3QZA

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


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.254 

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.195 

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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Xylose isomerase
A
388Streptomyces rubiginosusMutation(s): 0 
Gene Names: xylA
EC: 5.3.1.5
Find proteins for P24300 (Streptomyces rubiginosus)
Go to UniProtKB:  P24300
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D8U
Query on D8U

Download SDF File 
Download CCD File 
A
deuterium(1+)
D
GPRLSGONYQIRFK-DYCDLGHISA-N
 Ligand Interaction
DOD
Query on DOD

Download SDF File 
Download CCD File 
A
DEUTERATED WATER
D2 O
XLYOFNOQVPJJNP-ZSJDYOACSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.254 
  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.195 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 93.908α = 90.00
b = 99.503β = 90.00
c = 102.971γ = 90.00
Software Package:
Software NamePurpose
LAUENORMdata scaling
d*TREKdata scaling
nCNSrefinement
LAUENORMdata reduction
d*TREKdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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