[ccp4bb] WG: Postdoc / group leader position in Mass Spectrometry at University of Bayreuth
Dear colleagues, I apologize for this off topic post, but since MS has become so important for our community, I still hope to reach one or two candidates interested in our MS position . please forward if you know a candidate, thanks in advance . Best Clemens Postdoc / group leader position in protein/peptide Mass Spectrometry at University of Bayreuth We are currently looking for a highly motivated expert in protein mass spectrometry at the postdoc level for our laboratory at the Dept. of Biochemistry at University Bayreuth, Germany. Our work involves biochemical and structural studies on cellular signalling systems with relevance to aging mechanisms and aging-related diseases, in particular cyclic nucleotide signalling and deacylases of the Sirtuin family. The successful applicant will contribute MS work to these projects and, depending on his/her experience and independence, develop an independent line of research. The ideal candidate is highly self-motivated and independent, with a strong background in protein/peptide mass spectrometry and an interest in signalling mechanisms. We offer excellent research opportunities and a stimulating environment for mechanistic biochemical studies. Our laboratory is located in a new building at the University of Bayreuth and equipped with state-of-the-art laboratories for protein biochemistry, x-ray crystallography, and MS. The MS equipment comprises two HPLC couples ESI-MS, including a new high-resolution TripleTOF machine. Applications (including CV with publication list, research experience, PhD certificate, transcripts, and two names and contact information for references) should be sent as PDF or by mail to Prof. Dr. Clemens Steegborn University of Bayreuth Dept. Biochemistry, NW III Universitaetsstr. 30 95447 Bayreuth, Germany phone: ++49 0921 / 55 - 7831 email: mailto:sekretariat.bioche...@uni-bayreuth.de sekretariat.bioche...@uni-bayreuth.de web: http://www.biochemie.uni-bayreuth.de www.biochemie.uni-bayreuth.de -- Don't miss the 5th Murnau conference on structural biology - Focus topic: Signal transduction September 10-13, 2014 Murnau am Staffelsee, Germany http://www.murnauconference.de/2014/index.html --- Prof. Dr. Clemens Steegborn University of Bayreuth Dept. Biochemistry, NW III Universitaetsstr. 30 95447 Bayreuth, Germany phone: ++49 0921 / 55 - 7831 fax: ++49 0921 / 55 - 7832 email: mailto:clemens.steegb...@uni-bayreuth.de clemens.steegb...@uni-bayreuth.de web: http://www.biochemie.uni-bayreuth.de/ www.biochemie.uni-bayreuth.de
[ccp4bb] WG: Murnau conference on Structural Biology
Dear colleagues, I would like to remind you that registration for the Murnau conference on Structural Biology will end soon (July 31st). At the meeting from September 10 to 13, we will have eminent scientist as speakers from various fields of structural biology (see http://www.murnauconference.de/2014/schedule.html for the program), and there are several additional slots for oral presentations that will be filled through selection from the submitted abstracts. For more information on this meeting please have a look at http://www.murnauconference.de/2014/ I'm looking forward to meeting you in Murnau! With best regards Clemens --- Prof. Dr. Clemens Steegborn University of Bayreuth Dept. Biochemistry, NW III Universitaetsstr. 30 95447 Bayreuth, Germany phone: ++49 0921 / 55 - 7831 fax: ++49 0921 / 55 - 7832 email: mailto:clemens.steegb...@uni-bayreuth.de clemens.steegb...@uni-bayreuth.de web: http://www.biochemie.uni-bayreuth.de/ www.biochemie.uni-bayreuth.de
[ccp4bb] Murnau conference on structural biology, Sept 10-13
Dear colleagues, We'd like to bring to your attention this year's 5th Murnau conference on structural biology. This biennial structural biology meeting takes place in Murnau, a picturesque village at one of the lakes south from Munich, Germany. The meeting this year will be held from Sept 10th to 13th and will have a focus on signal transduction, but it will also cover sessions on broader structural subjects - please visit the meeting web site for further information: http://www.murnauconference.de/2014/index.html http://www.murnauconference.de/2014/index.html We'd be happy to welcome many of you in September! With best wishes, Clemens Steegborn Oliver Einsle -- Don't miss the 5th Murnau conference on structural biology - Focus topic: Signal transduction September 10-13, 2014 Murnau am Staffelsee, Germany http://www.murnauconference.de/2014/index.html --- Prof. Dr. Clemens Steegborn University of Bayreuth Dept. Biochemistry, NW III Universitaetsstr. 30 95447 Bayreuth, Germany phone: ++49 0921 / 55 - 7831 fax: ++49 0921 / 55 - 7832 email: mailto:clemens.steegb...@uni-bayreuth.de clemens.steegb...@uni-bayreuth.de web: http://www.biochemie.uni-bayreuth.de/ www.biochemie.uni-bayreuth.de
[ccp4bb] AW: [ccp4bb] Calcium ions in enzymes
