Hi Ian dod you try without link and standard ACE atom naming. Refmac should be able to deal N-terminal activation and few other things. At least it was the intention when it was written. Bugs may have been (self)introduced to prevent this from happening. If it is so then I would like to know.
Regards Garib On 13 Feb 2014, at 22:57, Ian Tickle <[email protected]> wrote: > > All, I'm having problems refining a structure with an N-terminal acetylated > MET residue. I'm trying it with both Refmac & Buster. Buster works fine & > gives perfect planar geometry for the ACE-MET linkage. Refmac gives a > pyramidal acetyl group after refinement which to my eyes is wrong (sp2 C > atom?). > > I have this line in my input PDB: > > LINKR C ACE A 0 N MET A 1 > ACE_C-N > > which as I understand it should solve the problem. However, looking at the > CIF entry for the ACE_C-N link I see restraints defined for bonds, angles & > torsion angles but not for the CC(=O)N plane. So the problem seems to be > that the planar restraints for this link group are missing - or are they > defined elsewhere? Anyway I added planar restraints to the ACE_C-N link > entry & it solves the problem, at least for regularisation - I still have the > same problem with refinement. Refmac in regularisation mode now gives the > correct (planar) geometry for the ACE-MET linkage. I'm just puzzled why > no-one has noticed this, after all post-translational acetylation is surely > not that uncommon (according to Wikipedia > 80% of human proteins are N-term > acetylated!). > > Further, looking at the entry for ACE I see: > > ACE ACE 'ACETYL GROUP ' non-polymer 7 3 > . > > ACE O O O 0.000 0.000 0.000 0.000 > ACE C C C1 0.000 -1.044 -0.606 0.000 > ACE H H H 0.000 -1.978 -0.069 0.000 > ACE CH3 C CH3 0.000 -1.041 -2.113 0.000 > ACE H3 H H 0.000 -0.541 -2.464 0.865 > ACE H2 H H 0.000 -2.038 -2.468 0.000 > ACE H1 H H 0.000 -0.540 -2.464 -0.864 > > Where did the extra H atom (3rd atom) come from? Acetyl is CH3C=O: the extra > H atom would make it acetaldehyde which of course has nothing whatsoever to > do with acetylation! Is this the reason for the lack of planar link > restraints (though that wouldn't explain why the other link restraints are > present)? > > Any insights appreciated! > > Cheers > > -- Ian Dr Garib N Murshudov MRC-LMB Francis Crick Avenue Cambridge CB2 0QH UK Web http://www.mrc-lmb.cam.ac.uk, http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/
