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Title: Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences

Paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and diamagnetic residual dipolar couplings can now be used in the program REFMAC5 from CCP4 as structural restraints together with X-ray crystallographic data. These NMR restraints can reveal differences between solid state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. The program REFMAC5 from CCP4 was modified to allow the simultaneous use of X-ray crystallographic data and paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and/or diamagnetic residual dipolar couplings. Incorporation of these long-range NMR restraints in REFMAC5 can reveal differences between solid-state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. Since NMR and X-ray data are complementary, when a single structure is consistent with both sets of data and still maintains reasonably ‘ideal’ geometries, the reliability of the derived atomic model is expected to increase. The program was tested on five different proteins: the catalytic domain of matrix metalloproteinase 1, GB3, ubiquitin, free calmodulin and calmodulin complexed with a peptide. In some cases the joint refinement produced a single model consistent with bothmore » sets of observations, while in other cases it indicated, outside the experimental uncertainty, the presence of different protein conformations in solution and in the solid state.« less
Authors:
; ; ;  [1] ;  [2] ;  [3] ;  [1] ;  [2]
  1. University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (Finland) (Italy)
  2. (Finland) (Italy)
  3. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH (United Kingdom)
Publication Date:
OSTI Identifier:
22347708
Resource Type:
Journal Article
Resource Relation:
Journal Name: Acta Crystallographica. Section D: Biological Crystallography; Journal Volume: 70; Journal Issue: Pt 4; Other Information: PMCID: PMC4306559; PMID: 24699641; PUBLISHER-ID: dz5299; OAI: oai:pubmedcentral.nih.gov:4306559; Copyright (c) Rinaldelli et al. 2014; This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
Denmark
Language:
English
Subject:
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; ATOMS; COUPLING; COUPLINGS; CRYSTALS; GEOMETRY; MATHEMATICAL SOLUTIONS; METALS; MOLECULES; NUCLEAR MAGNETIC RESONANCE; ORIENTATION; RELIABILITY; SOLIDS; SOLUTIONS; X RADIATION