1X8M | pdb_00001x8m

X-ray structure of pectin degrading enzyme 5-keto 4-deoxyuronate isomerase from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb1X8M/pdb

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


• Deposited: 2004-08-18 Released: 2004-09-21 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.280 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.257 (Depositor), 0.254 (DCC) 
• R-Value Observed: 
  0.259 (Depositor) 

Literature

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

Fedorov, A.A., Fedorov, E.V., Almo, S.C.

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: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Biological Assembly 6  

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

Biological assembly 6 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 193.97 kDa 
• Atom Count: 12,126 
• Modeled Residue Count: 1,554 
• Deposited Residue Count: 1,728 
• 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, C, D, E, F	288	Escherichia coli	Mutation(s): 0  Gene Names: kduI EC: 5.3.1.17
UniProt
Find proteins for Q46938 (Escherichia coli (strain K12)) Explore Q46938  Go to UniProtKB:  Q46938

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.280 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.257 (Depositor), 0.254 (DCC) 
• R-Value Observed: 0.259 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.011	α = 90
b = 101.011	β = 90
c = 179.41	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-09-21 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2004-09-21
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Structure summary
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references