[ccp4bb] Postdoctoral position at the European Institute of Oncology, Milano

2013-01-07 Thread Marina Mapelli
Postdoctoral research position in Structural Biology of Asymmetric Cell Division A postdoctoral research position is available in the group of Marina Mapelli at the European Institute of Oncology in Milano (http://www.ifom-ieo-campus.it/research/mapelli.php). The main interest of the group

Re: [ccp4bb] Who invented PDB format?

2013-01-07 Thread Frank von Delft
Thanks all for the quick replies! Thanks too for the gazillion contributions to the long long thread - helping me win my bet that people simply wouldn't be able to resist... :) On 07/01/2013 06:51, Felix Frolow wrote: ###

[ccp4bb] About NCS and inhibitors

2013-01-07 Thread Xiaopeng Hu
Dear All, We recently resolved an enzyme/inhibitor complex structure. The enzyme contains two NCS related active site and we did find extra density in both of them.However we observed that the two inhbitor moleculors are not NCS related, but partly overlaped if make a NCS moleculor. Has anyone

Re: [ccp4bb] About NCS and inhibitors

2013-01-07 Thread Felix Frolow
Why not? They can be mutually excluding! If one is in, the second can be. This phenomenon brakes a local symmetry. FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta

Re: [ccp4bb] About NCS and inhibitors

2013-01-07 Thread Felix Frolow
I apologise for typing blinbly: if one is in, the second can't be FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail:

Re: [ccp4bb] About NCS and inhibitors

2013-01-07 Thread Joel Sussman
Dear All, Something like what Felix wrote is seen in the crystal structure of recombinant human acetylcholinesterase (rhAChE) (PDB-ID: 3lii), with two molecules are seen in the asymmetric unit. * In one molecule, the active-site gorge (where inhibitors normally lie) is occupied with part of a

Re: [ccp4bb] Ammonium phosphate as cryoprotectant

2013-01-07 Thread Enrico Stura
Joy, Try 80% saturated Lithium sulfate (2.5M) instead. Just transfer the crystals and if it does not work let me have more precise crystallization conditions and I will post you other options. Enrico. On Thu, 03 Jan 2013 18:33:05 +0100, Joy joybeiy...@gmail.com wrote: Dear All, May I

Re: [ccp4bb] About NCS and inhibitors

2013-01-07 Thread Edward A. Berry
But I think the original poster meant partially overlapped after applying the ncs- operator- i.e. they are not ncs related but occupy partly the same position (in the two non-overlapping copies of the binding site). Then I guess it depends how clear the density is- If the density is not very

Re: [ccp4bb] About NCS and inhibitors

2013-01-07 Thread Nat Echols
On Mon, Jan 7, 2013 at 1:28 AM, Xiaopeng Hu huxp...@mail.sysu.edu.cn wrote: We recently resolved an enzyme/inhibitor complex structure. The enzyme contains two NCS related active site and we did find extra density in both of them.However we observed that the two inhbitor moleculors are not

Re: [ccp4bb] About NCS and inhibitors

2013-01-07 Thread Boaz Shaanan
Just a naive question: why apply NCS to ligands at all? Their contribution to the number of parameters and hence to the param/obs ratio, the main argument for applying NCS, is negligible, isn't it? Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva

Re: [ccp4bb] Ammonium phosphate as cryoprotectant

2013-01-07 Thread Joy
Dear Bryan, Thank you very much for the comments, I have tried glycerol and it did affect the resolution, at the same time, through reading former posts, I find that sucrose might not be a good choice for crystals grown in salt, I will definitely try adding glycerol stepwise, but at the

Re: [ccp4bb] Ammonium phosphate as cryoprotectant

2013-01-07 Thread Joy
Dear Enrico, Thank you very much for the comments, will definitely try it later. Best, Joy -Original Message- From: Enrico Stura [mailto:est...@cea.fr] Sent: 2013年1月7日 10:16 To: CCP4BB@jiscmail.ac.uk; Joy Subject: Re: [ccp4bb] Ammonium phosphate as cryoprotectant Joy, Try 80%

Re: [ccp4bb] Ammonium phosphate as cryoprotectant

2013-01-07 Thread Enrico Stura
On Mon, 07 Jan 2013 18:30:32 +0100, Joy joybeiy...@gmail.com wrote: Dear Bryan, Thank you very much for the comments, I have tried glycerol and it did affect the resolution, at the same time, through reading former posts, I find that sucrose might not be a good choice for crystals grown

Re: [ccp4bb] About NCS and inhibitors

2013-01-07 Thread Edward A. Berry
The idea is (whether it's valid or not) to apply the information from both sites simultaneously. If the density is pretty ambiguous and one side tends to drift off into an alternate conformation and the other drifts off into another conformation, but you have every reason to believe that the

Re: [ccp4bb] About NCS and inhibitors

2013-01-07 Thread Ethan Merritt
On Monday, January 07, 2013 12:10:17 pm Edward A. Berry wrote: The idea is (whether it's valid or not) to apply the information from both sites simultaneously. If the density is pretty ambiguous and one side tends to drift off into an alternate conformation and the other drifts off into

Re: [ccp4bb] About NCS and inhibitors

2013-01-07 Thread Nick Huang
Yes, it is very common. I solved two of them at 2-3 A resolution and saw my colleague had one with 1.4 A resolution (can't remember the name of the protein). Please see references J Med Chem. 2010 Jul 22;53(14):5229-39. doi: 10.1021/jm100377f. Complexes of bacterial nicotinate mononucleotide