, at 7:20, Toufic El Arnaout tou...@inmesolabs.netmailto:tou...@inmesolabs.net wrote: Congratulations to Robert Lefkowitz and Brian Kobilka: Nobel Prize in Chemistry, 2012! Congrats to the protein structure community. toufic el arnaout
Re: [ccp4bb] Nobel Prize 2012
Had the fortunate opportunity to hear him speak about the crystallography at the Pittsburgh Diffraction Conference last week. Great work and well done! Francis On Oct 10, 2012, at 8:54 AM, Bosch, Juergen wrote: Yes agreed great work - more of that please. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://lupo.jhsph.edu On Oct 10, 2012, at 7:20, Toufic El Arnaout tou...@inmesolabs.net wrote: Congratulations to Robert Lefkowitz and Brian Kobilka: Nobel Prize in Chemistry, 2012! Congrats to the protein structure community. toufic el arnaout - Francis E. Reyes PhD 215 UCB University of Colorado at Boulder
Re: [ccp4bb] Nobel Prize 2012
Perhaps a more complete list (now not up to date!) for crystallography can be found at http://www.iucr.org/people/nobel-prize I note however that the ebi chart is for structural biology related prizes. Colin -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frances C. Bernstein Sent: 10 October 2012 16:36 To: ccp4bb Subject: Re: [ccp4bb] Nobel Prize 2012 Your nice historic chart of Nobel prizes missed Hauptman and Karle in 1985. Frances Bernstein = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339FAX: 1-631-286-1999 = On Wed, 10 Oct 2012, Gary Battle wrote: Dear all, You can learn more about this important family of receptors by exploring their structures within the PDB archive. http://pdbe.org/nobel2012 The crystal structures of the beta2 adrenergic receptor were determined using X-ray diffraction by Kobilka's group. The structures http://pdbe.org/2rh1, http://pdbe.org/2r4r and http://pdbe.org/2r4s were published and released in 2007. Subsequently, the structure of a G protein (Gs) bound to the beta2 adrenergic receptor http://pdbe.org/3sn6 was determined using X-ray diffraction by the same group at a resolution of 3.2 A and published in 2011, providing important insights into how GPCRs activate G proteins. On 10/10/2012 15:17, Vandna Kukshal wrote: many congratulations to protein structure community ... On Wed, Oct 10, 2012 at 6:20 AM, Toufic El Arnaout tou...@inmesolabs.net wrote: Congratulations to Robert Lefkowitz and Brian Kobilka: Nobel Prize in Chemistry, 2012! Congrats to the protein structure community. toufic el arnaout -- Vandana kukshal -- Gary Battle Outreach Coordinator Protein Data Bank in Europe (PDBe) EMBL-EBI Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD Tel: 01223 49-4654 email: bat...@ebi.ac.uk http://www.facebook.com/proteindatabank http://twitter.com/PDBeurope -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
Re: [ccp4bb] On maps and doubts
btw, this thread has one of my favorite titles ever... JPK On Tue, Oct 9, 2012 at 4:11 AM, Eleanor Dodson eleanor.dod...@york.ac.ukwrote: This is interesting. In principle m and D should provide an optimum map, and at high resolution they do a reasonable job. The answer about occupancy is a good point. You don't say what resolution your data is at, but maybe it is rather low? I suspect that below ~ 3A the estimates of both m and D are somewhat unreliable - they are fitted to resolution curves and are influenced severely by scaling problems, all of which are more serious at low resolution. What about consulting Garib! He must be near by.. Eleanor On 4 Oct 2012, at 20:17, Israel Sanchez wrote: Hello everyone, I would like to share my experience with one dataset and request some advice on which is the best way to prove a conformational change seen in a density map. The first issue arose when we were looking for an extra ribosomal factor added to a crystalized ribosome. After careful data collection and refinement (I/sigma last shell 1.2, 3.1A and CC1/2 around 22%) the sigma-A-weighted maps 2mFo-DFc and Fo-Fc does not show any clear difference density that we could interpret as the expected factor. Interestingly, a computed map with coefficients 3mFo-2DFc started to show some features that clearly could be explained as a fragment of the factor. The density improved even more with a B-sharpened map. We have seen this behavior before and I was wondering if someone else is using this kind of maps and may could explain the reason behind this density improvement. Is it a crazy idea to go even higher like 4mFo-3DFc? The second query has to do with which is the best way to prove that a conformational change is present in an specific residue (in this case and RNA base) in your structure. To my knowledge, a classic omit map with simulated annealing would do the job regarding removing the model bias. Actually, I found an interesting alternative in PHENIX called a Kick map, were a series of maps computed from a ramdoinised set of models yields a averaged map ideally free from model bias. Does anyone has a preference for any of those schemes? Are there more alternative to prove a conformational change in a model phased with a molecular replacement solution? Thank you very much in advance. -- Israel Sanchez Fernandez PhD Ramakrishnan-lab MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