We had a case where Calcium facilitates productive ATP binding (Nat Struct Mol Biol. 12 (2005), 32-7) ... not sure whether one would call that a catalytic function, but it's certainly not structural Best Clemens -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Wei Liu Gesendet: Freitag, 31. Mai 2013 12:26 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Calcium ions in enzymes Dear all, As we all know, many proteins contain calcium ions. Does anyone know if there are reported cases where calcium ions play a catalytic role rather than a structural role in enzymes? Best Wei Liu
[ccp4bb] AW: [ccp4bb] cell disruptor / homogenizer - final summary
P.S.: The C5 is what we had in Bochum. Also not perfect, but I guess theres no perfect machine .. Von: Clemens Steegborn [mailto:clemens.steegb...@ruhr-uni-bochum.de] Gesendet: Donnerstag, 28. März 2013 13:58 An: 'Clemens Steegborn'; 'CCP4BB@JISCMAIL.AC.UK' Betreff: AW: [ccp4bb] cell disruptor / homogenizer - final summary Since my previous summary on cell disruption equipment elicited a pretty clear response, I want to give a final update: Several methods and machines were mentioned (see below), but the Avestin Emulsiflex C5 is now the clear winner, with five happy users and no really negative comment. Thanks again to everyone for this helpful feedback! Happy Holidays Clemens Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Clemens Steegborn Gesendet: Dienstag, 26. März 2013 19:21 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] AW: [ccp4bb] cell disruptor / homogenizer - summary Dear colleagues, To summarize the feedback on cell disruptors: One person found the Emulsiflex performance worth the maintenance required, there were no comments at all on Fluidizer and TS 0.75! As alternatives, French press (Glenn Milles), beadbeaters (Biospec), Panda homegenizer (GEA Niro Soavi), and nitrogen cavitation in a pressure bomb (http://www.ncbi.nlm.nih.gov/pubmed/21041386) were suggested. Thanks for the comments and suggestions. Best Clemens Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Clemens Steegborn Gesendet: Montag, 25. März 2013 10:17 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] cell disruptor / homogenizer Dear colleagues, We are currently looking for new cell disruptor/homogenizer equipment, mainly for E.coli work. We currently have a Branson sonifier and a Microfluidics Fluidizer the latter one keeps causing trouble, and we think about a replacement. We previously also used an Avestin C-5 Emulsiflex, required quite some maintenance, and I inquired about a Constant Systems TS 0.75 and got mixed responses from users (not to mention their outrageous pricing). My question: What is your experience with Fluidizer, Emulsiflex, TS 0.75? Is there any other great (low maintenance, affordable especially concerning follow-up costs: repairs, replacement parts) equipment I missed? Thanks in advance for your comments Best regards Clemens
[ccp4bb] AW: [ccp4bb] cell disruptor / homogenizer - final summary
Since my previous summary on cell disruption equipment elicited a pretty clear response, I want to give a final update: Several methods and machines were mentioned (see below), but the Avestin Emulsiflex C5 is now the clear winner, with five happy users and no really negative comment. Thanks again to everyone for this helpful feedback! Happy Holidays Clemens Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Clemens Steegborn Gesendet: Dienstag, 26. März 2013 19:21 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] AW: [ccp4bb] cell disruptor / homogenizer - summary Dear colleagues, To summarize the feedback on cell disruptors: One person found the Emulsiflex performance worth the maintenance required, there were no comments at all on Fluidizer and TS 0.75! As alternatives, French press (Glenn Milles), beadbeaters (Biospec), Panda homegenizer (GEA Niro Soavi), and nitrogen cavitation in a pressure bomb (http://www.ncbi.nlm.nih.gov/pubmed/21041386) were suggested. Thanks for the comments and suggestions. Best Clemens Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Clemens Steegborn Gesendet: Montag, 25. März 2013 10:17 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] cell disruptor / homogenizer Dear colleagues, We are currently looking for new cell disruptor/homogenizer equipment, mainly for E.coli work. We currently have a Branson sonifier and a Microfluidics Fluidizer the latter one keeps causing trouble, and we think about a replacement. We previously also used an Avestin C-5 Emulsiflex, required quite some maintenance, and I inquired about a Constant Systems TS 0.75 and got mixed responses from users (not to mention their outrageous pricing). My question: What is your experience with Fluidizer, Emulsiflex, TS 0.75? Is there any other great (low maintenance, affordable especially concerning follow-up costs: repairs, replacement parts) equipment I missed? Thanks in advance for your comments Best regards Clemens
