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: [log in to unmask]
>
> 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:
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> Toledo OH 43614-2598 web:
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>
> ********************************************************
>
>
>
>
> ____________________________________________________________________________________________________________
>
>
> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Jim Fairman
> Sent: Tuesday, March 24, 2009 11:25 AM
> To: [log in to unmask]
> 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 <[log in to unmask]> 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 <[log in to unmask]>:
> > 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 [log in to unmask] [log in to unmask]
>
>
>
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