On Tuesday, 18 July 2017 00:01:59 CDaddy wrote:
> I am a structural biologist who is teaching X-ray crystallography. Recently I
> noticed that BrlR structure (5XQL) was solved using molecular replacement
> with a search model of very low similarity. I am very interested in this
> structure because I think this a very good example to show students how to
> solve phase problem using molecular replacement, especially when the model
> and the target protein share a low sequence identity. However, when I
> downloaded the data from PDB, I found that I cannot solve the phase problem
> using Phaser as mentioned by the authors. During this procedure BmrR
> (PDB:1R8E) was used as the search model. I tried to consult the authors for
> help but receive no response by now. Since the description of this issue in
> the literature is very brief, could anyone please spend a little time on this
> molecular replacement and give me some advices on this issue? I like to learn
> some valuable tricks. Your assistance will be highly appreciated.
I have no familiarity with either structure, but even a cursory glance at the
cartoon depiction of 5XQL in the PDB suggests that you would want to chop
it into at least 3 pieces in order to use it for molecular replacement.
Did you try placing the N- and C- terminal domains separately after
chopping out the long connecting helix?
Ethan
--
Ethan A Merritt, Dept of Biochemistry
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