[ccp4bb] AW: [ccp4bb] cell disruptor / homogenizer - summary
Dear colleagues, To summarize the feedback on cell disruptors: One person found the Emulsiflex performance worth the maintenance required, there were no comments at all on Fluidizer and TS 0.75! As alternatives, French press (Glenn Milles), beadbeaters (Biospec), Panda homegenizer (GEA Niro Soavi), and nitrogen cavitation in a pressure bomb (http://www.ncbi.nlm.nih.gov/pubmed/21041386) were suggested. Thanks for the comments and suggestions. Best Clemens Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Clemens Steegborn Gesendet: Montag, 25. März 2013 10:17 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] cell disruptor / homogenizer Dear colleagues, We are currently looking for new cell disruptor/homogenizer equipment, mainly for E.coli work. We currently have a Branson sonifier and a Microfluidics Fluidizer the latter one keeps causing trouble, and we think about a replacement. We previously also used an Avestin C-5 Emulsiflex, required quite some maintenance, and I inquired about a Constant Systems TS 0.75 and got mixed responses from users (not to mention their outrageous pricing). My question: What is your experience with Fluidizer, Emulsiflex, TS 0.75? Is there any other great (low maintenance, affordable especially concerning follow-up costs: repairs, replacement parts) equipment I missed? Thanks in advance for your comments Best regards Clemens
[ccp4bb] cell disruptor / homogenizer
Dear colleagues, We are currently looking for new cell disruptor/homogenizer equipment, mainly for E.coli work. We currently have a Branson sonifier and a Microfluidics Fluidizer - the latter one keeps causing trouble, and we think about a replacement. We previously also used an Avestin C-5 Emulsiflex, required quite some maintenance, and I inquired about a Constant Systems TS 0.75 and got mixed responses from users (not to mention their outrageous pricing). My question: What is your experience with Fluidizer, Emulsiflex, TS 0.75? Is there any other great (low maintenance, affordable - especially concerning follow-up costs: repairs, replacement parts) equipment I missed? Thanks in advance for your comments Best regards Clemens
[ccp4bb] AW: [ccp4bb] Citations in supplementary material
Hi Bert, rReferences in Science do NOT contain article titles, like in quite a number of other journals (e.g. JBC, just to mention one of them) . and I agree that it's a pain to find out whether a reference is really of interest to you - but I also agree that it's so much more convenient for the journals that we won't be able to change it . Best Clemens Von: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] Im Auftrag von Van Den Berg, Bert Gesendet: Monday, November 22, 2010 3:45 PM An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Citations in supplementary material ?? I don't know if I understand the question, but don't most journals have references that do include the article titles? Science, Nature, Cell, NSMB, PNAS, JMB, Structure all have references titlesas they should. Bert On 11/22/10 9:35 AM, John R Helliwell jrhelliw...@gmail.com wrote: Dear Jacob, Additional content, like article titles, whether print or online, need to be checked properly for accuracy. Article titles (if supplied by authors) can often need heavy checking, and online systems to check bibliographic information are not always reliable or comprehensive. This I think explains the paucity of article titles coverage in references lists of many/most Journals. Best wishes, John On Mon, Nov 22, 2010 at 12:16 PM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: It seems to me that this problem is really a hold-over from compromise with the exigencies of hard-copy publishing, i.e. a way to save physical space. Further, there seem to be many aspects of e-publication that have not adapted to the strengths/weaknesses of the new medium, which could and should be remedied. One aspect is citation format--why not capitalize on the luxury of having plenty of space? Maybe even the abstracts could be included (why not?). Another thing I mentioned in a previous email: why not remove length limitations? Let the authors have the space they need to say what needs to be said! I think EMBO actually espouses this idea, although I am not sure how far they would go (I am pretty sure they do not limit number of references, for example.) Anyway, it seems to be an interesting and historical time in the publishing world. JPK On Sun, Nov 21, 2010 at 8:07 PM, Francois Berenger beren...@riken.jp wrote: Hello, For me the citation format is also a major problem. When the title of the paper is not shown, it really hinders the work of trying to find which references are worthwhile reading. I think it may even have a negative impact on the number of citations a paper get. I don't know if it has been solved in recent issues of IUCr journals, so please forgive me if this is an old and dead topic. Regards, Francois. -- Professor John R Helliwell DSc
