1BHW | pdb_00001bhw

LOW TEMPERATURE MIDDLE RESOLUTION STRUCTURE OF XYLOSE ISOMERASE FROM MASC DATA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.10 Å
  • R-Value Free: 
    0.321 (Depositor) 
  • R-Value Work: 
    0.315 (Depositor) 
  • R-Value Observed: 
    0.315 (Depositor) 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history

Literature

Multiwavelength anomalous solvent contrast (MASC): derivation of envelope structure-factor amplitudes and comparison with model values.

Ramin, M.Shepard, W.Fourme, R.Kahn, R.

(1999) Acta Crystallogr D Biol Crystallogr 55: 157-167

  • DOI: https://doi.org/10.1107/S090744499800626X
  • Primary Citation Related Structures: 
    1BHW, 1BHY, 1BHZ

  • PubMed Abstract: 

    A previous article [Fourme et al. (1995). J. Synchrotron Rad. 2, 36-48] presented the theoretical foundations of MASC, a new contrast-variation method using multiwavelength anomalous scattering, and reported the first experimental results. New experiments have been conducted both at the ESRF (Grenoble, France) and at LURE-DCI (Orsay, France), using cryocooled crystals of three proteins of known structures and very different molecular weights. Amplitudes of {GammaT(h)}, the 'normal' structure factors of the anomalously scattering part of the crystal including the solvent zone and the ordered anomalous scattering sites (if any), have been extracted from multiwavelength data. In the very low resolution range (d >/= 20 A), the agreement between experimental {GammaT(h)} and model values calculated from the bulk solvent is all the more satisfactory since the molecular weight of the protein is high. For spacings between 10 and 20 A, the agreement between experimental {GammaT(h)} and model values is also satisfactory if one takes into account ordered anomalous scatterer sites. Such sites have been found in the three cases.


  • Organizational Affiliation
    • LURE (CNRS, CEA, MENRT), Université Paris-Sud, 91405 Orsay CEDEX, France.ramin@lure.u-psud.fr

Macromolecule Content 

  • Total Structure Weight: 173.59 kDa 
  • Atom Count: 12,248 
  • Modeled Residue Count: 1,568 
  • Deposited Residue Count: 1,572 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
XYLOSE ISOMERASE
A, B, C, D
393Actinoplanes missouriensisMutation(s): 0 
EC: 5.3.1.5
UniProt
Find proteins for P12851 (Actinoplanes missouriensis (strain ATCC 14538 / DSM 43046 / CBS 188.64 / JCM 3121 / NBRC 102363 / NCIMB 12654 / NRRL B-3342 / UNCC 431))
Explore P12851 
Go to UniProtKB:  P12851
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12851
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.10 Å
  • R-Value Free:  0.321 (Depositor) 
  • R-Value Work:  0.315 (Depositor) 
  • R-Value Observed: 0.315 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.91α = 90
b = 141.91β = 90
c = 227.48γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
CCP4data scaling
SCALAdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-11-04
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-02
    Changes: Database references, Other, Refinement description
  • Version 1.4: 2024-05-22
    Changes: Data collection