[phenixbb] molecular replacement of protein/DNA complex

Randy Read rjr27 at cam.ac.uk
Fri Jan 6 09:27:19 PST 2012


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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