[ccp4bb] Postdoc position at the University of Bayreuth, Germany
Postdoc Position in Protein Crystallography A postdoctoral research position in protein crystallography is available in the group of Clemens Steegborn at the University of Bayreuth, Germany. Research in the laboratory is focused on understanding the molecular signaling mechanisms involved in aging processes and disease. In particular, we study deacetylases of the Sirtuin family and the cyclic nucleotide signaling network. We use protein crystallography, combined with biochemical and enzymological methods and bioinformatics approaches, to obtain a molecular understanding of these interconnected signaling systems and to develop compounds for their modulation. We are looking for a Postdoc with experience in protein x-ray crystallography to join our team studying the regulation of Sirtuins. Our laboratory at the University of Bayreuth offers access to state-of-the art equipment for protein biochemistry and crystallography, and a stimulating environment for research in structural biology, with two collaborating protein crystallography units (Steegborn lab and Blankenfeldt lab). We further have access to state-of the art synchrotron beamlines, and strongly interact with other labs within the Research Institute for Biomacromolecules (spectroscopy, NMR, bioinformatics) and the Department of Chemistry and Biology (cell biology, genetics, synthetic chemistry). Our lab offers excellent research opportunities and a stimulating environment for research in Structural Biology. The ideal candidate is a highly motivated Ph.D. with an interest in medically relevant questions. Experience in protein purification crystallization and x-ray structure analysis is ABSOLUTELY MANDATORY. Additional experience in molecular biology would be an asset. Applications (including CV, research experience, and at least two names and contact information for references) should be sent, preferably per email as PDF attachment, to clemens.steegb...@uni-bayreuth.de mailto:clemens.steegb...@rub.de Evaluation of applications will start by December 1st. --- Prof. Dr. Clemens Steegborn University of Bayreuth Dept. Biochemistry, NW I Universitaetsstr. 30 95447 Bayreuth, Germany phone: ++49 0921 / 55 - 2421 fax: ++49 0921 / 55 - 2432 email: mailto:clemens.steegb...@uni-bayreuth.de clemens.steegb...@uni-bayreuth.de web: http://www.biochemie.uni-bayreuth.de www.biochemie.uni-bayreuth.de
[ccp4bb] PhD student position in Structural Biology
PhD student position in Structural Biology We are currently looking for a highly motivated Ph.D. student for our laboratory at the Dept. of Biochemistry at University Bayreuth, Germany. Our work involves biochemical and structural studies on cellular signalling systems with relevance to aging mechanisms or disease. The PhD project will cover studies on cyclic nucleotide signalling mechanisms, one of the main fields of interest of the group (for related publications, see PNAS 105, 15720-5; JMB 362, 623-39; NSMB 12, 32-7). Our newly established laboratory is located at the University of Bayreuth and equipped with state-of-the-art facilities. We can offer excellent research opportunities and a stimulating environment for research in structural biology. The ideal candidate is a highly motivated student with strong interest in structural biology and prior experience in protein biochemistry. Additional experience in molecular biology and/or protein crystallization would be an asset. Applications (including CV, research experience, and two names and contact information for references) should be sent to Dr. Clemens Steegborn Ruhr-Universität Bochum MA 2/141 Universitätsstr. 150 44801 Bochum Germany Email: clemens.steegb...@rub.de --- Jun.-Prof. Dr. Clemens Steegborn Ruhr-University Bochum Physiological Chemistry, MA 2/141 Universitaetsstr. 150 44801 Bochum , Germany phone: ++49 234 32 27041 fax: ++49 234 32 14193 email: mailto:clemens.steegb...@rub.de clemens.steegb...@rub.de
[ccp4bb] AW: [ccp4bb] Colored proteins :)
Cytochrome c Best CSt -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] Im Auftrag von Artem Evdokimov Gesendet: Wednesday, October 21, 2009 2:25 AM An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Colored proteins :) Hello CCP4 folks! I have a quick question - could you suggest a few naturally intensely colored proteins? Colors based on small molecule co-factors (i.e. metal ions, flavonoids, etc.) are perfectly fine for my needs :) I already looked into GFP and its relatives, (bacterio)rodopsin, azurins/pseudoazurins, and hemoglobins - but I would appreciate more examples. I am sure there's a nice review out there somewhere but so far I've not found it. Thank you, Artem
[ccp4bb] AW: [ccp4bb] Disulfide bond survival in the presence of DTT?
