4QE5

Room temperature X-ray structure of D-xylose isomerase in complex with two Mg2+ ions and L-ribulose

• PDB DOI: https://doi.org/10.2210/pdb4QE5/pdb

• Classification: ISOMERASE
• Organism(s): Streptomyces rubiginosus
• Mutation(s): No 


• Deposited: 2014-05-15 Released: 2014-09-03 
• Deposition Author(s): Kovalevsky, A.Y., Langan, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.188 
• R-Value Work: 0.158 
• R-Value Observed: 0.148 

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.48 kDa 
• Atom Count: 3,391 
• Modelled Residue Count: 388 
• Deposited Residue Count: 388 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xylose isomerase	A	388	Streptomyces rubiginosus	Mutation(s): 0  EC: 5.3.1.5
UniProt
Find proteins for P24300 (Streptomyces rubiginosus) Explore P24300  Go to UniProtKB:  P24300

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RUU	D [auth A]	alpha-L-ribulofuranose C5 H10 O5 LQXVFWRQNMEDEE-VAYJURFESA-N
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.188 
• R-Value Work: 0.158 
• R-Value Observed: 0.148 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.928	α = 90
b = 99.687	β = 90
c = 103.03	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHASER	phasing
SHELXL-97	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-03 
Deposition Author(s): Kovalevsky, A.Y., Langan, P.

Revision History  

• Version 1.0: 2014-09-03
  Type: Initial release
  
• Version 1.1: 2014-09-10
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Structure summary