3WJS | pdb_00003wjs

Crystal structure of GYE (old yellow enzyme)

• PDB DOI: https://doi.org/10.2210/pdb3WJS/pdb

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


• Deposited: 2013-10-14 Released: 2014-09-24 
• Deposition Author(s): Yuan, Y.A., Yin, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Literature

Crystal structure of GYE (old yellow enzyme)

Yuan, Y.A., Yin, B.

To be published.

Biological Assembly 1  

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

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 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 39.74 kDa 
• Atom Count: 2,422 
• Modeled Residue Count: 315 
• Deposited Residue Count: 361 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH oxidase	A	361	Gluconobacter oxydans	Mutation(s): 0  Gene Names: nox
UniProt
Find proteins for A1E8I9 (Gluconobacter oxydans) Explore A1E8I9  Go to UniProtKB:  A1E8I9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HG	D [auth A]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N
PGE	B [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.886	α = 90
b = 138.886	β = 90
c = 145.091	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-24 
Deposition Author(s): Yuan, Y.A., Yin, B.

Revision History  

• Version 1.0: 2014-09-24
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary