2X5J

Crystal structure of the Apoform of the D-Erythrose-4-phosphate dehydrogenase from E. coli

• PDB DOI: https://doi.org/10.2210/pdb2X5J/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2010-02-09 Released: 2011-02-16 
• Deposition Author(s): Moniot, S., Didierjean, C., Boschi-Muller, S., Branlant, G., Corbier, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.266 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Structural Characterization of Erythrose-4- Phosphate Dehydrogenase from Escherichia Coli: Peculiar Features When Compared to Phosphorylating Gapdhs

Moniot, S., Didierjean, C., Boschi-Muller, S., Branlant, G., Corbier, C.

To be published.

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 (software)

Macromolecule Content

• Total Structure Weight: 149.77 kDa 
• Atom Count: 10,801 
• Modelled Residue Count: 1,310 
• Deposited Residue Count: 1,356 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE	A [auth O], B [auth P], C [auth Q], D [auth R]	339	Escherichia coli K-12	Mutation(s): 0  EC: 1.2.1.72
UniProt
Find proteins for P0A9B6 (Escherichia coli (strain K12)) Explore P0A9B6  Go to UniProtKB:  P0A9B6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth O], F [auth P], G [auth Q], H [auth R]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.266 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.3	α = 90
b = 110.7	β = 90
c = 138	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-16 
Deposition Author(s): Moniot, S., Didierjean, C., Boschi-Muller, S., Branlant, G., Corbier, C.

Revision History  

• Version 1.0: 2011-02-16
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary