3GNX | pdb_00003gnx

Structure of dehydrated D-xylose isomerase from streptomyces rubiginosus

• PDB DOI: https://doi.org/10.2210/pdb3GNX/pdb

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


• Deposited: 2009-03-18 Released: 2010-03-23 
• Deposition Author(s): Gramiccia, F., Schiltz, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Dehydration-induced structural phase transition in crystals of D-xylose isomerase from streptomyces rubiginosus

Gramiccia, F., Besnard, C., Schiltz, M.

To be published.

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: 86.77 kDa 
• Atom Count: 6,516 
• Modeled Residue Count: 770 
• Deposited Residue Count: 774 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xylose isomerase	A, B [auth E]	387	Streptomyces pseudogriseolus	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
XYL	C [auth A], F [auth E]	Xylitol C5 H12 O5 HEBKCHPVOIAQTA-SCDXWVJYSA-N
MN	D [auth A], E [auth A], G [auth E], H [auth E]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.853	α = 90
b = 87.65	β = 90
c = 94.531	γ = 90

Software Package:

Software Name	Purpose
STOE	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-23 
Deposition Author(s): Gramiccia, F., Schiltz, M.

Revision History  

• Version 1.0: 2010-03-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Derived calculations, Structure summary
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary