molecular replacement of protein/DNA complex

From: Wei Shi
Date: 6 January 2012 16:57

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