Re: [ccp4bb] Mg or water?
I doubt that you can tell the difference between Mg and water just from the height of the density, but Mg2+ is always octahedrally coordinated with Mg-O bond lengths ~2.0A At 2.9A resolution you may not be able to distinguish Phil On 14 Dec 2011, at 22:45, bie gao wrote: Hi every, I'm working with 2 crystal forms of a protein from 2 different crystallization conditions. Condition 1 has 100mM MgCl2. Condition 2 doesn't. Both are ~2.9 angstrom. The 2 structures are virtually identical except in condition1, there is a clear positive density surrounded by a Glu side chain carboxyl and a couple of main carboxyl groups. (Again, condition 2 doesn't have this density). My initial thought is that a Mg atom is incorporated and it fits well. But the problem is we can not role out the possibility of a water molecule. Refining with Mg gives a b-factor of 42 (about average for the whole protein). The b-factor is 21 when refining with a water. Both cases there is no positive/negative density at contour=2.0. Based on the current data, is there any other role we can apply to see how likely it is a Mg or water. Or anomalous scattering is the only way? Thanks for your suggestions. Best, Gao
Re: [ccp4bb] Hydrophobic interactions
Dear amit sir you can go through this server .. http://pic.mbu.iisc.ernet.in http://pic.mbu.iisc.ernet.in/index.html . PIC server can calculate many interactions within and between the protein molecules. ..PIC: Protein Interactions Calculator K. G. Tina, R. Bhadra, and N. Srinivasan,NAR 2007 best regards On Thu, Dec 15, 2011 at 2:04 AM, Luthra,Amit alut...@uchc.edu wrote: Hi Everyone I have to calculate hydrophobic interactions in pdb files. Is any server available for this type of calculation? ** ** Thanks in advance ** ** Amit -- Vandana kukshal
Re: [ccp4bb] Hydrophobic interactions
LIGPLOT will show this graphically, if the correct parameters are set in ligplot.prm, but not state the interactions explicitly: http://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/ The relevant lines in ligplot.prm: PLOT PARAMETERS --- Y- Include: Hydrophobic interactions - (Y/N)? HTH, Iain On Wednesday,Dec 14 12:34 PM, Luthra,Amit wrote: Hi Everyone I have to calculate hydrophobic interactions in pdb files. Is any server available for this type of calculation? Thanks in advance Amit
Re: [ccp4bb] Mg or water?
At 2A I think you will see the difference between the 2A bond Mg-GLU and the likely 2.8A HOH-GLU. Look at your difference map - put a peak there and check distances to surrounding atoms. Marjorie Hardings metal protein server gives a guide to other putative Mg binding. Eleanor On 12/15/2011 08:10 AM, Phil Evans wrote: I doubt that you can tell the difference between Mg and water just from the height of the density, but Mg2+ is always octahedrally coordinated with Mg-O bond lengths ~2.0A At 2.9A resolution you may not be able to distinguish Phil On 14 Dec 2011, at 22:45, bie gao wrote: Hi every, I'm working with 2 crystal forms of a protein from 2 different crystallization conditions. Condition 1 has 100mM MgCl2. Condition 2 doesn't. Both are ~2.9 angstrom. The 2 structures are virtually identical except in condition1, there is a clear positive density surrounded by a Glu side chain carboxyl and a couple of main carboxyl groups. (Again, condition 2 doesn't have this density). My initial thought is that a Mg atom is incorporated and it fits well. But the problem is we can not role out the possibility of a water molecule. Refining with Mg gives a b-factor of 42 (about average for the whole protein). The b-factor is 21 when refining with a water. Both cases there is no positive/negative density at contour=2.0. Based on the current data, is there any other role we can apply to see how likely it is a Mg or water. Or anomalous scattering is the only way? Thanks for your suggestions. Best, Gao
[ccp4bb] Post-Doctoral Position in Singapore: Chromatin Structure-Activity and Anticancer Drug Development
Post-Doctoral Position in Singapore: Chromatin Structure-Activity and Anticancer Drug Development We are seeking a highly motivated scientist keen on engaging in exciting projects at the cutting edge of structural biology and medicinal biochemistry (http://www.sbs.ntu.edu.sg/AboutSBS/Faculty/Davey/Pages/Home.aspx). The fellow would be involved in projects entailing crystallographic and functional studies of nucleosome-transcription factor assemblies and the design and characterization of chromatin-targeting anticancer agents. This provides a special opportunity for a unique and stimulating research experience over a multitude of disciplines. The position is available from April 1, 2012 and the preferred candidate would have Ph.D. training in X-ray crystallography and protein (and/or nucleic acid) overexpression and purification. The starting salary would be commensurate with the candidate’s qualifications and experience. To apply, please send your CV and a short statement of research interests by e-mail to da...@ntu.edu.sgmailto:da...@ntu.edu.sg . Dr. Curt Alexander Davey Division of Structural Biology Biochemistry School of Biological Sciences Nanyang Technological University (NTU) 60 Nanyang Drive, SBS-04s-44 Singapore 637551 da...@ntu.edu.sgmailto:da...@ntu.edu.sg Web: http://www.sbs.ntu.edu.sg/AboutSBS/Faculty/Davey/Pages/Home.aspx Tel: (65) 6592 1549 Fax: (65) 6791 3856 CONFIDENTIALITY: This email is intended solely for the person(s) named and may be confidential and/or privileged. If you are not the intended recipient, please delete it, notify us and do not copy, use, or disclose its content. Towards A Sustainable Earth: Print Only When Necessary. Thank you.
