Re: [ccp4bb] Problem with Coot reading monomer library file.
Dear Eric, Thank you very much for your suggestion. It worked. Dear Paul, Thank you for your kind offer with the help (and for writing such a wonderful program + providing users with support!). I will compare the cif files and see if I can pick out the differences... Sincerely, Peter Hi Peter, Did you try making a cif using the Dundee Prodrg server? http://davapc1.bioch.dundee.ac.uk/prodrg/ Eric -- Eric Ortlund, Ph.D.Assistant ProfessorDepartment of BiochemistryEmory University School of Medicine1510 Clifton Road, NE, Room G235Atlanta, GA 30322Tel 404-727-5014 Fax 404-727-2738eric.ortl...@emory.edu Date: Sat, 29 Aug 2009 07:02:12 +0100 From: paul.ems...@bioch.ox.ac.uk To: pc...@hotmail.com Subject: Re: [ccp4bb] Problem with Coot reading monomer library file. Peter Chan wrote: Dear Crystallographers, I've been spending 10 hours trying (googling, manually editting cif files based on templates in Coot's library, asking around, rtfm and reading this bbs) to figure out why Coot the geometric restraints wouldn't load. I can think of no reason why 0.1 would work and 0.6 would not. If you want me to investigate, please send the PDB and cif dictionary. Regards, Paul. _ Stay in the loop and chat with friends, right from your inbox! http://go.microsoft.com/?linkid=9671354
[ccp4bb] Refmac Problem - Permission Denied
I would appreciate if any one has any ideas on this I have a strange NFS related problem, if anyone has any ideas... I am running refmac with the ccp4 directories mounted on an nfs share (v4) mounted under /usr/local I get the following error... #CCP4I TERMINATION STATUS 0 Last system error message: Permission denied Refmac_5.5.0072: Open failed: File: /usr/local/ccp4-6.1.1/ lib/data/monomers/mon_lib_ind.cif However, to test this I have changed the permissions to 777 and uid and gid to the user's account. The user can see the file, and can even edit the file on the remote server. and yet it still fails. If I run refmac from the users account on the nfs server directly, then it runs with no problem. This is running under CentOS 5.3, fully patched etc, with SE linux turned off David N. M. Jones, Ph.D. Associate Professor Dept. of Pharmacology Univ. of Colorado Denver 12801 East 17th Ave MS 8303, PO Box 6511 Aurora, CO 80045 e-mail david.jo...@ucdenver.edu Tel. (303) 724-3600 Cell(303) 916-7246
Re: [ccp4bb] Refmac Problem - Permission Denied
Does it work with NFS v.3? Cheers. --Original Message-- From: David Jones Sender: CCP4 bulletin board To: CCP4BB@JISCMAIL.AC.UK ReplyTo: David Jones Subject: [ccp4bb] Refmac Problem - Permission Denied Sent: Aug 29, 2009 3:32 PM I would appreciate if any one has any ideas on this I have a strange NFS related problem, if anyone has any ideas... I am running refmac with the ccp4 directories mounted on an nfs share (v4) mounted under /usr/local I get the following error... #CCP4I TERMINATION STATUS 0 Last system error message: Permission denied Refmac_5.5.0072: Open failed: File: /usr/local/ccp4-6.1.1/ lib/data/monomers/mon_lib_ind.cif However, to test this I have changed the permissions to 777 and uid and gid to the user's account. The user can see the file, and can even edit the file on the remote server. and yet it still fails. If I run refmac from the users account on the nfs server directly, then it runs with no problem. This is running under CentOS 5.3, fully patched etc, with SE linux turned off David N. M. Jones, Ph.D. Associate Professor Dept. of Pharmacology Univ. of Colorado Denver 12801 East 17th Ave MS 8303, PO Box 6511 Aurora, CO 80045 e-mail david.jo...@ucdenver.edu Tel. (303) 724-3600 Cell(303) 916-7246 Roger Rowlett Professor Dept. of Chemistry Colgate University
Re: [ccp4bb] Active aggregates?
Dear James, Could you provide the reference of your success story? My protein also formed large soluble aggregates and I am desperate for such successful stories! By the way, have your performed DLS to your protein? What about the polydispensity? Is it lower than 20%? Thanks in advance! Sincerely, Xuan Yang 2009/8/27 James Stroud xtald...@gmail.com Just try crystallizing it. What is a crystal but a massive aggregate? That they are still soluble and active is great news. As a grad student, I had a similar phenomenon with an early project. I showed a gel in group meeting where both activity and aggregation were obvious, said the aggregate was no problem, got ridiculed when I said I was going to throw it in trays despite what anyone said, had giant crystals after a few trays, and solved the structure with miras. Get the structure and then worry about why it's aggregating. The structure will probably provide you with the clues you need. On Aug 26, 2009, at 5:55 PM, ose toyoyuki wrote: Dear all, This is a question on how to cope with the protein that seems to form massive aggregates in solution but enzymatically active. I'm working on a protein whose molecular weight is around 70kDa and can be divided into two domains (say A and B domains). We expressed this protein in E.coli fused with GST and purified using some chromatography. The GST affinity chromatography works well and proteinase digestion to remove the tag does wonders too. The purified protein was confirmed to be active enough, we can detect both activities from these two domains. But the retention time from the gel filtration clearly shows it is awfully aggregated (comes out at the void region). DLS measurement indicates the averaged diameter is around 45 nm, which I feel is a bit too long. Analytical ultracentrifuge result implies that the distribution of the molecular species is wide, some portion got precipitated with 1K rcf (means the molecular weight is more than 5MDa) and the rest is ranging from 1MD to 5MDa with a peak at 1MDa. I made new two constructs covering the A and B domains respectively, both of them are active again, but only the A domain has got the same symptom as the intact protein. The B domain seems to exist as a monomer in solution. Here come my questions, (I) How can I interpret this phenomenon? (II) Is there anything we can try to change the situation? (III) Does it make sense to try crystallization? (probably not).(IV) Has anyone got such experience? I tried the methylation on lysine side chains, I also tried the buffer with 0.2M arginine or 10% glycerol but the all the results just seem hopeless. The protein before the proteinase treatment also comes out at the void region from the gel filtration. cheers toyoyuki --? Toyoyuki Ose o...@sci.hokudai.ac.jp Graduate School of Life Science Hokkaido University N21W11 Kita-ku, Sapporo 001-0021 Japan
Re: [ccp4bb] Active aggregates?
Dear Ose, I think we have met similar problems. My protein is relatively small, ~17kD, but it could form aggregates larger than 100nm. A classic Protein Science paper in 2003 by DR Smith titled Crystal structures of fusion proteins with large-affinity tags offered me great help. With MBP tag and optimized linker my protein became significantly less aggregated (~10nm). However, this is still far from a guarantee for success since it is still quite difficult to obtain crystals, although Jovine's group reported a recent success about ZP-N. By the way, can you observe a monomer peak during ultracentrifuge? In terms of DLS, how about the polydispensity? HPV E6 also aggregates to similar size, but the granules were relatively homogeneous. More importantly, it was observed that in cell the protein could still form such large aggregates. Maybe for some proteins, they were just meant to be like this. And based on my very limited knowledge, most structures of such proteins remained as the higher-hanging fruit. Last but not the least, J Jancarik, et al. designed a elegant protocol (2004，Acta Cryst. D60. 1670-1673.) to find the optimized buffer that could increase the solubiltiy and homogeneity, whichmight be helpful too. Good luck! Xuan Yang 2009/8/27 ose toyoyuki o...@castor.sci.hokudai.ac.jp Dear all, This is a question on how to cope with the protein that seems to form massive aggregates in solution but enzymatically active. I'm working on a protein whose molecular weight is around 70kDa and can be divided into two domains (say A and B domains). We expressed this protein in E.coli fused with GST and purified using some chromatography. The GST affinity chromatography works well and proteinase digestion to remove the tag does wonders too. The purified protein was confirmed to be active enough, we can detect both activities from these two domains. But the retention time from the gel filtration clearly shows it is awfully aggregated (comes out at the void region). DLS measurement indicates the averaged diameter is around 45 nm, which I feel is a bit too long. Analytical ultracentrifuge result implies that the distribution of the molecular species is wide, some portion got precipitated with 1K rcf (means the molecular weight is more than 5MDa) and the rest is ranging from 1MD to 5MDa with a peak at 1MDa. I made new two constructs covering the A and B domains respectively, both of them are active again, but only the A domain has got the same symptom as the intact protein. The B domain seems to exist as a monomer in solution. Here come my questions, (I) How can I interpret this phenomenon? (II) Is there anything we can try to change the situation? (III) Does it make sense to try crystallization? (probably not).(IV) Has anyone got such experience? I tried the methylation on lysine side chains, I also tried the buffer with 0.2M arginine or 10% glycerol but the all the results just seem hopeless. The protein before the proteinase treatment also comes out at the void region from the gel filtration. cheers toyoyuki --? Toyoyuki Ose o...@sci.hokudai.ac.jp Graduate School of Life Science Hokkaido University N21W11 Kita-ku, Sapporo 001-0021 Japan
Re: [ccp4bb] Active aggregates?
Hi Toyoyuki, If your protein bind to metal ions you could try low concentration of chelating agents in the purification and storage buffer. Take a look at the following reference: Chelating Agents Stabilize the Monomeric State of the Zinc Binding Human Papillomavirus 16 E6 Oncoprotein Degenkolbe et al., Biochemistry, 2003, 42 (13), pp 3868–3873 Few years back, based on the above mentioned paper, keeping low amount of EGTA (note: NOT eDta) and DTT helped me to stabilize a Zinc binding RING domain as dimer instead of soluble aggregate. Of course, every protein is different but above reference might help you. If you lucky enough to identify a chelating agent that prevent aggregation of your protein, you might also try to include that chemical in the expression media. Good luck and all the best, -Partha Partha Sampathkumar NYSGXRC, Lilly Biotechnology Center San Diego CA 92121 PS: At that time I purified this particular RING domain over NiNTA column. Since both EGTA and DTT are not good for the NiNTA resin I kept required higher concentration of both waiting for the protein in the 1.7ml eppendroff tubes that were used to collection elution fractions. On Sat, Aug 29, 2009 at 7:52 PM, Xuan Yang pattisy...@gmail.com wrote: Dear James, Could you provide the reference of your success story? My protein also formed large soluble aggregates and I am desperate for such successful stories! By the way, have your performed DLS to your protein? What about the polydispensity? Is it lower than 20%? Thanks in advance! Sincerely, Xuan Yang 2009/8/27 James Stroud xtald...@gmail.com Just try crystallizing it. What is a crystal but a massive aggregate? That they are still soluble and active is great news. As a grad student, I had a similar phenomenon with an early project. I showed a gel in group meeting where both activity and aggregation were obvious, said the aggregate was no problem, got ridiculed when I said I was going to throw it in trays despite what anyone said, had giant crystals after a few trays, and solved the structure with miras. Get the structure and then worry about why it's aggregating. The structure will probably provide you with the clues you need. On Aug 26, 2009, at 5:55 PM, ose toyoyuki wrote: Dear all, This is a question on how to cope with the protein that seems to form massive aggregates in solution but enzymatically active. I'm working on a protein whose molecular weight is around 70kDa and can be divided into two domains (say A and B domains). We expressed this protein in E.coli fused with GST and purified using some chromatography. The GST affinity chromatography works well and proteinase digestion to remove the tag does wonders too. The purified protein was confirmed to be active enough, we can detect both activities from these two domains. But the retention time from the gel filtration clearly shows it is awfully aggregated (comes out at the void region). DLS measurement indicates the averaged diameter is around 45 nm, which I feel is a bit too long. Analytical ultracentrifuge result implies that the distribution of the molecular species is wide, some portion got precipitated with 1K rcf (means the molecular weight is more than 5MDa) and the rest is ranging from 1MD to 5MDa with a peak at 1MDa. I made new two constructs covering the A and B domains respectively, both of them are active again, but only the A domain has got the same symptom as the intact protein. The B domain seems to exist as a monomer in solution. Here come my questions, (I) How can I interpret this phenomenon? (II) Is there anything we can try to change the situation? (III) Does it make sense to try crystallization? (probably not).(IV) Has anyone got such experience? I tried the methylation on lysine side chains, I also tried the buffer with 0.2M arginine or 10% glycerol but the all the results just seem hopeless. The protein before the proteinase treatment also comes out at the void region from the gel filtration. cheers toyoyuki --? Toyoyuki Ose o...@sci.hokudai.ac.jp Graduate School of Life Science Hokkaido University N21W11 Kita-ku, Sapporo 001-0021 Japan
