1MZR | pdb_00001mzr

Structure of dkga from E.coli at 2.13 A resolution solved by molecular replacement

• PDB DOI: https://doi.org/10.2210/pdb1MZR/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2002-10-09 Released: 2003-10-28 
• Deposition Author(s): Abergel, C., Jeudy, S., Monchois, V., Claverie, J.M., Bacterial targets at IGS-CNRS, France (BIGS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 
  0.220 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.170 (DCC) 

Starting Model: experimental

Literature

Crystal structure of Escherichia coli DkgA, a broad-specificity aldo-keto reductase.

Jeudy, S., Monchois, V., Maza, C., Claverie, J.M., Abergel, C.

(2006) Proteins 62: 302-307

• PubMed: 16284956 
• DOI: https://doi.org/10.1002/prot.20710
• Primary Citation of Related Structures:  
  1MZR

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Organizational Affiliation: 
• Information Génomique et Structurale, CNRS, Marseille, France.

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.

Macromolecule Content 

• Total Structure Weight: 68.03 kDa 
• Atom Count: 5,008 
• Modeled Residue Count: 550 
• Deposited Residue Count: 592 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,5-diketo-D-gluconate reductase A	A, B	296	Escherichia coli	Mutation(s): 0  Gene Names: yqhe EC: 1.1.1 (PDB Primary Data), 1.1.1.2 (UniProt), 1.1.1.346 (UniProt)
UniProt
Find proteins for Q46857 (Escherichia coli (strain K12)) Explore Q46857  Go to UniProtKB:  Q46857

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth A], G [auth B], H [auth B], I [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free:  0.220 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.170 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.177	α = 90
b = 145.697	β = 90
c = 79.511	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-10-28 
Deposition Author(s): Abergel, C., Jeudy, S., Monchois, V., Claverie, J.M., Bacterial targets at IGS-CNRS, France (BIGS)

Revision History  

• Version 1.0: 2003-10-28
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description