[buster-discuss] Dimethylysine restraints

[Oliver Smart]

On Mon, 2 Jul 2012, Axelrod, Herbert L. wrote:

> Hi, I am trying to refine a protein in which the lysine residues have 
> been reductively methylated. In the input coordinate file, I have 
> re-named the LYS residues to MLY. To setup restraints for MLY residues, 
> I have implemented PDB2TNT to output a restraints dictionary for MLY 
> using the idealized coordinates found in Ligand Expo. When I try to 
> input this dictionary using the -l option of BUSTER, I get the following 
> error message in ab_pdb2tnt
>
>
> ############################# 1. initial checks ##############################
>
>
> ####################### 2. creating TNT sequence file ########################
>
>
> ########################### 3. processing residues ###########################
>
>
> ###################### 4. processing missing restraints ######################
>
>
> ####################### 5. remove duplicate restraints #######################
>
>
> ERROR : [pdb2tnt-0023] something wrong when excluding
>         "GEOMETRY [ ]*MLY [ ]*BOND[A-Z]*.* [ ]*N [ ]*CA"
>         restraint from ./01-BUSTER/Cycle-1/my.geom
>
>
> Obviously there is something amiss in my refinement strategy, and was 
> wondering if anyone could suggest the proper strategy to setup 
> restraints and implement BUSTER refinement for proteins containing 
> methylated lysine residues.
>
> Many Thanks,
>
> Herb Axelrod
> Staff Scientist
> Stanford Synchrotron Radiation Lightsource
>
> _______________________________________________


Herb,

Sorry you hit this problem. The simple answer to your question is that
BUSTER already has restraints for MLY residues. So using pdb entry 4egl
as a test (as it contains a MLY residue

refine -p 4egl/4egl.pdb -m 4egl/4egl.mtz \
        -d 4egl_test_01_nodic >  4egl_test_01_nodic.log

runs with the latest 11072011 release of BUSTER and produces quite 
reasonable results.

But the distributed restraints for MLY are based on old methods
(PDB2TNT). Our new method "grade" generally produces better results,
producing restraints based on CSD structures and applying restraints on 
torsions. The easiest way to use grade is to go to

http://grade.globalphasing.org

(Herb - noticed from the logs you have done this!). Doing this for MLY 
produces the attached results, that can be unpacked with

tar xvf MLY.gradeserver_all.tgz

to use the MLY restraints with BUSTER it is necessary to get BUSTER to 
forget its existing MLY restraints that are in the library "exoticaa.dat".
This can be done by

refine -p 4egl/4egl.pdb -m 4egl/4egl.mtz \
    -d 4egl_test_03_grade_MLY_noexoticaa \
   StandardDictionaries="protgeo_eh99 nuclgeo bcorrel contact idealdist_contact" \
   StandardDictionariesAll="protgeo_eh99 nuclgeo sugar cofactor_geo othergeo bcorrel contact idealdist_contact assume connect" \
   -l MLY/MLY.grade_PDB_ligand.cif > 4egl_test_03_grade_MLY_noexoticaa.log

this also works (please make sure that you have the latest BUSTER 
release).

Regards,

Oliver

| Dr Oliver Smart                             |
| Global Phasing Ltd., Cambridge UK           |
| http://www.globalphasing.com/people/osmart/ |
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