6XEQ

Crystal structure of the tetrameric 6-phosphogluconate dehydrogenase from Gluconobacter oxidans

• PDB DOI: https://doi.org/10.2210/pdb6XEQ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Gluconobacter oxydans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-06-13 Released: 2020-12-02 
• Deposition Author(s): Maturana, P., Roversi, P., Castro-Fernandez, V., Herrera-Morande, A., Garratt, R.C., Cabrera, R.
• Funding Organization(s): Comision Nacional Cientifica y Technologica (CONICYT)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.286 
• R-Value Work: 0.246 
• R-Value Observed: 0.248 

Literature

Crystal structure of the 6-phosphogluconate dehydrogenase from Gluconobacter oxydans reveals tetrameric 6PGDHs as the crucial intermediate in the evolution of structure and cofactor preference in the 6PGDH family [version 1; peer review: 1 approved, 1 approved with reservations]

Maturana, P., Tobar-Calfucoy, E., Fuentealba, M., Roversi, P., Garratt, R., Cabrera, R.

(2021) Wellcome Open Res 6

• DOI: https://doi.org/10.12688/wellcomeopenres.16572.1

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 Evidence: SAXS

Macromolecule Content

• Total Structure Weight: 153.71 kDa 
• Atom Count: 9,723 
• Modelled Residue Count: 1,271 
• Deposited Residue Count: 1,412 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-phosphogluconate dehydrogenase	A, B, C, D	353	Gluconobacter oxydans	Mutation(s): 0  Gene Names: GOX1705 EC: 1.1.1.343
UniProt
Find proteins for G5EBD7 (Gluconobacter oxydans (strain 621H)) Explore G5EBD7  Go to UniProtKB:  G5EBD7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth B], G [auth C], H [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.286 
• R-Value Work: 0.246 
• R-Value Observed: 0.248 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.061	α = 90
b = 125.675	β = 90
c = 166.273	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data reduction
pointless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-12-02 
Deposition Author(s): Maturana, P., Roversi, P., Castro-Fernandez, V., Herrera-Morande, A., Garratt, R.C., Cabrera, R.

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Funding Organization	Location	Grant Number
Comision Nacional Cientifica y Technologica (CONICYT)	Chile	FONDEQUIP EQM140151

Revision History  

• Version 1.0: 2020-12-02
  Type: Initial release
  
• Version 1.1: 2021-06-23
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description