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
