Re: [ccp4bb] Rfree flag
Dear All, Thank you Folmer and Fred for your suggestions. Mine is an isomorphous crystal. I had refined without using the same set of Rfree reflections, finally getting larger difference between the R and Rfree. I hope considering the same Rfree set would solve this problem. Thank you With regards Kavya Although it is not mandatory, I think it would be a very good idea, especially if you have the exact same spacegroup and the native and ligand-bound forms of your protein are essentially the same. If you do not use the same reflections, you are actually not reporting an independent (free) R-factor. Best regards, Folmer Hello, I think this depends on the type of problem you are facing: if the 2 crystals are not isomorphous then you cannot have the same R-free sets; if the 2 crystals are isomorphous then either you do not worry about keeping the same R-free set (but then the starting structure must be perturbed enough to get rid of R-free bias during refinement), or you keep the same indices for the reflections in the 2 R-free sets (same reflections in your message) in which case there is no R-free bias at the beginning of refinement. By R-free bias I mean this: in your new (liganded) crystal form, there are reflections that have seen the Fo's during refinement of the native structure but that are in the R-free set in the ligand structure. This leads to bias. HTH, Fred. Dear users, Is it mandatory to use the same reflections for Rfree calculations of a ligand bound data as that of its native? Thank you With Regards Kavya -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
Re: [ccp4bb] Rfree flag
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Kavya, As far as I understand the PDBRedo project attempts to make the reflections unbiased from the structure by a random shift of coordinates (e.g. 'NOISE' keyword in pdbset, although I am not aware of an investigation about whether this actually does make remove bias. It is safest to keep the same Rfree-set. Regards, Tim On 02/28/2013 06:54 AM, Kavyashree Manjunath wrote: Dear users, Is it mandatory to use the same reflections for Rfree calculations of a ligand bound data as that of its native? Thank you With Regards Kavya - -- - -- 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 Mozilla - http://enigmail.mozdev.org/ iD8DBQFRLyQ2UxlJ7aRr7hoRAsHBAJ43K7f2lcSZwm6fD1pH8+grvrOqRACg1bdi PUUKJaUv8C4JgmcPNM6H9+U= =J47i -END PGP SIGNATURE-
[ccp4bb] correction to: Post Doctoral Position at Imperial College London in Structural Biology
Dear all, the recent advertisement for a postdoc position in the Freemont/Zhang labs at Imperial had a small error in the job code needed to find it online. The correct code is NS 2013 047 IL Use it at http://www3.imperial.ac.uk/employment (Job search) to apply for the position. Closing date is 25 Mar midnight GMT. The entire advertisement is repeated below. Sorry about the confusion. Andreas Post Doctoral Position at Imperial College London in Structural Biology Imperial College London Department of Life Sciences Faculty of Natural Sciences Research Associate Salary: £32,100 - £35,620 per annum We wish to recruit a Research Associate for up to 24 months in the first instance with possible extension to up to five years to work in the research group of Professor Paul Freemont and Professor Xiaodong Zhang (http://www.msf.bio.ic.ac.uk/index.php) in the Centre for Structural Biology, Department of Life Sciences at the South Kensington Campus of Imperial College London. Our research group comprise research fellows, research associates and PhD students from a diverse range of background including molecular biology, biochemistry, X-ray crystallography, electron microscopy, physics and engineering. We employ a multi-disciplinary approach to study the structures and mechanisms of large macromolecular complexes. Funded by a CRUK programme grant to Professor Paul Freemont and Professor Xiaodong Zhang, you will join a multi-disciplinary group to investigate the structure and mechanism of the AAA ATPase p97. p97 is a versatile participant of the ubiquitin proteasome system, interacting with a larger network of adaptor proteins to mediate a variety of cellular processes including ER associated degradation, autophagy and DNA damage repair. Successful candidates must hold a PhD in a structural biology or biochemistry discipline or an equivalent level of research, industrial or commercial experience and have demonstrated capacity for innovative high quality structural biological research. Previous research experience in a structural biological laboratory environment covering X-ray crystallography or electron microscopy single particle analysis is essential. The successful candidate must also have an advanced knowledge of protein biochemistry and structural biology. Experience in supervision and training of junior research staff and students and in writing scientific research papers would be advantageous. The successful candidate must be able to work effectively within a team, have the ability to develop and apply new concepts, and have a creative approach to problem-solving. They will also be expected to demonstrate excellent verbal and written communication skills, and be able to write clearly and succinctly for publication. For informal enquiries please contact Professor Paul Freemont (p.freem...@imperial.ac.uk) or Professor Xiaodong Zhang (xiaodong.zh...@imperial.ac.uk) Our preferred method of application is online via our website http://www3.imperial.ac.uk/employment (please select “Job Search” then enter the job title or vacancy reference number – NS 2013 047 IL - including spaces into “Keywords”). Please complete and upload an application form as directed. *** Professor Paul Freemont Co-director of Macromolecular Structure and Function Group Department of Life Sciences Sir Ernst Chain Building - Wolfson Laboratories South Kensington Campus London SW7 2AZ, UK www.msf.bio.ic.ac.uk Tel: 02075945327 Email: p.freem...@imperial.ac.uk
Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04
Hi Ed, It looks as though you have not sourced $CCP4/include/ccp4.setup. This needs to be customized and sourced before you configure and make CCP4. Adam
Re: [ccp4bb] Rfree flag
Hi Tim, Our approach is a bit different. We first try to establish whether the R-free set is biased, by checking whether R-free is surprisingly low compared to R given the data parameter ratio. If this is the case (or if we chose a new R-free set for some reason, e.g. because it was too small) PDB_REDO resets the B-factors to 0.5*(Wilson B-factor) and then does more cycles of refinement to ensure it converges. This should get rid of the bias. We compared this to the 'perturb coordinates' approach and in most cases there wasn't any difference. In some cases the perturbed coordinates were outside the radius of convergence of Refmac (the version 5.2 or perhaps 5.4) particularly in cases with NCS. So coordinate perturbation was just not worth it. This was before NCS restraints were properly implemented in PDB_REDO (hurray for local NCS/LSSR!), so this issue must be much smaller now. Of course the rebuilding round of PDB_REDO followed by more refinemnt, will cause enough model perturbation if the above results are not convincing enough ;) We also do full (well, k-fold) cross-validation for small data sets in which the different test sets are all-but-one completely biased. Here, too, the B-factor resetting works well enough. That said we might add a few extra cycles of refinement here to be on the safe side. Cheers, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent: Thursday, February 28, 2013 10:33 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Rfree flag -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Kavya, As far as I understand the PDBRedo project attempts to make the reflections unbiased from the structure by a random shift of coordinates (e.g. 'NOISE' keyword in pdbset, although I am not aware of an investigation about whether this actually does make remove bias. It is safest to keep the same Rfree-set. Regards, Tim On 02/28/2013 06:54 AM, Kavyashree Manjunath wrote: Dear users,y Is it mandatory to use the same reflections for Rfree calculations of a ligand bound data as that of its native? Thank you With Regards Kavya - -- - -- 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 Mozilla - http://enigmail.mozdev.org/ iD8DBQFRLyQ2UxlJ7aRr7hoRAsHBAJ43K7f2lcSZwm6fD1pH8+grvrOqRACg1bdi PUUKJaUv8C4JgmcPNM6H9+U= =J47i -END PGP SIGNATURE-
Re: [ccp4bb] disulfide engineering
Along these lines, what reagents do people use to promote disuflide bonds, i.e., the anti-DTT? JPK On Thu, Feb 28, 2013 at 2:06 AM, David Briggs drdavidcbri...@gmail.comwrote: You might want to try Disulfide by design http://cptweb.cpt.wayne.edu/DbD2/ Cheers Dave On Feb 28, 2013 6:55 AM, Careina Edgooms careinaedgo...@yahoo.com wrote: Dear CCP4 members I wish to engineer a disulfide bond at the dimer interface of a protein I am working with. Does anyone know of any available software to assist with this? Best Careina -- *** Jacob Pearson Keller, PhD Postdoctoral Associate HHMI Janelia Farms Research Campus email: j-kell...@northwestern.edu ***
