3WBY

Crystal structure of Gox0644 D53A mutant in complex with NADPH

• PDB DOI: https://doi.org/10.2210/pdb3WBY/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Gluconobacter oxydans 621H
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-05-22 Released: 2014-05-28 
• Deposition Author(s): Yuan, Y.A., Wang, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.326 
• R-Value Work: 0.218 
• R-Value Observed: 0.224 

Literature

Crystal structure of Gox0644 D53A mutant in complex with NADPH

Yuan, Y.A., Wang, C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 65.51 kDa 
• Atom Count: 4,454 
• Modelled Residue Count: 542 
• Deposited Residue Count: 564 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative 2,5-diketo-D-gluconic acid reductase	A, B	282	Gluconobacter oxydans 621H	Mutation(s): 1  Gene Names: GOX0644 EC: 1.1.1
UniProt
Find proteins for Q5FT75 (Gluconobacter oxydans (strain 621H)) Explore Q5FT75  Go to UniProtKB:  Q5FT75

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	C [auth A], D [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.326 
• R-Value Work: 0.218 
• R-Value Observed: 0.224 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.638	α = 90
b = 76.587	β = 90
c = 125.624	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-28 
Deposition Author(s): Yuan, Y.A., Wang, C.

Revision History  

• Version 1.0: 2014-05-28
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations