[phenixbb] protein-ligand complex structure
pafonine at lbl.gov
Fri Oct 25 13:17:30 PDT 2013
it's difficult to tell what's happening without looking at files. First,
I would compute ligand OMIT map. Then fit ligand into it and refined
ligands coordinates and ADPs. If you see negative density around ligand
after refinement among other reasons this may indicate that the ligand
or parts of it have multiple conformations in which case you need to
model them as such or at least refine group occupancy of the one copy.
If ligand crosses a special position then it becomes a different story.
If you send me files (data, model, cifs if any) and indicate which
ligands are in question I will have a look. Please send files to my
email directly, not the entire mailing list.
On 10/25/13 9:28 AM, Wei Shi wrote:
> Also, as suggested by Dr Terwilliger, I deleted the ligands and refine
> only the protein structure. When I go over the protein structure, I
> could see some region didn't fit the density well, so I am thinking of
> mutating those regions to alanines and do a refinement in phenix
> (default settings + NCS restraints + Secondary structural restraints +
> Optimize X-ray/stereochemistry weight +Optimize X-ray/ADP weight), and
> see whether I could see better density. Any suggestions or ideas about
> how to improve the protein structural model? Thank you so much!
> On Fri, Oct 25, 2013 at 12:15 PM, Wei Shi <wei.shi118 at gmail.com
> <mailto:wei.shi118 at gmail.com>> wrote:
> Thank you guys for the suggestions!
> For Dr Bosch's question, every monomer binds two ligands, and the
> first binding site is different from the second binding site. The
> ligand is placed differently for the two binding sites for each
> monomer, but for the symmetrical sites in the dimer protein, the
> ligand is placed in the same conformation, even though the density
> of the ligand in the second monomer is not good enough to place the
> Thank you so much!
> On Thu, Oct 24, 2013 at 10:31 PM, Bosch, Juergen <jubosch at jhsph.edu
> <mailto:jubosch at jhsph.edu>> wrote:
> Hi Wei,
> have you considered modeling two conformations of your ligand in
> the four sites ?
> On Oct 24, 2013, at 10:19 PM, Wei Shi wrote:
>> Hi all,
>> I am working on a structure of protein-ligand complex. Four
>> ligands are placed for the dimer protein and the density for
>> the two ligands of the first monomer is better than the
>> density for the other two ligands of the second monomer.
>> Ligand is moved to fit density better in Coot (and for two
>> ligands of the first monomer, they fits the density almost
>> perfectly), but after a refinement in phenix (default settings
>> + NCS restraints + Secondary structural restraints + Optimize
>> X-ray/stereochemistry weight +Optimize X-ray/ADP weight), some
>> part of the ligand which fits density good before moved out of
>> the density again...Besides, it always shows green density in
>> Coot for the ligand region even in places where the ligand is
>> in density...
>> Any suggestions or ideas about how to fit the ligand better
>> and why the density for ligands of the second monomer is worse
>> than that for the first monomer and why the ligands would move
>> out of density after refinement?
>> Is it because the protein model is not good enough to get the
>> ligand density good? There is a conformational change upon
>> ligand binding, and I rebuilt some part of the protein
>> manually, and the density for a region of about 30 residues is
>> not very good, and I tried to mutate those to alanies and
>> refine, but it didn't help me see the density better...
>> Any suggestions or ideas on how to improve this
>> protein-complex structural model? Thank you so much!
>> The statistics for the current best model is as follows, and
>> the resolution of the dataset is 2.8Å.
>> start final
>> R-work: 0.3359 0.2993
>> R-free: 0.3619 0.3558
>> RMS(angles): 1.03 1.55
>> RMS(bonds): 0.006 0.007
>> MolProbity validation
>> Ramachandran outliers: 4.7% (Goal: < 0.2%)
>> Ramachandran favored: 85.3% (Goal: > 98%)
>> Rotamer outliers: 4.5% (Goal: 1%)
>> C-beta outliers: 0 (Goal: 0)
>> Clashscore: 7.43
>> Overall score: 2.56
>> Thank you so much!
>> phenixbb mailing list
>> phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
> Jürgen Bosch
> Johns Hopkins University
> Bloomberg School of Public Health
> Department of Biochemistry & Molecular Biology
> Johns Hopkins Malaria Research Institute
> 615 North Wolfe Street, W8708
> Baltimore, MD 21205
> Office: +1-410-614-4742 <tel:%2B1-410-614-4742>
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