1XRU | pdb_00001xru

Crystal Structure of 5-keto-4-deoxyuronate Isomerase from Eschericia coli

• PDB DOI: https://doi.org/10.2210/pdb1XRU/pdb

• Classification: ISOMERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-10-15 Released: 2005-04-05 
• Deposition Author(s): Crowther, R.L., Georgiadis, M.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.191 (Depositor), 0.161 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Literature

The crystal structure of 5-keto-4-deoxyuronate isomerase from Escherichia coli

Crowther, R.L., Georgiadis, M.M.

(2005) Proteins 61: 680-684

• PubMed: 16152643 
• DOI: https://doi.org/10.1002/prot.20598
• Primary Citation Related Structures: 
  1XRU

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Organizational Affiliation: 
• The Waksman Institute, Rutgers University, Piscataway, New Jersey, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 64.36 kDa 
• Atom Count: 4,890 
• Modeled Residue Count: 562 
• Deposited Residue Count: 564 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase	A, B	282	Escherichia coli	Mutation(s): 11  Gene Names: kduI EC: 5.3.1.17
UniProt
Find proteins for Q46938 (Escherichia coli (strain K12)) Explore Q46938  Go to UniProtKB:  Q46938

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	D [auth A], F [auth B]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.191 (Depositor), 0.161 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.972	α = 90
b = 102.972	β = 90
c = 176.862	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-04-05 
Deposition Author(s): Crowther, R.L., Georgiadis, M.M.

Revision History  

• Version 1.0: 2005-04-05
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary