1XID

MODES OF BINDING SUBSTRATES AND THEIR ANALOGUES TO THE ENZYME D-XYLOSE ISOMERASE

• PDB DOI: https://doi.org/10.2210/pdb1XID/pdb

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


• Deposited: 1994-03-07 Released: 1994-06-22 
• Deposition Author(s): Carrell, H.L., Glusker, J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Observed: 0.157 

Literature

Modes of binding substrates and their analogues to the enzyme D-xylose isomerase.

Carrell, H.L., Hoier, H., Glusker, J.P.

(1994) Acta Crystallogr D Biol Crystallogr 50: 113-123

• PubMed: 15299449 
• DOI: https://doi.org/10.1107/S0907444993009345


• PubMed Abstract: 
  

  Studies of binding of substrates and inhibitors of the enzyme D-xylose isomerase show, from X-ray diffraction data at 1.6-1.9 A resolution, that there are a variety of binding modes. These vary in the manner in which the substrate or its analogue extend, on binding, across the carboxy end of the (betaalpha)(8)-barrel structure. These binding sites are His54 and the metal ion (magnesium or manganese) that is held in place by Glul81, Asp245, Glu217 and Asp287. Possible catalytic groups have been identified in proposed mechanisms and their role in the binding of ligands is illustrated.

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Organizational Affiliation: 

The Institute for Cancer Research, The Fox Chase Cancer Center, Philadelphia, PA 19111, USA.

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: 43.54 kDa 
• Atom Count: 3,359 
• Modelled Residue Count: 387 
• Deposited Residue Count: 388 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-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
ASC	D [auth A]	ASCORBIC ACID C6 H8 O6 CIWBSHSKHKDKBQ-JLAZNSOCSA-N
MN	B [auth A], C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Observed: 0.157 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.8	α = 90
b = 99.74	β = 90
c = 103	γ = 90

Software Package:

Software Name	Purpose
PROLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-06-22 
Deposition Author(s): Carrell, H.L., Glusker, J.P.

Revision History  

• Version 1.0: 1994-06-22
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other
• Version 2.1: 2024-02-14
  Changes: Data collection, Database references, Structure summary