Hi Brad, For DosR, a stable disulfide bond was reported even in presence of 150 mM DTT - was reduced only after Thermal denaturation. see J Mol Biol. 2008 Nov 21;383(4):822-36 Best Clemens Von: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] Im Auftrag von Brad Bennett Gesendet: Tuesday, August 11, 2009 12:06 AM An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Disulfide bond survival in the presence of DTT? Hi all- Got a perplexing thiol chemistry/phasing issue. To prevent non-native disulfide bonds from forming between free Cys but to preserve native disulfides, I have heard of using a very low (say 0.5 mM) concentration of DTT. I've recently come across a paper where the assignment of 3 disulfides in a protein structure was carried out by calculating a 4A resolution anomalous difference map (detecting the sulfur anomalous signal with 1.7A x-rays). However, at every step in the protein prep and in the crystallization solution, there exists mM concentrations of DTT. Every protein is different, so the microenvironment and the protection of a disulfide will be different for every one you come across. But I am surprised that a disulfide can withstand that much DTT. I guess the proof is in the pudding, which would be the anomalous peaks observed in the maps. What is the upper limit on DTT (or B-ME or TCEP) concentration that people have used and still maintained native disulfides? Thanks- Brad
[ccp4bb] AW: [ccp4bb] Crystallization Reagent
Hi Paul, Check out http://www.jenabioscience.com/ Best Clemens -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] Im Auftrag von Paul Smith Gesendet: Tuesday, August 11, 2009 7:46 PM An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Crystallization Reagent Does anyone know of a source of AMP-N-PP? Thanks, --Paul
[ccp4bb] Postdoc position in protein crystallography
Postdoc Position in Protein Crystallography A research position in protein crystallography at the postdoc level is available in the group of Clemens Steegborn in Bochum, Germany. Research in the laboratory is focused on understanding the molecular signaling mechanisms involved in aging processes and disease. In particular, we study mitochondrial signaling proteins and the cyclic nucleotide signaling network formed by nucleotdyl cyclases and their counterparts, phosphodiesterases. We use protein crystallography, combined with biochemical and enzymological methods and bioinformatics approaches, to obtain a molecular understanding of these interconnected signaling systems. We are looking for a Postdoc with experience in protein x-ray crystallography to join our team studying cyclic nucleotide signaling mechanisms (see, e.g., PNAS 105, 15720-5; J. Med. Chem. 51, 4456-64; NSMB 12, 32-7). Our laboratory is located at the Medical School of Ruhr-University Bochum. It offers access to state-of-the art equipment and facilities, and a stimulating environment for research in structural biology. The group strongly interacts with Eckhard Hofmann's group, sharing crystallography equipment and holding joint seminars, and is associated with the Max-Planck-Institute of Molecular Physiology in Dortmund giving us access to state-of the art x-ray facilities and synchrotron beamlines. Our lab offers excellent research opportunities and a stimulating environment for research in Structural Biology. The ideal candidate is a highly motivated Ph.D. with an interest in medically relevant questions. Experience in protein purification crystallization and x-ray structure analysis is ABSOLUTELY MANDATORY. Additional experience in molecular biology would be an asset. Applications (including CV, research experience, and at least two names and contact information for references) should be sent, preferably per email as PDF attachment, to mailto:clemens.steegb...@rub.de clemens.steegb...@rub.de Evaluation of applications will start by June 9th. --- Jun.-Prof. Dr. Clemens Steegborn Ruhr-University Bochum Physiological Chemistry, MA 2/141 Universitaetsstr. 150 44801 Bochum, Germany phone: ++49 234 32 27041 fax: ++49 234 32 14193 email: clemens.steegb...@rub.de
[ccp4bb] AW: [ccp4bb] Twinned data and maps
