2XF8

Structure of the D-Erythrose-4-Phosphate Dehydrogenase from E. coli in complex with a NAD cofactor analog (3-Chloroacetyl adenine pyridine dinucleotide) and sulfate anion

• PDB DOI: https://doi.org/10.2210/pdb2XF8/pdb

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


• Deposited: 2010-05-20 Released: 2011-06-08 
• 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: 2.95 Å
• R-Value Free: 
  0.280 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.239 (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)

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 602.58 kDa 
• Atom Count: 40,244 
• Modelled Residue Count: 5,156 
• Deposited Residue Count: 5,408 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	338	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3CD	AA [auth G], DA [auth I], GA [auth K], JA [auth M], MA [auth O], R [auth A], U [auth C], X [auth E]	3-(CHLOROACETYL) PYRIDINE ADENINE DINUCLEOTIDE C22 H28 Cl N6 O14 P2 XIQCGHNADRRDKB-RBEMOOQDSA-O
SO4	BA [auth H], CA [auth I], EA [auth J], FA [auth K], HA [auth L], IA [auth M], KA [auth N], LA [auth O], NA [auth P], Q [auth A], S [auth B], T [auth C], V [auth D], W [auth E], Y [auth F], Z [auth G]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free:  0.280 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.18	α = 91.3
b = 111.66	β = 96.11
c = 135.47	γ = 88.44

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-08 
Deposition Author(s): Moniot, S., Didierjean, C., Boschi-Muller, S., Branlant, G., Corbier, C.

Revision History  

• Version 1.0: 2011-06-08
  Type: Initial release
  
• Version 1.1: 2011-06-09
  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: 2024-11-20
  Changes: Structure summary