[phenixbb] molecular replacement of protein/DNA complex

[Wei Shi]

Thank you so much, Randy! I am now trying to fix one protein with the DNA
and search for a second copy of the protein.

Best,
Wei

On Fri, Jan 6, 2012 at 12:27 PM, Randy Read <rjr27 at cam.ac.uk> wrote:

> Hi,
>
> You could try deleting parts of the model from the solution (e.g. one copy
> of the protein, or the DNA component) and see whether the likelihood score
> increases (that part is therefore wrong in the model) or decreases (that
> part was probably right).  It may be that, say, the DNA and one copy of the
> protein are correct.  In that case, you could fix that partial solution and
> search for a second copy of the protein.
>
> In searching for a second copy of the protein, the rotate around option
> might be very useful.  It sounds like you know the correct orientation
> within about 30 degrees or so, so you could allow the orientation to vary
> by that much.
>
> Alternatively, you might be able to push the MR with separate pieces of
> protein and DNA, in particular by lowering the threshold for orientations
> you accept for the subsequent translation search.
>
> Good luck!
>
> Randy Read
>
> On 6 Jan 2012, at 16:53, Wei Shi wrote:
>
> Hi all,
>
> I have been trying to solve a protein-DNA complex structure using
> molecular replacement. I suspect two copies of protein bind one piece of
> the DNA, and the angle between the two copies of protein is somewhere
> between 130 to 180 degrees. I could get molecular replacement solution
> using a search model of protein/DNA complex I made with deletion in part of
> the protein and with the angle between the two proteins about 145 degrees.
> Only 1 copy of this two-protein/one-DNA complex is expected in the ASU.
> Below is the statistics for the solution.
>
> RFZ=2.9 TFZ=6.9 PAK=0 LLG=111 TFZ==14.6 LLG=111
>
> And when I open the pdb file and generate symmetry mates, no clashes and I
> could see contacts between the end of DNA, but space instead of contacts
> between layers of the protein/DNA complex. I suspect that the angle between
> the two proteins I use in the search model is not quite right. No solution
> if I search with DNA and protein separately. I am trying to find a way to
> move the protein a little bit around the original solution and see whether
> that can help me make the solution better. I just read that “ROTate AROUnd
> option of the brute rotation serch” and “NMAPdb” might do this?  Does
> anyone have any suggestions about what I could try? Thank you so much!
>
> Best,
> Wei
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>
> ------
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research      Tel: + 44 1223 336500
> Wellcome Trust/MRC Building                   Fax: + 44 1223 336827
> Hills Road                                    E-mail: rjr27 at cam.ac.uk
> Cambridge CB2 0XY, U.K.                       www-structmed.cimr.cam.ac.uk
>
>
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