Re: [ccp4bb] Pore Dimension Convention
On 14/12/11 23:14, Jacob Keller wrote: is there a convention for denoting/measuring pore sizes in protein structures? Maybe inter-atom distances minus van der Waals radii? AFAIK, the standard method is HOLE (Smart, Goodfellow, Wallace, 1993 (for example)). The method has been implemented in Coot using energy-lib.cif from the Refmac dictionary for the atom-type radii and is available (in 0.7-pre) by using the `hole' function. http://lmb.bioch.ox.ac.uk/coot/doc/coot/hole.html#hole (it's not on the caver page, which is why I mention it here). Paul.
Re: [ccp4bb] Pore Dimension Convention
Replying to my own post :-( ... I forgot to mention that I wrote a GUI for it: http://lmb.bioch.ox.ac.uk/coot/extras/test-hole.scm Screeny here: http://lmb.bioch.ox.ac.uk/coot/screenshots/Screenshot-Coot-hole.png
[ccp4bb] Dec 16, 2011 deadline- User proposal submission for Collaborative Crystallography at BCSB
Dear Users, The deadline for Feb/April 2012 Collaborative Crystallography proposals will be *Dec 16, 2011. * Through the Collaborative Crystallography Program (CC) at the Advanced Light Source (ALS), scientists can send protein crystals to Berkeley Center for Structural Biology (BCSB) staff researchers for data collection and analysis. The CC Program can provide a number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; and * Reduced travel costs. To apply, please submit a proposal through the ALS General User proposal review process for beamtime allocation. Proposals are reviewed and ranked by the Proposal Study Panel, and beamtime is allocated accordingly. BCSB staff schedule the CC projects on Beamlines 5.0.1 and 5.0.2 to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography - How To Apply: To learn more, go to: http://www.als.lbl.gov/als/quickguide/becomealsuser.html To submit a proposal, go to: http://alsusweb.lbl.gov/. Scroll down to *Structural Biology beamlines (includes protein SAXS)* and click on New Proposal. Enter your proposal information, with attention to the following details: * For question 3/First choice, select 5.0.1 (Monochromatic); for question 3/Second choice, select 5.0.2 (MAD). * Check box (yes) in response to question (7) Do you want collaborative crystallography (beamline 5.0.1 or 5.0.2 only) * In question 4, please describe a specific research project with a clear end point. In order to request CC time for Feb/April 2012 allocation period, proposals must be submitted by *Dec 16, 2011.* The deadline for CC proposals for the time period May/June 2012 will be Mar 15, 2012. Regards, Banumathi Sankaran
Re: [ccp4bb] Mg or water?
Thank you all for the help. These are the key factors I collected so far: 1. Distance, Mg--O is shorter (2.0 -- 2.4A) 2. Coordination, Mg is octahedrally coordinated. 3. B factors, local B factors (i.e. the residues that coordinate with the ion) should be similar. 4. Use Mn++ to replace Mg. I will look into these more. Best, Gao On Wed, Dec 14, 2011 at 5:45 PM, bie gao gao...@gmail.com wrote: Hi every, I'm working with 2 crystal forms of a protein from 2 different crystallization conditions. Condition 1 has 100mM MgCl2. Condition 2 doesn't. Both are ~2.9 angstrom. The 2 structures are virtually identical except in condition1, there is a clear positive density surrounded by a Glu side chain carboxyl and a couple of main carboxyl groups. (Again, condition 2 doesn't have this density). My initial thought is that a Mg atom is incorporated and it fits well. But the problem is we can not role out the possibility of a water molecule. Refining with Mg gives a b-factor of 42 (about average for the whole protein). The b-factor is 21 when refining with a water. Both cases there is no positive/negative density at contour=2.0. Based on the current data, is there any other role we can apply to see how likely it is a Mg or water. Or anomalous scattering is the only way? Thanks for your suggestions. Best, Gao
