5DT9

Crystal structure of a putative D-Erythronate-4-Phosphate Dehydrogenase from Vibrio cholerae

• PDB DOI: https://doi.org/10.2210/pdb5DT9/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-09-17 Released: 2015-09-30 
• Deposition Author(s): Stogios, P.J., Skarina, T., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 0.240 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Literature

Crystal structure of a putative D-Erythronate-4-Phosphate Dehydrogenase from Vibrio cholerae

Stogios, P.J.

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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 44.27 kDa 
• Atom Count: 3,188 
• Modelled Residue Count: 379 
• Deposited Residue Count: 387 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Erythronate-4-phosphate dehydrogenase	A	387	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0  Gene Names: pdxB, VC_2108 EC: 1.1.1.290
UniProt
Find proteins for Q9KQ92 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KQ92  Go to UniProtKB:  Q9KQ92

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	B [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	M [auth A], N [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 0.240 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: P 4₃ 2₁ 2
• Diffraction Data: https://doi.org/10.18430/M35DT9

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.775	α = 90
b = 145.775	β = 90
c = 62.031	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
Coot	model building
PHENIX	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-30 
Deposition Author(s): Stogios, P.J., Skarina, T., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2015-09-30
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description