[ccp4bb] Problem with ligand refinement in REFMAC5

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-06-14

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Subject: Problem with ligand refinement in REFMAC5
From: Andreas Hörnberg andreas {- dot -} hornberg {- at -} UCMP {- dot -} UMU {- dot -} SE
Date: 2007-06-14

Dear all!

I have two questions:

First - I am refining a structure containing a modified residue with a
ligand bound. This ligand is present in two stereoisomers and it seems
like we have both in the structure. When refining the structure with ALIG
and BLIG (each with 0.5 occupancy) defined in the coordinate file, REFMAC5
moves the ligands apart. In the ligand there is an electron rich atom with
a clearly defined position in the electron density map (observed at 9
sigma). Prior to refinement, the electron rich atom from the two
stereoisomers are positioned in the centre of the strong density feature.
After ten cycles of refinement the atoms are separated (by about 1 Å) and
found in two different positions, neither of them coinciding with the
strong density. I don’t understand why the stereoisomers are moved apart.
The REFMAC log file does not give any warnings about close contacts
between the atoms, but still they are moved during refinement and I don’t
know how to avoid this! Any help is much appreciated!

To contribute to the confusion, the second problem is actually quite the
opposite…

I have a non-covalent ligand bound in two alternative, partly overlapping
sites. The sites induce distinct structural changes of the protein. For
example, a Trp is moved to sandwich the ligand in one of the sites whereas
this conformation of the Trp is not consistent with the second binding
site.

I’ve tired to refine this structure using REFMAC5 and naming the Trp
ATRP/BTRP and the corresponding ligand ALIG/BLIG in the coordinate file.
Since the ATRP density map is stronger, the BTRP moves towards this
density, even though this is create clashes between the BTRP and the BLIG.
The program doesn’t seem to link the two sites of the ligand with the
corresponding conformations of the Trp.

Is it possible to link the ALIG to the ATRP conformation of the protein
and ligand?

Sincerely,

Andreas

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: B-factor sharpening in CCP4 or Coot
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-06-14

Next message:
Subject: Re: Eden & SUSE linux libfftw.so.2
From: Adam Ralph aralph {- at -} MATHS {- dot -} NUIM {- dot -} IE
Date: 2007-06-14