[ccp4bb] FW: [ccp4bb] disulfide engineering
Rather than looking at anti-DTT it is more important to set up an appropriate redox system. This can be a combination of reduced and oxidised glutathione or cysteine. If you check some of the commercial protein refolding screens this should give you an idea about relative concentrations. Best regards, Paul.. - Dr. Paul A. McEwan Senior Scientist (Structural Biology) Evotec (UK) Ltd. 114 Innovation Drive | Milton Park | Abingdon | Oxfordshire | OX14 4SA email: paul.mce...@evotec.com mailto:paul.mce...@evotec.com Tel: +44 (0)1235 861561 Fax:+44 (0)1235 863139 direct line: +44 (0)1235 838802 www.evotec.com http://www.evotec.com From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob Keller Sent: 28 February 2013 11:09 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] disulfide engineering Along these lines, what reagents do people use to promote disuflide bonds, i.e., the anti-DTT? JPK On Thu, Feb 28, 2013 at 2:06 AM, David Briggs drdavidcbri...@gmail.com wrote: You might want to try Disulfide by design http://cptweb.cpt.wayne.edu/DbD2/ Cheers Dave On Feb 28, 2013 6:55 AM, Careina Edgooms careinaedgo...@yahoo.com wrote: Dear CCP4 members I wish to engineer a disulfide bond at the dimer interface of a protein I am working with. Does anyone know of any available software to assist with this? Best Careina -- *** Jacob Pearson Keller, PhD Postdoctoral Associate HHMI Janelia Farms Research Campus email: j-kell...@northwestern.edu *** Evotec (UK) Ltd is a limited company registered in England and Wales. Registration number:2674265. Registered office: 114 Milton Park, Abingdon, Oxfordshire, OX14 4SA, United Kingdom.
[ccp4bb] PhD studentship at UoLiverpool/CICbioGUNE
Dear Colleagues, We are offering an exciting PhD studentship on the structural biology of RNA degradation and translational repression. The project combines state-of-the-art technologies in cryo-electron microscopy and X-ray crystallography and is a collaboration between the Spanish research institute CICbioGUNE in Bilbao and the University of Liverpool. The studentship covers approximately two years of research at each institute. If you are aware of high-calibre candidates who might be interested, please bring this opportunity to their attention. Full details can be found at: http://www.findaphd.com/search/ProjectDetails.aspx?PJID=41553LID=829 Please note that this studentship is only available to EU/UK students. With best regards, U of Liverpool Mark Caddick Olga Mayans (cadd...@liv.ac.uk) CICbioGUNE Sean Connell Paola Fuccini (sconn...@cicbiogune.es)
Re: [ccp4bb] disulfide engineering
Along these lines, what reagents do people use to promote disuflide bonds, i.e., the anti-DTT? Glutathione (red) + Glutathione (ox), redox potential is adjusted by varying the ratio. Best, Clemens JPK On Thu, Feb 28, 2013 at 2:06 AM, David Briggs drdavidcbri...@gmail.comwrote: You might want to try Disulfide by design http://cptweb.cpt.wayne.edu/DbD2/ Cheers Dave On Feb 28, 2013 6:55 AM, Careina Edgooms careinaedgo...@yahoo.com wrote: Dear CCP4 members I wish to engineer a disulfide bond at the dimer interface of a protein I am working with. Does anyone know of any available software to assist with this? Best Careina -- *** Jacob Pearson Keller, PhD Postdoctoral Associate HHMI Janelia Farms Research Campus email: j-kell...@northwestern.edu *** -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 31 84031 -
Re: [ccp4bb] FW: [ccp4bb] [ccp4bb] disulfide engineering
