[ccp4bb]: RE: cis peptide

["Fukami, Takaaki {NRRC~Tokyo}" <TAKAAKI.FUKAMI@Roche.COM>]

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Hi Guan,

I encountered the same situation.
In my case, a cis-Lys was located between prolines.

It was required that an initial structure (coordinates to be refined) 
should have a cis conformation, although the top/par files were correct.
When I fed coordinates to CNX in which the peptide was in a trans
conformation,
the conformation didn't changed to cis although there were obvious peaks 
in its FoFc map.


If you defined a new residue for your cis-His, I guess you're using
a non-standard residue name for it.  If you're using TOPPAR/protein.link, 
you should add your residue name in a list in the .link file.


If you're using TOPPAR/protein.top and TOPPAR/protein_rep.param files,
the easist way I think is to modify the protein_rep.param as below.
(add last 4 lines)  You don't need define a special residue for cis-pept.

{ very tight/rigid dihedrals }
dihe X    C    NH1  X     $kdih_rigid   1     0.0 ! omega torsion angle and
ARG...
dihe CH1E C    N    CH1E  $kdih_rigid   2   180.0 ! allow cis PRO
dihe CH2E C    N    CH1E  $kdih_rigid   2   180.0
dihe CH2G C    N    CH1E  $kdih_rigid   2   180.0

dihe CH1E C    NH1  CH1E  $kdih_rigid   2   180.0 ! allow cis Pept
dihe CH2G C    NH1  CH1E  $kdih_rigid   2   180.0 !
dihe CH1E C    NH1  CH2G  $kdih_rigid   2   180.0 ! cis GLY
dihe CH2G C    NH1  CH2G  $kdih_rigid   2   180.0 !



Hope it helps.


Takaaki Fukami
Protein Crystallography / Structural Chemistry Group
Nippon Roche Research Center, Kamakura
T: +81-467-45-3484
F: +81-467-45-6824
Mail: Takaaki.Fukami@Roche.com


> -----Original Message-----
> From: GUAN [mailto:grj@pewdc.ibp.ac.cn]
> Sent: Friday, April 06, 2001 6:49 PM
> To: ccp4bb@dl.ac.uk
> Subject: 
> 
> 
> ***  For details on how to be removed from this list visit the  ***
> ***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***
> 
> Dear all:
> when I refine my structure, I can definitely see a cis peptide
> bond between proline and histidine. (it is very obvious from the 
> 2fo-fc.map at R=17.1% and Rf=19.1%). This is a non-proline cis
> peptide because it is formed by CO of proline and NH of histidine.
> 
> I am using CNS to refine the structure, and I changed the name of
> proline and defined the bond and dihedral parameters in the toppar
> files for this peptide bond, but it seems not successful in the map.
> It has not put the N atom to the density it should be.
>  
> Does anyone have experiences on the refinement of non-proline cis
> peptide bond, or know how to deal with it? And where can I find the
> bond and dihedral parameters for non-proline cis peptide bond?
> 
> Thanks in advance.
> Rong-Jin guan
>