3QZA

Joint neutron and X-ray structure of apo-D-Xylose Isomerase at pH=5.9


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.254 

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.254 

wwPDB Validation 3D Report Full Report


This is version 1.4 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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Xylose isomeraseA388Streptomyces rubiginosusMutation(s): 0 
Gene Names: xylA
EC: 5.3.1.5
Find proteins for P24300 (Streptomyces rubiginosus)
Explore P24300 
Go to UniProtKB:  P24300
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D8U
Query on D8U

Download CCD File 
A
deuterium(1+)
D
GPRLSGONYQIRFK-DYCDLGHISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.254 
  • Space Group: I 2 2 2
  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.254 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.908α = 90
b = 99.503β = 90
c = 102.971γ = 90
Software Package:
Software NamePurpose
nCNSrefinement
d*TREKdata scaling
d*TREKdata reduction
LAUENORMdata reduction
LAUENORMdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-17
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Refinement description
  • Version 1.2: 2018-04-25
    Changes: Data collection
  • Version 1.3: 2018-06-06
    Changes: Data collection, Experimental preparation, Refinement description
  • Version 1.4: 2019-03-13
    Changes: Data collection