3KCJ

Room temperature neutron structure of apo-D-Xylose Isomerase (refined jointly with X-ray structure 3KBJ)


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.173 

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Identification of the Elusive Hydronium Ion Exchanging Roles with a Proton in an Enzyme at Lower pH Values

Kovalevsky, A.Y.Hanson, B.L.Mason, S.A.Yoshida, T.Fisher, S.Z.Mustyakimov, M.Forsyth, V.T.Blakeley, M.P.Keen, D.A.Langan, P.

(2011) Angew Chem Int Ed Engl 50: 7520-7523


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Xylose isomerase388Streptomyces rubiginosusMutation(s): 0 
Gene Names: xylA
EC: 5.3.1.5
UniProt
Find proteins for P24300 (Streptomyces rubiginosus)
Explore P24300 
Go to UniProtKB:  P24300
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24300
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.173 
  • Space Group: I 2 2 2
  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.179 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.04α = 90
b = 99.52β = 90
c = 102.47γ = 90
Software Package:
Software NamePurpose
nCNSrefinement
RETREATdata reduction
RETREATdata scaling
nCNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-07-27
    Changes: Data collection
  • Version 1.3: 2011-08-17
    Changes: Database references
  • Version 1.4: 2017-11-01
    Changes: Refinement description
  • Version 1.5: 2024-02-21
    Changes: Data collection, Database references