Literature DB >> 7520085

Simultaneous refinement of the structure of BPTI against NMR data measured in solution and X-ray diffraction data measured in single crystals.

C A Schiffer1, R Huber, K Wüthrich, W F van Gunsteren.   

Abstract

The structure of the bovine pancreatic trypsin inhibitor (BPTI) has been determined to high resolution by both NMR spectroscopy in solution and X-ray diffraction in crystals. The root-mean-square difference calculated between the two structures for the polypeptide backbone is 0.9 A. Several amino acid side-chains, of which all but one are charged or polar, have different conformations. We find that by refining one structure simultaneously against both the NMR and crystallographic data sets, it can accommodate both. Different starting configurations were used, including the X-ray structure 5pti, an NMR conformer, and the X-ray structure in the full unit cell with extra solvent placed in the bulk solvent region. The X-ray structures quickly converged to accommodate the NMR data in addition to the crystallographic data. Starting from an NMR conformer, however, the convergence to accommodate the more abundant X-ray data in addition to the NMR data is much slower.

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Year:  1994        PMID: 7520085     DOI: 10.1006/jmbi.1994.1533

Source DB:  PubMed          Journal:  J Mol Biol        ISSN: 0022-2836            Impact factor:   5.469


  9 in total

1.  Joint refinement as a tool for thorough comparison between NMR and X-ray data and structures of HU protein.

Authors:  M L Raves; J F Doreleijer; H Vis; C E Vorgias; K S Wilson; R Kaptei
Journal:  J Biomol NMR       Date:  2001-11       Impact factor: 2.835

2.  Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR.

Authors:  R Bryn Fenwick; Henry van den Bedem; James S Fraser; Peter E Wright
Journal:  Proc Natl Acad Sci U S A       Date:  2014-01-13       Impact factor: 11.205

Review 3.  Integrative, dynamic structural biology at atomic resolution--it's about time.

Authors:  Henry van den Bedem; James S Fraser
Journal:  Nat Methods       Date:  2015-04       Impact factor: 28.547

4.  On the use of time-averaging restraints when deriving biomolecular structure from ³J -coupling values obtained from NMR experiments.

Authors:  Lorna J Smith; Wilfred F van Gunsteren; Niels Hansen
Journal:  J Biomol NMR       Date:  2016-09-15       Impact factor: 2.835

5.  Cluster analysis of consensus water sites in thrombin and trypsin shows conservation between serine proteases and contributions to ligand specificity.

Authors:  P C Sanschagrin; L A Kuhn
Journal:  Protein Sci       Date:  1998-10       Impact factor: 6.725

6.  Synergy of NMR, computation, and X-ray crystallography for structural biology.

Authors:  Blair R Szymczyna; Rebecca E Taurog; Mark J Young; Jamie C Snyder; John E Johnson; James R Williamson
Journal:  Structure       Date:  2009-04-15       Impact factor: 5.006

7.  A general method for the unbiased improvement of solution NMR structures by the use of related X-ray data, the AUREMOL-ISIC algorithm.

Authors:  Konrad Brunner; Wolfram Gronwald; Jochen M Trenner; Klaus-Peter Neidig; Hans Robert Kalbitzer
Journal:  BMC Struct Biol       Date:  2006-06-26

8.  On the Use of Side-Chain NMR Relaxation Data to Derive Structural and Dynamical Information on Proteins: A Case Study Using Hen Lysozyme.

Authors:  Lorna J Smith; Wilfred F van Gunsteren; Niels Hansen
Journal:  Chembiochem       Date:  2020-12-14       Impact factor: 3.164

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

Authors:  Mauro Rinaldelli; Enrico Ravera; Vito Calderone; Giacomo Parigi; Garib N Murshudov; Claudio Luchinat
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2014-03-19
  9 in total

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