Hi Walter, You should definitely detwin data for map calculation if you have a significant twinning fraction (and only for maps; keep using the twinned data set for refinement). We use the CCP4 program detwin. BUT if Shelxl gives bad density, maybe that's simply what you have, a bad density map - because output from Shelx is already detwinned! BTW, we observed that different programs handled different cases differently well; I would suggest ALWAYS to try more than one program, and also to try Phenix ... Best Clemens -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] Im Auftrag von Walter Kim Gesendet: Monday, March 16, 2009 7:22 AM An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Twinned data and maps Hi again, Thanks for your insight into refinement tools for twinned data. I have a couple of twinned data sets that are nearly perfectly pseudomerohedrally twinned. I've begun to refine my data in Refmac5 (using the automated twin refinement), CNS (using the twin inputs) and Shelxl; I'm testing out the different refinement programs to evaluate the best strategy for the refinement. However, I would like to start making maps. 1. Refmac5 - outputs an mtz that is model-biased 2. CNS - maps made via model_map_twin.inp are poor 3. Shelxl - the maps generated in coot from the.fcf file are poor Are there better ways to make cleaner maps with my twinnned data that are less model-biased that I can try to build into? Should I detwin the data and make maps from that (but continue to refine against the twinned data)? Thanks, Walter
[ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Twinned data and maps
Yes, Phenix default output (for twinned data) is detwinned, like the one from Shelxl; didn't know for the new Refmac twin option - but I understand from this posting and Garib's that it also detwins if the twin option is used ... So considering that the Shelxl-derived density looked bad, I definitely agree with Tassos (and apparently didn't make that point clear enough) that other reasons for bad density than twinning have to be considered ... Best Clemens -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] Im Auftrag von Eleanor Dodson Gesendet: Monday, March 16, 2009 12:52 PM An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] AW: [ccp4bb] Twinned data and maps But dont all twinned refinement programs output detwinned terms for a map? Certainly REFMAC and SHELX do. Eleanor Clemens Steegborn wrote: Hi Walter, You should definitely detwin data for map calculation if you have a significant twinning fraction (and only for maps; keep using the twinned data set for refinement). We use the CCP4 program detwin. BUT if Shelxl gives bad density, maybe that's simply what you have, a bad density map - because output from Shelx is already detwinned! BTW, we observed that different programs handled different cases differently well; I would suggest ALWAYS to try more than one program, and also to try Phenix ... Best Clemens -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] Im Auftrag von Walter Kim Gesendet: Monday, March 16, 2009 7:22 AM An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Twinned data and maps Hi again, Thanks for your insight into refinement tools for twinned data. I have a couple of twinned data sets that are nearly perfectly pseudomerohedrally twinned. I've begun to refine my data in Refmac5 (using the automated twin refinement), CNS (using the twin inputs) and Shelxl; I'm testing out the different refinement programs to evaluate the best strategy for the refinement. However, I would like to start making maps. 1. Refmac5 - outputs an mtz that is model-biased 2. CNS - maps made via model_map_twin.inp are poor 3. Shelxl - the maps generated in coot from the.fcf file are poor Are there better ways to make cleaner maps with my twinnned data that are less model-biased that I can try to build into? Should I detwin the data and make maps from that (but continue to refine against the twinned data)? Thanks, Walter
[ccp4bb] AW: [ccp4bb] Broken chain in Pymol display
Hi Joe, check chainID and segID; there might be a break in one of them not noticed by phenix because it uses the other one, but then leading to an apparent backbone break in coot because it uses the other one ... Best Clemens -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Joe Xtal Sent: Monday, March 02, 2009 5:08 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Broken chain in Pymol display Hi all, I tried to display a refined structure (final steps in phenix.refine) in Pymol, but several places are not connected. BTW, the structure displays normally in Coot and bond angle and length deviation are below 1.0 and 0.006, respectively. Thank you, Joe
[ccp4bb] Ph.D. and Postdoc positions in Structural Biology
Ph.D. and Postdoc positions in Structural Biology Several research positions in Structural Biology are available at Ruhr-University Bochum at the Ph.D. and Postdoc level in the groups of Eckhard Hofmann and Clemens Steegborn. The laboratories are located at Ruhr-University Bochum and offer state-of-the art equipment and facilities and a stimulating environment for research in structural biology. For details on the research focus of the labs please see below. Applications (including CV, research experience, and at least two names and contact information for references) should be sent, preferably per email as PDF attachment, to either mailto:clemens.steegb...@rub.de clemens.steegb...@rub.de or mailto:eckhard.hofm...@bph.rub.de eckhard.hofm...@bph.rub.de. Please indicate in your cover letter whether you wish to apply to one specific lab or for a position in either group. Evaluation of applications will start by February 9th. Steegborn lab Research in the Steegborn laboratory is focused on understanding the molecular signaling mechanisms involved in aging processes and disease, and how to modulate these processes with drugs. In particular, we study the ROS-activated mitochondrial apoptosis initiator p66shc and the Sirtuin family of metabolic sensors with emphasis on mitochondrial family members. A second focus is the metabolic sensor 'soluble adenylyl cyclase' and the cyclic nucleotide signaling network it forms with guanylyl cyclases and their counterparts, phosphodiesterases. We use protein crystallography, combined with biochemical and enzymological methods and bioinformatics approaches, to obtain a detailed, molecular understanding of these interconnected signaling systems and to exploit our findings for the development of specific modulators. We are now looking for a Postdoc with experience in protein x-ray crystallography to join our team studying cyclic nucleotide signaling mechanisms (see, e.g., PNAS 105, 15720-5; J. Med. Chem. 51, 4456-64; NSMB 12, 32-7); exceptional candidates for a Ph.D. student position might also be considered. Crystals and diffraction data set are already available for some projects. Our laboratory is located at the Medical School of Ruhr-University Bochum which harbours outstanding research groups and facilities. The group strongly interacts with Eckhard Hofmann's group, sharing crystallography equipment and holding joint seminars, and is further associated with the Max-Planck-Institute of Molecular Physiology in Dortmund giving us access to state-of the art x-ray facilities and synchrotron beamlines. Our lab offers excellent research opportunities and a stimulating environment for research in Structural Biology. The ideal candidate is a highly motivated Ph.D. with an interest in medically relevant questions. Experience in protein purification crystallization and x-ray structure analysis is ABSOLUTELY MANDATORY. Additional experience in molecular biology would be an asset. Hofmann lab One focus in our lab is the study of the role of carotenoids in the process of light harvesting. This includes structural work on integral membrane and soluble proteins and their genetic and biochemical modification. Another focus is on the functional analysis of membrane transport proteins, especially in the combination of structural and FTIR-spectroscopic methods to better understand the coupling of ATP hydrolysis with the transport process. Our group is well equipped for protein purification and crystallography, including AEKTA FPLC systems, nanodrop crystallization robot, crystal imaging system, rotating anode generator with confocal mirrors and a MAR IP. Frequent access to the SLS and the ESRF is guaranteed. Due to the strong collaboration within the chair of biophysics, the combination of different biophysical techniques is applied to most projects. As we participate in two collaborative research centers (SFB480 and SFB642) we are involved in several ongoing projects with collaborating groups covering different areas such as peroxisome biogenesis, bilin biosynthetic enzymes or bacterial reaction centers. In a collaboration with Dr. Stephan Pollmann (Plant Physiology, Ruhr-University Bochum) our work focuses on enzymes involved in the biosynthesis of plant wound hormones, such as 12-oxo-phytodienoic acid and jasmonic acid (see e.g. Hofmann et al. Plant Cell 18, 3201-3217, Schaller et al. FEBS J. 275, 2428-2441, Hofmann Pollmann Plant.Phys.Biochem. 46, 302-308). Two DFG-funded doctoral positions are available in our groups: The candidate in the Hofmann group will focus on the structural investigation of the enzymes and site specific mutants, while the candidate in the Pollmann group will mainly cover genetic (transgenic plants) and analytic aspects (HPLC, GC-MS) of the project. Both candidates are expected to closely interact. In addition a position on the postdoctoral level is available. The candidate will be involved in several projects with external groups
[ccp4bb] suggestions for UV spectrometer
