Hello Roger,
did you publish your results? Your case sounds very educational and might
be interesting for teaching purposes, so a reference would be a nice thing
to have.
Tim
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
On Tue, 24 Mar 2009, 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
