Having dealt with quite a few cases of more than one molecule in the
AU (including a couple of dreaded 12-meric assemblies... bleah), I am
still looking for the best way to identify proper NCS operators for
the myriad of potential combinations of fragments.
As has been said, it is generally worthwhile to identify the
equivalent portions of the molecules and appropriate NCS weights, not
only for potentially finding something interesting in terms of
biology, but also for doing the best possible refinement job.
I therefore wish there were better tools for this purpose. Overall, I
think this area has not received proper attention yet. But it should,
because I have the feeling that the impact of a great set of tools
would be immense.
Eternally hopeful - MM
--------------------------------------------------------------------------------
Mischa Machius, PhD
Associate Professor
Department of Biochemistry
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.; ND10.214A
Dallas, TX 75390-8816; U.S.A.
Tel: +1 214 645 6381
Fax: +1 214 645 6353
On Mar 24, 2009, at 1:22 PM, Roger Rowlett wrote:
I had a student solve a medium resolution (2.3 A) data set with
(unfortunately) 12 identical protein chains in the asymmetric unit.
To save a little time, and to take advantage of a large amount of
potential averaging we used NCS to do the initial phase of the
refinement. For 10 of the 12 chains, everything was hunky-dory. For
the 11th and 12th chains, however, there was an extremely messy area
of high-sigma difference map density that turned out to be a very
interesting ligand-binding interaction. Releasing the symmetry
constraints resulted in a very sharp map of the protein chain
rearrangement and bound ligand in the two "different" chains.
In general, even with homodimers and homotetramers in the ASU, we
find that there are often subtle but significant differences in
individual protein chains, especially around packing contacts and
external loops of the protein.
Cheers,
--
Roger S. Rowlett
Professor
Colgate University Presidential Scholar
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346
tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@mail.colgate.edu
Skrzypczak-Jankun, Ewa wrote:
I have seen proteins refined as ‘the same’, modeled to an averaged
map etc only to have one of them with much higher Bj because most
likely they are NOT the same so watch out by treating them as ‘the
same’ you are losing the very valuable information that you might
be looking for
Ewa
********************************************************
Dr Ewa Skrzypczak-Jankun
Associate Professor
University of Toledo Office:
Dowling Hall r.2257
Health Science Campus Phone:
419-383-5414
Urology Department Mail Stop #1091 Fax:
419-383-3785
3000 Arlington Ave. e-mail:
ewa.skrzypczak-jan...@utoledo.edu
Toledo OH 43614-2598 web:
http://golemxiv.dh.meduohio.edu/~ewa
********************************************************
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf
Of Jim Fairman
Sent: Tuesday, March 24, 2009 11:25 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] two identical proteins in one asymmetric unit
Sang Hoon,
Each molecule in the asymmetric unit is most likely different. I
work on a protein that crystallizes as a homodimer with 2 molecules
per asymmetric unit and there are some differences between the two
(eg: electron density visible for the 14 N-terminal residues in one
molecule, but not the other).
Cheers, Jim
On Tue, Mar 24, 2009 at 11:03 AM, Folmer Fredslund
<folm...@gmail.com> wrote:
Dear Sang
They are really different!
And I guess you would probably want to use NCS restraints depending
on
your resolution.
Regards,
Folmer
2009/3/24 Sang Hoon Joo <s...@duke.edu>:
> I am refining my crystal structure in which I have two identical
> chains in one asymmetric unit.
> Space group is H32 and each chain yields me a biological trimer
as expected.
> The problem is, do I have to assume they are identical, or they are
> really different.
> After each cycle of refinement, if I try to align two molecules I
get
> ~ 0.17 RMSD.
> --
> Sang Hoon Joo, PhD
> Postdoctoral Associate
> Duke University
> 239 Nanaline H. Duke
> Box 3711, DUMC
> Durham, NC 27710
>
--
Jim Fairman
Graduate Research Assistant
Department of Biochemistry, Cellular, and Molecular Biology (BCMB)
University of Tennessee -- Knoxville
216-368-3337 jfair...@utk.edu james.fair...@case.edu
