4DUO

Room-temperature X-ray structure of D-Xylose Isomerase in complex with 2Mg2+ ions and xylitol at pH 7.7

Structural Biology Knowledgebase: 4DUO SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.200
  • R-Value Work: 0.141

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DUO

Classification: isomerase / isomerase inhibitor

Total Structure Weight: 43484.49

Macromolecule Entities
Molecule Chains Length Organism Details
Xylose isomerase A 388 Streptomyces rubiginosus EC#: 5.3.1.5 IUBMB
Gene Name(s): xylA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
XYL
Query on XYL

A D-XYLITOL
C5 H12 O5
HEBKCHPVOIAQTA-SCDXWVJYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.200
  • R-Value Work: 0.141
  • Space Group: I 2 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 93.79 α = 90.00
b = 99.62 β = 90.00
c = 102.83 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-02-22
  • Released Date: 2012-08-29
  • Deposition author(s): Kovalevsky, A.Y., Hanson, L., Langan, P.

Revision History

  • 2012-10-03
    Type: Citation | Details: Citation update