We have had some good luck with hydrogen peroxide [for technical details plus validation via a crystal structure see Van der Meeren et al JBC 288(2):1214-1225, (2013)]. best of luck Savvas On 28 Feb 2013, at 12:14, McEwan, Paul paul.mce...@evotec.com wrote: Rather than looking at “anti-DTT” it is more important to set up an appropriate redox system. This can be a combination of reduced and oxidised glutathione or cysteine. If you check some of the commercial protein refolding screens this should give you an idea about relative concentrations. Best regards, Paul.. - Dr. Paul A. McEwan Senior Scientist (Structural Biology) Evotec (UK) Ltd. 114 Innovation Drive | Milton Park | Abingdon | Oxfordshire | OX14 4SA email: paul.mce...@evotec.com Tel: +44 (0)1235 861561 Fax:+44 (0)1235 863139 direct line: +44 (0)1235 838802 www.evotec.com From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob Keller Sent: 28 February 2013 11:09 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] disulfide engineering Along these lines, what reagents do people use to promote disuflide bonds, i.e., the anti-DTT? JPK On Thu, Feb 28, 2013 at 2:06 AM, David Briggs drdavidcbri...@gmail.com wrote: You might want to try Disulfide by design http://cptweb.cpt.wayne.edu/DbD2/ Cheers Dave On Feb 28, 2013 6:55 AM, Careina Edgooms careinaedgo...@yahoo.com wrote: Dear CCP4 members I wish to engineer a disulfide bond at the dimer interface of a protein I am working with. Does anyone know of any available software to assist with this? Best Careina -- *** Jacob Pearson Keller, PhD Postdoctoral Associate HHMI Janelia Farms Research Campus email: j-kell...@northwestern.edu *** Evotec (UK) Ltd is a limited company registered in England and Wales. Registration number:2674265. Registered Office: 114 Milton Park, Abingdon, Oxfordshire, OX14 4SA, United Kingdom
Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04
Adam, I am not compiling CCP4, just refmac. IIUC, all that sourcing ccp4.setup does is it sets $CLIB for refmac makefile to find libccp4c and libccp4f. And presumably lapack and libblas, but that's a separate issue. On Thu, 2013-02-28 at 10:28 +, Adam Ralph wrote: Hi Ed, It looks as though you have not sourced $CCP4/include/ccp4.setup. This needs to be customized and sourced before you configure and make CCP4. Adam -- Bullseye! Excellent shot, Maurice. Julian, King of Lemurs.
Re: [ccp4bb] disulfide engineering
In the literature, you can find examples of air oxidation, oxidized glutathione (alone), mixture of reduced and oxidized glutathione, and hydrogen peroxide. The correct concentrations have to be found empirically. We are just now mushing through this with an engineered disulfide variant. Air oxidation partially worked for us--one of the engineered disulfides worked, one did not. ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 2/28/2013 7:55 AM, Clemens Grimm wrote: Along these lines, what reagents do people use to promote disuflide bonds, i.e., the anti-DTT? Glutathione (red) + Glutathione (ox), redox potential is adjusted by varying the ratio. Best, Clemens JPK On Thu, Feb 28, 2013 at 2:06 AM, David Briggs drdavidcbri...@gmail.comwrote: You might want to try Disulfide by design http://cptweb.cpt.wayne.edu/DbD2/ Cheers Dave On Feb 28, 2013 6:55 AM, Careina Edgooms careinaedgo...@yahoo.com wrote: Dear CCP4 members I wish to engineer a disulfide bond at the dimer interface of a protein I am working with. Does anyone know of any available software to assist with this? Best Careina -- *** Jacob Pearson Keller, PhD Postdoctoral Associate HHMI Janelia Farms Research Campus email: j-kell...@northwestern.edu *** -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 31 84031 -
Re: [ccp4bb] disulfide engineering
Dera Careina going back to the original software question, I think you may be able to use the Rasmot-3D Pro server http://biodev.cea.fr/rasmot3d/ Nucleic Acids Res. 2009 Jul;37(Web Server issue):W459-64. doi: 10.1093/nar/gkp304. Epub 2009 May 5. RASMOT-3D PRO: a 3D motif search webserver. Debret G, Martel A, Cuniasse P. Source Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), iBiTec-S, DSV, CEA, CE-Saclay, 91191 Gif Sur Yvette Cedex, France. This allows you to upload coordinates containing a a motif (in your case two disulphide-bonded Cys residues from another protein), and the coordinates for a protein structure you wish to examine - in this case your dimeric coordinates. It will then search for pairs of CA-CB bonds in the protein that would be at the right relative angles and distances to form a disulphide if those residues were mutated to cysteines. There are a number of different conformations for disulphide bonds depending on the various torsion angles so you may need to choose a number of different search structures - though obviously 2-fold symmetric ones would be a good start. After your mutagenesis some of the suggestions that have already been made may allow you to oxidize them to a disulphide. best wishes Pete On 28 Feb 2013, at 14:52, Roger Rowlett wrote: In the literature, you can find examples of air oxidation, oxidized glutathione (alone), mixture of reduced and oxidized glutathione, and hydrogen peroxide. The correct concentrations have to be found empirically. We are just now mushing through this with an engineered disulfide variant. Air oxidation partially worked for us--one of the engineered disulfides worked, one did not. ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 2/28/2013 7:55 AM, Clemens Grimm wrote: Along these lines, what reagents do people use to promote disuflide bonds, i.e., the anti-DTT? Glutathione (red) + Glutathione (ox), redox potential is adjusted by varying the ratio. Best, Clemens JPK On Thu, Feb 28, 2013 at 2:06 AM, David Briggs drdavidcbri...@gmail.comwrote: You might want to try Disulfide by design http://cptweb.cpt.wayne.edu/DbD2/ Cheers Dave On Feb 28, 2013 6:55 AM, Careina Edgooms careinaedgo...@yahoo.com wrote: Dear CCP4 members I wish to engineer a disulfide bond at the dimer interface of a protein I am working with. Does anyone know of any available software to assist with this? Best Careina -- *** Jacob Pearson Keller, PhD Postdoctoral Associate HHMI Janelia Farms Research Campus email: j-kell...@northwestern.edu *** -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 31 84031 - Prof Peter Artymiuk Krebs Institute Department of Molecular Biology Biotechnology University of Sheffield Sheffield S10 2TN ENGLAND
Re: [ccp4bb] disulfide engineering
I don't know how much mileage you'd get out of it with your protein, but I was able to get very efficient disulfide linkage at the dimerization interface of my protein by dropping the salt to nearly nothing and running lots of buffer over it after immobilization on a cation exchange column (during purification). --p On 02/28/2013 06:09 AM, Jacob Keller wrote: Along these lines, what reagents do people use to promote disuflide bonds, i.e., the anti-DTT? JPK On Thu, Feb 28, 2013 at 2:06 AM, David Briggs drdavidcbri...@gmail.com mailto:drdavidcbri...@gmail.com wrote: You might want to try Disulfide by design http://cptweb.cpt.wayne.edu/DbD2/ Cheers Dave On Feb 28, 2013 6:55 AM, Careina Edgooms careinaedgo...@yahoo.com mailto:careinaedgo...@yahoo.com wrote: Dear CCP4 members I wish to engineer a disulfide bond at the dimer interface of a protein I am working with. Does anyone know of any available software to assist with this? Best Careina -- *** Jacob Pearson Keller, PhD Postdoctoral Associate HHMI Janelia Farms Research Campus email: j-kell...@northwestern.edu mailto:j-kell...@northwestern.edu ***
Re: [ccp4bb] disulfide engineering
Adding 1-10mM copper sulfate is often a good way to oxidize disulfide bonds, although some proteins cannot tolerate this treatment. Mike - Original Message - From: Jacob Keller j-kell...@fsm.northwestern.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Thursday, February 28, 2013 3:09:18 AM GMT -08:00 US/Canada Pacific Subject: Re: [ccp4bb] disulfide engineering Along these lines, what reagents do people use to promote disuflide bonds, i.e., the anti-DTT? JPK On Thu, Feb 28, 2013 at 2:06 AM, David Briggs drdavidcbri...@gmail.com wrote: You might want to try Disulfide by design http://cptweb.cpt.wayne.edu/DbD2/ Cheers Dave On Feb 28, 2013 6:55 AM, Careina Edgooms careinaedgo...@yahoo.com wrote: Dear CCP4 members I wish to engineer a disulfide bond at the dimer interface of a protein I am working with. Does anyone know of any available software to assist with this? Best Careina -- *** Jacob Pearson Keller, PhD Postdoctoral Associate HHMI Janelia Farms Research Campus email: j-kell...@northwestern.edu *** -- Michael C. Thompson Graduate Student Biochemistry Molecular Biology Division Department of Chemistry Biochemistry University of California, Los Angeles mi...@chem.ucla.edu
Re: [ccp4bb] disulfide engineering
I have used a copper solution that worked well. The details can be found in this paper: Nucleic Acids Res. 2004 Sep 30;32(17):5192-7. PMID: 15459288 PMCID: PMC521666 Yingyun Liu - Original Message - From: Roger Rowlett rrowl...@colgate.edu Date: Thursday, February 28, 2013 9:52 am Subject: Re: [ccp4bb] disulfide engineering To: CCP4BB@JISCMAIL.AC.UK In the literature, you can find examples of air oxidation, oxidized glutathione (alone), mixture of reduced and oxidized glutathione, and hydrogen peroxide. The correct concentrations have to be found empirically. We are just now mushing through this with an engineered disulfide variant. Air oxidation partially worked for us--one of the engineered disulfides worked, one did not. ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 2/28/2013 7:55 AM, Clemens Grimm wrote: Along these lines, what reagents do people use to promote disuflide bonds, i.e., the anti-DTT? Glutathione (red) + Glutathione (ox), redox potential is adjusted by varying the ratio. Best, Clemens JPK On Thu, Feb 28, 2013 at 2:06 AM, David Briggs drdavidcbri...@gmail.comwrote: You might want to try Disulfide by design Cheers Dave On Feb 28, 2013 6:55 AM, Careina Edgooms careinaedgo...@yahoo.com wrote: Dear CCP4 members I wish to engineer a disulfide bond at the dimer interface of a protein I am working with. Does anyone know of any available software to assist with this? Best Careina -- *** Jacob Pearson Keller, PhD Postdoctoral Associate HHMI Janelia Farms Research Campus email: j-kell...@northwestern.edu *** -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 31 84031 -
[ccp4bb] PhD CASE studentship
Dear Colleagues, We have an Industrial CASE BBSRC PhD Studentship on offer at the University of Reading. Please circulate this email to relevant colleagues and UG students. The CASE award is a collaborative project in the Schools of Food and Nutritional Sciences and Biological Sciences. The project title is Understanding the structure-function relationships of cold-adapted enzymes. The aim of this project is to use advanced protein engineering methodologies to develop cold adapted enzymes that can be quickly inactivated at temperatures less than 50oC. This work will use computational and structural biology approaches to aid understanding of structure, function and stability of cold adapted enzymes of commercial importance to our industrial partner. Using this knowledge, the structural and functional characteristics will be further enhanced, through protein engineering, targeting the development of enzymes that have high activity but can be quickly inactivated at low temperatures. The engineered enzymes will be experimentally analysed using a variety of biophysical techniques and their structures determined to verify the predictions. The enzymes will then be characterised, with particular emphasis on the specificity of the enzymes deactivation kinetics, and will then be evaluated regarding their commercial potential using a variety of substrates. The PhD candidate will develop expertise in a range of methodologies including enzymology, protein engineering, protein expression, fermentation, purification, chromatography and structural biology. The applicants should ideally have some experience in protein expression and/or protein structure and some knowledge of food biotechnology. Funding Details: The studentship will cover Home/EU Fees and pay a tax-free stipend of £15,226 per year for a period of up to 4 years. The studentship will begin in October 2013. Applicants should hold a minimum of a UK Honours Degree at 2:1 level or equivalent. Please note that due to restrictions on the funding, this studentship is for UK/EU applicants only. To be eligible for support, applicants must be 'UK Residents' as defined by the BBSRC; this includes EU citizens who have been resident in the UK for a period of 3 years for any purpose, including undergraduate studies, prior to the start of the studentship. To apply for this studentship please submit an application for a PhD in Food Science/Applied Biochemistry to the University of Reading at: http://www.reading.ac.uk/graduateschool/prospectivestudents/gs-how-to-apply.aspx Please quote the reference GS13-22 in the 'Scholarships applied for' box which appears within the Funding Section of your online application. Application Deadline: Friday, 22 March 2013 For further information please contact: Dr. Dimitris Charalampopoulos (d.charalampopou...@reading.ac.uk) Dr Kim Watson (k.a.wat...@reading.ac.uk)
[ccp4bb] stereo monitor for DELL T7600
Hi All, I am ordering a Dell workstation (Dell Precision,T7600n,MT,1300W) with 2GB nVIDIA Quadro 4000. Can anyone recommend to me which stereo monitor would be compatible with this model? I have some stereo models mentioned in previously ccp4bb email: - Zalman ZM-M215W 21.5in - Zalman ZM-M240W 24in - Samsung http://proteincrystallography.org/ccp4bb/message29933.htmlSyncMaster S27A750D 27in - LG D2342P 23in / LG D2542P 25in Any advice will be highly appreciated. Thanks so much in advance! Jl
[ccp4bb] West Coast Protein Crystallography Workshop 21!
