1S5M

Xylose Isomerase in Substrate and Inhibitor Michaelis States: Atomic Resolution Studies of a Metal-Mediated Hydride Shift

• PDB DOI: https://doi.org/10.2210/pdb1S5M/pdb

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


• Deposited: 2004-01-21 Released: 2004-02-10 
• Deposition Author(s): Fenn, T.D., Ringe, D., Petsko, G.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.98 Å
• R-Value Free: 0.129 
• R-Value Work: 0.111 

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,PQS (software)

Macromolecule Content

• Total Structure Weight: 43.19 kDa 
• Atom Count: 3,690 
• Modelled 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  Gene Names: XYLA 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
GLC	B [auth A]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
MN	C [auth A], D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
NA	E [auth A], F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.98 Å
• R-Value Free: 0.129 
• R-Value Work: 0.111 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.865	α = 90
b = 92.968	β = 90
c = 98.298	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: 2004-02-10 
Deposition Author(s): Fenn, T.D., Ringe, D., Petsko, G.A.

Revision History  

• Version 1.0: 2004-02-10
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Derived calculations, Version format compliance
• Version 1.3: 2018-01-31
  Changes: Experimental preparation
• Version 1.4: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.5: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.6: 2023-08-23
  Changes: Data collection, Database references, Refinement description, Structure summary