3GR8 | pdb_00003gr8

Structure of OYE from Geobacillus kaustophilus, orthorhombic crystal form

• PDB DOI: https://doi.org/10.2210/pdb3GR8/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Geobacillus kaustophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-25 Released: 2010-03-31 
• Deposition Author(s): Uhl, M.K., Gruber, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.213 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.180 (DCC) 

Starting Model: experimental

Literature

Old Yellow Enzyme-Catalyzed Dehydrogenation of Saturated Ketones

Schittmayer, M., Zach, S., Winkler, M., Winkler, A., Macheroux, P., Uhl, M.K., Gruber, K., Kambourakis, S., Rozzell, D., Glieder, A.

(2011) Adv Synth Catal 353: 268-274

• DOI: https://doi.org/10.1002/adsc.201000862

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 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 76.88 kDa 
• Atom Count: 5,689 
• Modeled Residue Count: 680 
• Deposited Residue Count: 680 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADPH dehydrogenase	A, B	340	Geobacillus kaustophilus	Mutation(s): 0  Gene Names: namA EC: 1.6.99.1
UniProt
Find proteins for Q5KXG9 (Geobacillus kaustophilus (strain HTA426)) Explore Q5KXG9  Go to UniProtKB:  Q5KXG9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	C [auth A], G [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
BTB	E [auth A], F [auth A]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.213 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.180 (DCC) 

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.394	α = 90
b = 151.93	β = 90
c = 143.744	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
DENZO	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-31 
Deposition Author(s): Uhl, M.K., Gruber, K.

Revision History  

• Version 1.0: 2010-03-31
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-09-03
  Changes: Database references
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description