All, The West Coast Protein Crystallography Workshop is fast approaching. We have a pretty full house with an outstanding line up of talks and posters! If you would still like to participate we can accommodate more people (see wcpcw.org). That said, we absolutely need your abstract first thing tomorrow morning to get it in the program. Only posters presentations are still available. We will be distributing the schedule tomorrow. Looking forward to seeing everybody. Best, John WCPCW 21 Organizer - *SECURITY/CONFIDENTIALITY WARNING: This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (fpc5p) -
Re: [ccp4bb] disulfide engineering
Thank you to everyone for the helpful suggestions From: Yingyun Liu yingyun...@jhu.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Thursday, February 28, 2013 10:29 PM Subject: Re: [ccp4bb] disulfide engineering I have used a copper solution that worked well. The details can be found in this paper: Nucleic Acids Res. 2004 Sep 30;32(17):5192-7. PMID: 15459288 PMCID: PMC521666 Yingyun Liu - Original Message - From: Roger Rowlett rrowl...@colgate.edu Date: Thursday, February 28, 2013 9:52 am Subject: Re: [ccp4bb] disulfide engineering To: CCP4BB@JISCMAIL.AC.UK In the literature, you can find examples of air oxidation, oxidized glutathione (alone), mixture of reduced and oxidized glutathione, and hydrogen peroxide. The correct concentrations have to be found empirically. We are just now mushing through this with an engineered disulfide variant. Air oxidation partially worked for us--one of the engineered disulfides worked, one did not. ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 2/28/2013 7:55 AM, Clemens Grimm wrote: Along these lines, what reagents do people use to promote disuflide bonds, i.e., the anti-DTT? Glutathione (red) + Glutathione (ox), redox potential is adjusted by varying the ratio. Best, Clemens JPK On Thu, Feb 28, 2013 at 2:06 AM, David Briggs drdavidcbri...@gmail.comwrote: You might want to try Disulfide by design Cheers Dave On Feb 28, 2013 6:55 AM, Careina Edgooms careinaedgo...@yahoo.com wrote: Dear CCP4 members I wish to engineer a disulfide bond at the dimer interface of a protein I am working with. Does anyone know of any available software to assist with this? Best Careina -- *** Jacob Pearson Keller, PhD Postdoctoral Associate HHMI Janelia Farms Research Campus email: j-kell...@northwestern.edu *** -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 31 84031 -
Re: [ccp4bb] stereo monitor for DELL T7600
What about the ASUS VG278HR Activ stereo with build in emitter, 27 in. Am 01.03.13 00:56, schrieb jlliu liu: Hi All, I am ordering a Dell workstation (Dell Precision,T7600n,MT,1300W) with 2GB nVIDIA Quadro 4000. Can anyone recommend to me which stereo monitor would be compatible with this model? I have some stereo models mentioned in previously ccp4bb email: - Zalman ZM-M215W 21.5in - Zalman ZM-M240W 24in - Samsunghttp://proteincrystallography.org/ccp4bb/message29933.html SyncMaster S27A750D 27in - LG D2342P 23in / LG D2542P 25in Any advice will be highly appreciated. Thanks so much in advance! Jl -- Joachim Reichelt Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Das HZI ist seit 2007 zertifiziertes Mitglied im audit berufundfamilie Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, Bundesministerium für Bildung und Forschung Stellvertreter: Rüdiger Eichel, Abteilungsleiter Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Ulf Richter, MBA Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477
