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: [email protected]
