Dear experts, Thank you for your helpful input. I think it's clear now to conclude that the alternative conformations exist on both Phe and Tyr residues.
Counter level = 1 sigma http://i50.tinypic.com/anzfrn.png Counter level = 0.7 sigma - the alternative conformation of Phe can be confirmed. http://i49.tinypic.com/5v57pi.jpg Counter level = 0.3 sigma - the alternative conformation of Tyr can be confirmed. http://i48.tinypic.com/11vh7he.jpg Thank you Dr. Herman for your additional comments. Yes I can confirm that the "in" position cannot be occupied by both residues since we had another structure in which Phe was mutated to Trp. In this structure, the Trp always has " in" conformation and Tyr always has "out" conformation. My best regards, Tri Ngo On Mon, Jul 30, 2012 at 4:45 PM, <[email protected]> wrote: > ** > Hi Bernard, > > When I wrote my comment, I considered the same, since correlated > alternative conformations are in my experience quite common. However, I do > not believe it is the case here. The Phe and Tyr can have two > conformations: an "in" conformation, pointing towards the other, and an > "out" conformation, pointing away from the other. There is no problem for > both side chains occupying the "out" position, but only one of them can > occupy the "in" conformation, since both side chains in this conformation > would clash. This means that the sum of the partial occupancies for the > "in" conformation can not be greater than one, which, as I recall > correctly, is also what is observed with ~0.3 for the "in" conformation and > ~0.7 for the "out" conformation. However, the partial occupancies need > not be the same for the Phe and the Tyr. > > My two cents, > Herman > > PS: I was told that in refmac clashes between parital occupancies are > ignored if their sum is less or equal than 1. > > ------------------------------ > *From:* CCP4 bulletin board [mailto:[email protected]] *On Behalf Of > *Bernhard > Rupp > *Sent:* Friday, July 27, 2012 5:02 PM > > *To:* [email protected] > *Subject:* Re: [ccp4bb] Alternative conformation of Phe and Tyr? > > Hmmm…I have a question for the experts: It seems to me from the figure > (although that is for Tri Ngo to verify), that**** > > these partial occupancies are correlated. When conformation A of TYR (in > the green density) is occupied,**** > > Phe B in the blue density probably cannot be occupied because of a VdW > clash. (Again, caveat that I can’t see that exactly from the static image) > **** > > I recall that Shelxl allows to constrain such occupancies, but how are > Refmac and Phenix dealing with that? How would I implement that? Are > clashes between partial occs just ignored?**** > > ** ** > > Even if I am wrong about the existence of a clash in this particular case, > such situations are not uncommon imho.**** > > ** ** > > Thx, BR**** > > *From:* CCP4 bulletin board [mailto:[email protected]] *On Behalf Of > *Pavel > Afonine > *Sent:* Friday, July 27, 2012 7:17 AM > *To:* [email protected] > *Subject:* Re: [ccp4bb] Alternative conformation of Phe and Tyr?**** > > ** ** > > Hi,**** > > ** ** > > you can't expect to see something with occupancy ~0.3 at the same cutoff > level as you use to see fully occupied sites. So most likely the solution > is to use a lower cutoff levels, as many suggested already. Two maps you > attached look totally expectable to me.**** > > ** ** > > Pavel**** > > On Fri, Jul 27, 2012 at 1:01 AM, Tri Ngo <[email protected]> wrote:**** > > Dear ccp4bb,**** > > ** ** > > I am working on refinement of an enzyme structure. I notice an alternative > conformation (gauche+ and gauche-) on both residues Phe and Tyr.**** > > ** ** > > Here is the image of electron density before refinement. Based on the > different map intensity, I am quite sure there is an alternative > conformation on both positions.**** > > ** ** > > http://i50.tinypic.com/29zaoap.jpg**** > > ** ** > > However, after running occupancy refinement by Phenix, I don't see the > density map at the gauche- conformation of Tyr residue. Please take a look > at the image 2.**** > > ** ** > > http://i50.tinypic.com/anzfrn.png**** > > ** ** > > So do you think the gauche- conformation of Tyr exists in this structure. > Should I keep it in the final model because there is no positive map there? > **** > > ** ** > > ** ** > > Thank you very much for your input.**** > > ** ** > > -- ** > > *Ngo Duc Tri***** > > * * > > PhD Student > Structural Biology Lab**** > > School of Medicine - Sungkyunkwan University - Korea**** > > Phone: 031-299-6150 - Cell: 010-7774-8210 **** > > ** ** > > ** ** > > -- * Ngo Duc Tri * PhD Student Structural Biology Lab School of Medicine - Sungkyunkwan University - Korea Phone: 031-299-6150 - Cell: 010-7774-8210
