4GE8

OYE1-W116I complexed with (s)-Carvone

• PDB DOI: https://doi.org/10.2210/pdb4GE8/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces pastorianus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-08-01 Released: 2012-08-29 
• Deposition Author(s): Pompeu, Y.A., Stewart, J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.170 
• R-Value Work: 0.137 
• R-Value Observed: 0.140 

Starting Model: experimental

Literature

X‑ray Crystallography Reveals How Subtle Changes Control the Orientation of Substrate Binding in an Alkene Reductase

Pompeu, Y.A., Sullivan, B., Stewart, J.D.

(2013) ACS Catal 3: 2376-2390

• DOI: https://doi.org/10.1021/cs400622e

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 46.78 kDa 
• Atom Count: 3,812 
• Modelled Residue Count: 399 
• Deposited Residue Count: 400 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADPH dehydrogenase 1	A	400	Saccharomyces pastorianus	Mutation(s): 1  Gene Names: OYE1 EC: 1.6.99.1
UniProt
Find proteins for Q02899 (Saccharomyces pastorianus) Explore Q02899  Go to UniProtKB:  Q02899

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	L [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
1PE	I [auth A], J [auth A], K [auth A], N [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
0WU	O [auth A]	(5S)-2-methyl-5-(prop-1-en-2-yl)cyclohex-2-en-1-one C10 H14 O ULDHMXUKGWMISQ-VIFPVBQESA-N
CL	C [auth A], D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	F [auth A], G [auth A], H [auth A], M [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.170 
• R-Value Work: 0.137 
• R-Value Observed: 0.140 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.928	α = 90
b = 140.928	β = 90
c = 42.484	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-29 
Deposition Author(s): Pompeu, Y.A., Stewart, J.D.

Revision History  

• Version 1.0: 2012-08-29
  Type: Initial release
  
• Version 1.1: 2013-10-09
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description