Hi Evgeny Thanks a lot for responding. It's a nice idea but sadly it doesn't work. For sure it makes the acetyl group planar at what was the A0-A1 link (now a single AME residue), but the amide group at the A1-A2 link is now pyramidal! Presumably now planar link restraints for this link are missing!
Also Buster now doesn't recognise the A1-A2 (AME-ASN) link. It would be nice to be able to use the same input PDB file for both programs. Ho hum! Cheers -- Ian On 14 February 2014 08:35, Evgeny Osipov <e.m.osi...@gmail.com> wrote: > Hello Ian and ccp4 community, > I think you must use modified residue, N-acetylmethionine with code AME, > instead of LINKR. > May be someone find this mildly useful: > there is a file called mon_lib_list.cif, located in > $CCP4/lib/data/monomers/list/ > If you are not sure about particular residue modification or three-letter > code for insertion in COOT-check this file > > P.S.: I hope you are still able to understand my runglish > 14.02.2014 02:57, Ian Tickle пишет: > > >> 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 >> > > > -- > Eugene Osipov > Junior Research Scientist > Laboratory of Enzyme Engineering > A.N. Bach Institute of Biochemistry > Russian Academy of Sciences > Leninsky pr. 33, 119071 Moscow, Russia > e-mail: e.m.osi...@gmail.com > >
