3OET

D-Erythronate-4-Phosphate Dehydrogenase complexed with NAD

• PDB DOI: https://doi.org/10.2210/pdb3OET/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-08-13 Released: 2010-08-25 
• Deposition Author(s): Filippova, E.V., Wawrzak, Z., Onopriyenko, O., Savchenko, A., Edwards, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 0.253 
• R-Value Work: 0.190 
• R-Value Observed: 0.193 

Starting Model: experimental

Literature

D-Erythronate-4-Phosphate Dehydrogenase complexed with NAD

Filippova, E.V., Wawrzak, Z., Onopriyenko, O., Savchenko, A., Edwards, A., Anderson, W.F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 generated by PISA (software)

Biological Assembly 6  

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

Biological assembly 6 generated by PISA (software)

Biological Assembly 7  

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

Biological assembly 7 generated by PISA (software)

Biological Assembly 8  

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

Biological assembly 8 generated by PISA (software)

Biological Assembly 9  

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

Biological assembly 9 generated by PISA (software)

Biological Assembly 10  

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

Biological assembly 10 generated by PISA (software)

Biological Assembly 11  

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

Biological assembly 11 generated by PISA (software)

Biological Assembly 12  

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

Biological assembly 12 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 340.16 kDa 
• Atom Count: 23,835 
• Modelled Residue Count: 2,987 
• Deposited Residue Count: 3,048 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Erythronate-4-phosphate dehydrogenase	A, B, C, D, E, F, G, H	381	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0  Gene Names: pdxB, STM2370 EC: 1.1.1.290
UniProt
Find proteins for P60802 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P60802  Go to UniProtKB:  P60802

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 0.253 
• R-Value Work: 0.190 
• R-Value Observed: 0.193 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/m33oet

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.279	α = 90
b = 167.765	β = 93.88
c = 103.949	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
CCP4	model building
MrBUMP	phasing
PHENIX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-3000	data scaling
CCP4	phasing
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-25 
Deposition Author(s): Filippova, E.V., Wawrzak, Z., Onopriyenko, O., Savchenko, A., Edwards, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2010-08-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-12-06
  Changes: Data collection
• Version 1.5: 2024-10-30
  Changes: Structure summary