Peptide bond to symmetry related molecule
Hi All, We are refining several structures in which the N-terminal residue of chain A appears to form a peptide bond to the C-terminal residue of its symmetry mate, chain A. In reality, the target protein consists of 4 identical helical repeats that pack end to end. Slippage and averaging over the 4 possible registers leads to the appearance of an infinitely long polymer in the crystal, with no breaks between protomers. Is it possible to enforce a peptide bond to symmetry mates in Phenix, and what is the easiest way to do this? I have found a several cases in the archives on how to deal with symmetry clashes, but struggling to figure out how to deal with a peptide bond. Thanks for your help! Best, Damian - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Damian Ekiert Assistant Professor Skirball Institute | NYU School of Medicine Depts. Cell Biology and Microbiology damian.ekiert@ekiertlab.org www.bhabhaekiertlab.org
Damian
Peptide bonds are usually automatic, however, because only bond restraints
are permitted across symmetry mates it can sometimes be "interesting". Have
you try refining and checking the .geo file for the bond restraints?
Please feel free to send the model file directly to me for testing purposes.
Cheers
Nigel
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Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : NWMoriarty@LBL.gov
Fax : 510-486-5909 Web : CCI.LBL.gov
ORCID : orcid.org/0000-0001-8857-9464
On Mon, Aug 23, 2021 at 7:19 AM Damian Ekiert
Hi Nigel, I hadn’t checked, but had a look now and I am only finding records that start with “nonbonded” (examples pasted below for the two connections that I would like to make). If you don’t mind having a look, I will send you some files on the side. Thanks! nonbonded pdb=" N LEU B 1 " pdb=" C PRO B 12 " model vdw sym.op. 3.003 3.350 -x-1,-x+y,-z-1/3 nonbonded pdb=" N ASP A 44 " pdb=" C VAL A 215 " model vdw sym.op. 1.560 3.350 -x-1,-x+y-1,-z-1/3 Best, Damian - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Damian Ekiert Assistant Professor Skirball Institute | NYU School of Medicine Depts. Cell Biology and Microbiology damian.ekiert@ekiertlab.org www.bhabhaekiertlab.org
Thanks Nigel and Pavel for your help with this. In case it is helpful to someone else down the road, the summary is: Generic bonds can be specified to a symmetry mate by editing the geometry_restraints.edits section of your .eff file. This will create a bond length restraint between any two atoms of interest, but restraining the angles, torsions, etc. is not currently possible. An example of how to specify such a bond is below: refinement.geometry_restraints.edits { n_44_selection = chain A and resname ASP and resid 44 and name N c_215_selection = chain A and resname VAL and resid 215 and name C bond { action = *add atom_selection_1 = $n_44_selection atom_selection_2 = $c_215_selection symmetry_operation = -x-1,-x+y-1,-z-1/3 distance_ideal = 1.335 sigma = 0.02 slack = None } } Best, Damian - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Damian Ekiert Assistant Professor Skirball Institute | NYU School of Medicine Depts. Cell Biology and Microbiology damian.ekiert@ekiertlab.org www.bhabhaekiertlab.org
participants (3)
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Damian Ekiert -
Nigel Moriarty -
Pavel Afonine