1MUW | pdb_00001muw

The 0.86 Angstrom Structure of Xylose Isomerase

• PDB DOI: https://doi.org/10.2210/pdb1MUW/pdb

• Classification: ISOMERASE
• Organism(s): Streptomyces olivochromogenes
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-09-24 Released: 2002-11-06 
• Deposition Author(s): Fenn, T.D., Ringe, D., Petsko, G.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.86 Å
• R-Value Free: 
  0.143 (Depositor), 0.109 (DCC) 
• R-Value Work: 
  0.124 (Depositor), 0.103 (DCC) 
• R-Value Observed: 
  0.126 (Depositor) 

Starting Model: experimental

Literature

Active Site Dynamics at 0.86A: Crystallographic Analysis of a Metal-Mediated Hydride Shift

Fenn, T.D., Ringe, D., Petsko, G.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 43.03 kDa 
• Atom Count: 3,910 
• Modeled Residue Count: 386 
• Deposited Residue Count: 386 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
XYLOSE ISOMERASE	A	386	Streptomyces olivochromogenes	Mutation(s): 0  EC: 5.3.1.5
UniProt
Find proteins for P15587 (Streptomyces olivochromogenes) Explore P15587  Go to UniProtKB:  P15587

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	B [auth A], C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG	D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
OH	F [auth A]	HYDROXIDE ION H O XLYOFNOQVPJJNP-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.86 Å
• R-Value Free:  0.143 (Depositor), 0.109 (DCC) 
• R-Value Work:  0.124 (Depositor), 0.103 (DCC) 
• R-Value Observed: 0.126 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.906	α = 90
b = 92.883	β = 90
c = 98.321	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-11-06 
Deposition Author(s): Fenn, T.D., Ringe, D., Petsko, G.A.

Revision History  

• Version 1.0: 2002-11-06
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Refinement description