[ccp4bb] Jean-Luc Ferrer
It is with a deep sadness that we learned the passing away of our dear colleague and friend, Dr Jean-Luc Ferrer, on April 21st in Grenoble, after a long struggle against his disease. Jean-Luc was an internationally known and highly respected scientist in protein crystallography.Jean-Luc had led the Synchrotron Group (GSY) at the IBS, a research group bridging instrumental and methodological development in large research infrastructures and structural biology projects. He was in charge of the French national (CRG) beamline FIP-BM30A at the ESRFsince 2001. He has always been inventive, dynamic and determined to highlight the advantages of synchrotron radiation for protein crystallography. Pioneer in the automation of crystallography beamlines, he has been the driving force to develop the first sample loader based on a robotic arm with the idea of using it directly as a goniometer. This paved the way to “in plate” diffraction experiments and its use for intensive ligand screening. He was also a co-funder of the NatX-ray company in Grenoble and San Diego and was strongly involved in several teaching programs and international workshops. Since the shutdown of the ESRF to complete its latest upgrade program, Jean-Luc had been in charge to rebuild the FIP beamline in order to provide the best service to the community, which will become BM07-FIP2. Jean-Luc will be forever missed and remembered. David Cobessi, on the behalf of the whole IBS staff and the RéNaFoBiS network members To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] linking PLP-Lys
Dear Rajesh, You do not need to define a link between Lys and PLP: PLP linked to Lys is LLP. You can find examples in PDB. LLP is recognized by Phenix and Refmac. Kind regards, David On 07/23/2012 07:30 PM, Rajesh Kumar wrote: Dear All, My friend needs a help. What is the best way to connect Lys to PLP with covalent bond. I am sure there are many ways do it. My friend would appreciate if you could simplify and explain this so that he could learn it without difficulties. Also I could learn I appreciate your time and help Thanks Rajesh -- David Cobessi Institut de Biologie Structurale 41, Rue Jules Horowitz 38027 Grenoble Cedex-1, France Tel:33(0)438789613 33(0)608164340 Fax:33(0)438785122
Re: [ccp4bb] strict structure based alignment
Dear Christian, PDBefold superimposes the structures and generates the sequence alignment in fasta(??) format. You can then read this file in Multialign for example to get the sequence alignment and then add the secondary structures to the sequence alignment using ESPript for example. David On 07/13/2012 04:30 PM, Christian Roth wrote: Dear all, I want align a couple or protein structures by secondary structure matching to one target and want get a kind of aminoacid alignment file e.g. what residue fit the other, without adjustments due to sequence based alignments. I tried Strap, but as far as I understood it, it takes also the sequence into account. I tried also Rapido, but this does only a pairwise comparison. Superpose does align it nicely (ccp4 based or Coot based) but there seems to be no option to print the sequence alignment in a file and it is again just a pairwise comparison . Is there an other program which does something similar? Best Regards Christian -- David Cobessi Institut de Biologie Structurale 41, Rue Jules Horowitz 38027 Grenoble Cedex-1, France Tel:33(0)438789613 33(0)608164340 Fax:33(0)438785122
Re: [ccp4bb] information received through the AFC: iycr2014
English version: http://www.un.org/ga/search/view_doc.asp?symbol=A/66/L.51 David On 07/04/2012 01:50 PM, Vellieux Frederic wrote: Dear colleagues, Information just received here through the AFC channels: the UN general assembly has declared that 2014 will be the international year of crystallography. Their statement (in French) as an attachment (sorry about including an attachment). F. Vellieux
[ccp4bb] PhD position - Institut de Biologie Structurale (Grenoble)
A PhD position funded by a grant is available in the Synchrotron Group headed by Dr Jean-Luc Ferrer at Institut de Biologie Structurale (IBS http://www.ibs.fr/spip.php?lang=en) at Grenoble, starting in October 2012. The project will focus on the structural and biochemical characterizations of proteins from plant and protein interactions. The successful candidate will be employed for a period of three years, with a gross salary of around 1700 EUR/month. We search for candidates holding a MSc degree in biochemistry. Experience in protein purification, and/or background in protein crystallography will be an advantage. IBS is close to the European large instruments, the ILL http://www.ill.eu/ and the ESRF http://www.esrf.eu/. Please send CV and 2 reference letters to david.cobe...@ibs.fr and jean-luc.fer...@ibs.fr -- David Cobessi Institut de Biologie Structurale 41, Rue Jules Horowitz 38027 Grenoble Cedex-1, France Tel:33(0)438789613 33(0)608164340 Fax:33(0)438785122
Re: [ccp4bb] crystallization of a macromolecular complex
Hi Jan, Have you tried to change the pH? Crystallization at 4°C? David Jan Rash wrote: Dear All, This is about the crystallization of the macromolecular complex which is highly soluble and shows no signs of the aggregation (even at high concentration). We have tried several salts, precipitants and even high protein concentration (around 20g/L) for its crystallization without any genuine hit. Any suggestions for growing the crystals of this macromolecular complex will be highly appreciated. Thanks, Jan
Re: [ccp4bb] Regarding BMCD
Have you tried: http://xpdb.nist.gov:8060/BMCD4/index.faces It works for me. David Nishant Varshney wrote: Dear all, I have bee trying to access the biomolecular crystallization database BMCD for quite sometime now, no matter which route I access it through the page shows an error as the server can not be contacted. I would like to know whether its a problem only I am coming across.Moreover, is there any registration or license required to access BMCD? if there is, I am not aware of it. Your help will be appreciated. Regards Nishant /NISHANT KUMAR VARSHNEY/ /C/O Dr. C.G. Suresh,/ /Biochemical Sciences Division,/ /National Chemical Laboratory,/ /Pune-411008, Maharastra,/ /India./ Share files, take polls, and make new friends - all under one roof. Click here. http://in.rd.yahoo..com/tagline_groups_8/*http://in.promos.yahoo.com/groups/ -- David Cobessi Institut de Biologie Structurale 41, Rue Jules Horowitz 38027 Grenoble Cedex-1, France Tel:33(0)438789613 33(0)608164340 Fax:33(0)438785122
Re: [ccp4bb] Refolding of Denatured Protein
Sanjiv Kumar wrote: I am working on a membrane protein. There was problem with the normal purification of the protein so I have tired to purify it under denaturing conditions (Using 8M Urea). Luckily I could purify the protein in large quantity. But now the problem is that I am not able to refold the protein by step wise removing 8M Urea by dialysis (8M, 6M, 4M, 2M, 1M, 0.5M and 0M urea). It is showing aggregation at very high urea concentration say 2M urea. Kindly suggest any alternate method that I can try for refolding of this protein. It is a prokaryotic protein, cloned in pET28a and expressed in BL21 DE3. Please Help. Sanjiv Kumar Dear Sanjiv, I guess that the protein is well expressed in the membranes if there is only (if I could say) a problem with the purification, and that you are also able to solubilize the membranes and extract the protein with detergents. Have you tried several detergents for the purification? Or several buffers with or without salt? David -- David Cobessi Institut de Biologie Structurale 41, Rue Jules Horowitz 38027 Grenoble Cedex-1, France Tel:33(0)438789613 33(0)608164340 Fax:33(0)438785122
Re: [ccp4bb] Refolding of Denatured Protein
Sanjiv Kumar wrote: I have not tried purifying this protein either with detergent or with /Guanidine Hydrochloride. I can try with both /Guanidine HCl and detergent. Since I got good purification with the 8M urea, I was thinking if this protein could be refolded and used further. Isn't removal of detergent more difficult then Urea? Sanjiv Kumar Lab. No. 411, Functional Genomics Unit, Institute of Genomics and Integrative Biology, New Delhi-110007 India Is it a transmembrane protein or not? or just a protein associated to the membrane (with a GPI anchor for example)? If it is a transmembrane protein, you should try to use detergents for extraction and during the purification. David -- David Cobessi Institut de Biologie Structurale 41, Rue Jules Horowitz 38027 Grenoble Cedex-1, France Tel:33(0)438789613 33(0)608164340 Fax:33(0)438785122
Re: [ccp4bb] Building structure in COOT
Liew Chong Wai wrote: Hi, Good day I am currently building my structure by using COOT. My protein is a tetramer protein and I have fit my protein sequence into one of the monomer of the homologous model. May I know how can I replace other monomer with the amended monomer?? Thanks *Chong-wai* Hi Chong-wai, Several possibilities to generate the tetramer from the monomer, let say A. You can calculate the RT matrices ( in CCP4 or using LSQMAN and MOLEMAN2 or using O for example) to superpose the monomer A onto B, C and D and then apply these matrices to the amended monomer (A) in order to generate the tetramer. You can also superpose the monomer A onto B in COOT by using SSM or LSQ and save the new position as monomer B in COOT etc... and then you can generate 4 monomers and the tetramer. Do not forget to change the chain ID before refinement. Best regards, David -- David Cobessi Institut de Biologie Structurale 41, Rue Jules Horowitz 38027 Grenoble Cedex-1, France Tel:33(0)438789613 33(0)608164340 Fax:33(0)438785122
Re: [ccp4bb] Transfer Rfree flag
riya doreen wrote: Hello: Can someone tell me if there is a relatively straightforward way of transferring Free R flags between two CNS format reflection files ? Thanks Dear Riya, You can do it either by using CNS (merge.inp: keep the flags Rfree(A: dataset A), Fobs(B: dataset B) for example) or CCP4 (CNS---MTZ and use cad). David -- David Cobessi Institut de Biologie Structurale 41, Rue Jules Horowitz 38027 Grenoble Cedex-1, France Tel:33(0)438789613 33(0)608164340 Fax:33(0)438785122
