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 conformation is the same on both sides, applying NCS allows you to
refine a single conformation that is consistent with both.
More generally, is there any reason to not? I suppose ligands
may be more likely than amino acids to violate NCS, but good
practices would say examine each residue for violations.
You could say, why enforce NCS on the 27'th residue of each chain, since
their contribution to the number of parameters is small.
(mind you,there may be good reasons to not constrain ligands
that I m not aware of, if so I hope someone speak up)
eab
Boaz Shaanan wrote:
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 84105
Israel
E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710
________________________________________
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Edward A. Berry
[ber...@upstate.edu]
Sent: Monday, January 07, 2013 6:12 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] About NCS and inhibitors
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
clear and if the protein residues of the active site do follow ncs, I would try
rebuilding ligand b to match a and (separately) a to match b and refining
with ncs applied to the ligand; and see if the resulting fit looks just as good.
eab
Joel Sussman wrote:
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 peptide loop from a
symmetrically related rhAChE.
* While the corresponding region of the other copy of rhAChE is void of this
peptide.
See figs 15-16 in:
Dvir, H., Silman, I., Harel, M., Rosenberry, T. L.& Sussman, J. L. (2010).
"Acetylcholinesterase: From 3D structure to
function" /Chemico-Biological Interactions/ *187*, 10-22.
* So, in essence, no reason to ever assume that two copies in asymmetric unit
will be identical, or have identical
inhibitors bound, or 'surrogate inhibitors' (like in this case) bound.
Sometimes differences are due to difference in
crystal packing
Best regards,
Joel
On 7 Jan 2013, at 11:58, Felix Frolow wrote:
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: mbfro...@post.tau.ac.il<mailto:mbfro...@post.tau.ac.il>
Tel: ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608
On Jan 7, 2013, at 11:48 , Felix
Frolow<mbfro...@post.tau.ac.il<mailto:mbfro...@post.tau.ac.il>> wrote:
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 Crystallographica F, co-editor
e-mail: mbfro...@post.tau.ac.il<mailto:mbfro...@post.tau.ac.il>
Tel: ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608
On Jan 7, 2013, at 11:28 , Xiaopeng
Hu<huxp...@mail.sysu.edu.cn<mailto:huxp...@mail.sysu.edu.cn>> wrote:
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 else observed this before?
Thanks for any help and suggestion!
Best,
Xiaopeng Hu