Hi Tim, The Shimadzu UV2401PC comes at a reasonable price and has all features you might possible need in a Biochemistry lab. And if you like the option to use small sample volumes, I would suggest to by a TrayCell from Helma - you put it in a regular photometer, it guides the light through a microliter chamber and back into the photometer (it is essentially a cuvette with optics and a 1 or 5 microliter chamber). Costs a few hundred Euros . If you're sure you will never need regular cuvettes - go for Nanodrop. If you want more flexibility, Shimadzu plus TrayCell . Best Clemens --- Jun.-Prof. Dr. Clemens Steegborn Ruhr-University Bochum Physiological Chemistry, MA 2/141 Universitaetsstr. 150 44801 Bochum, Germany phone: ++49 234 32 27041 fax: ++49 234 32 14193 email: [EMAIL PROTECTED]
[ccp4bb] Ph.D. Position in Structural Biology / Bochum, Germany
Ph.D. Student Position in Structural Biology in Bochum, Germany We are looking for a highly motivated Ph.D. student interested in biochemical and structural studies on intracellular signaling systems with relevance to aging diseases. Our laboratory (for more info: http://www.ruhr-uni-bochum.de/physiolchem/steegborn/index.html) is located at the Medical School of Ruhr-University Bochum which harbors excellent research groups and facilities. The group is further associated with the Max-Planck-Institute of Molecular Physiology in Dortmund and provides a stimulating environment for research in structural biology. Excellent students in Biochemistry, Biology, Chemistry, or Physics are welcome. Skills in either molecular biology or protein chemistry purification or protein crystallography would be an asset. Please send applications (including CV, research experience, and at least two names and contact information for references) either as pdf files to [EMAIL PROTECTED] or as hardcopy to the address given below. Prof. Dr. Clemens Steegborn Ruhr-University Bochum Dept. Physiol. Chemistry, MA 2/141 Universitaetsstr. 150 44801 Bochum, Germany phone: 0049 234 32 27041 fax: 0049 234 32 14193 email: [EMAIL PROTECTED]
[ccp4bb] Postdoc and Ph.D. student positions
Postdoctoral Position in Structural Biology / Biochemistry We are looking for a highly motivated Postdoc for our laboratory at the Institute for Physiological Chemistry at Ruhr-University Bochum, Germany. Our work involves biochemical and structural studies on cellular signaling systems with relevance to cancer, metabolic diseases, or aging. A main focus of the group is the mechanism of metabolic sensing and cyclic nucleotide signaling. Our laboratory is located at the Medical School of the Ruhr-University Bochum which harbours outstanding research groups and facilities. The group is further associated with the Max-Planck-Institute of Molecular Physiology in Dortmund giving us access to state-of the art x-ray facilities and synchrotron beamlines. Our lab offers excellent research opportunities and a stimulating environment for research in structural biology. The ideal candidate is a highly motivated Ph.D. with an interest in medically relevant questions; experience in protein biochemistry and protein crystallization is mandatory. Additional experience in molecular biology would be an asset. Applications (including CV, research experience, and two names and contact information for references) should be sent to Dr. Clemens Steegborn Ruhr-University Bochum MA 2/141 Universitaetsstr. 150 44801 Bochum Germany Email: mailto:[EMAIL PROTECTED][EMAIL PROTECTED] mailto:[EMAIL PROTECTED][EMAIL PROTECTED] Jun.-Prof. Dr. Clemens Steegborn Ruhr-University Bochum Dept. Physiol. Chemistry, MA 2/141 Universitaetsstr. 150 44801 Bochum, Germany phone: 0049 234 32 27041 fax: 0049 234 32 14193 email: [EMAIL PROTECTED]
Re: [ccp4bb] AKTA prime
Dear Frank, AKTA prime delivers a max. pressure of 1 MPa. The 24 ml SEC columns can be run at pressures up to 1.5 (S200) or even 3 MPa (superose 12). If your column is in pretty good shape, expect to reach 0.9 MPa at 0.4 ml/min for S200. So you can use an AKTA prime, but ... Best Clemens At 11:16 PM 2/13/2007, you wrote: Dear all, I need to decide between buying an AKTA prime and an AKTA FPLC from GE health care. I understand AKTA prime is a low-pressure system, but because it is too much cheaper than AKTA FPLC, it is still very attractive to me. I will mainly use it for Nickel columns and gel filtration columns, and I am worried about the latter. Is it true that using AKTA prime, you can only run the 24 ml Superdex 200 column at 0.1 or 0.2 ml/min? Could anyone who has used AKTA prime give me some feedbacks? I would appreciate it. Best, Frank Need Mail bonding? Go to the Yahoo! Mail QA for great tips from Yahoo! Answers users. Jun.-Prof. Dr. Clemens Steegborn Ruhr-University Bochum Dept. Physiol. Chemistry, MA 2/141 Universitaetsstr. 150 44801 Bochum, Germany phone: 0049 234 32 27041 fax: 0049 234 32 14193 email: [EMAIL PROTECTED]
