[phenixbb] molecular replacement of protein/DNA complex

Wei Shi wei.shi118 at gmail.com
Fri Jan 6 08:53:51 PST 2012

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!

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