4YIL | pdb_00004yil

OYE1 W116A COMPLEXED WITH (Z)-METHYL 3-CYANO-3-(4-FLUOROPHENYL)ACRYLATE IN A NON PRODUCTIVE BINDING MODE

• PDB DOI: https://doi.org/10.2210/pdb4YIL/pdb

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


• Deposited: 2015-03-02 Released: 2016-01-20 
• Deposition Author(s): Santangelo, S., Brenna, E., Stewart, J.D., Powell III, R.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 
  0.189 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Opposite Enantioselectivity in the Bioreduction of (Z)-beta-Aryl-beta-cyanoacrylates Mediated by the Tryptophan 116 Mutants of Old Yellow Enzyme 1: Synthetic Approach to (R)- and (S)-beta-Aryl-gamma-lactams

Brenna, E., Crotti, M., Gatti, F.G., Monti, D., Parmeggiani, F., Powell III, R.W., Santangelo, S., Stewart, J.D.

(2015) Adv Synth Catal 357: 1849-1860.

• DOI: https://doi.org/10.1002/adsc.201500206

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 45.28 kDa 
• Atom Count: 3,791 
• Modeled Residue Count: 397 
• Deposited Residue Count: 397 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADPH dehydrogenase 1	A	397	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
4D3	E [auth A]	methyl (2Z)-3-cyano-3-(4-fluorophenyl)prop-2-enoate C11 H8 F N O2 SKAOSLYCNKRRPS-RMKNXTFCSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free:  0.189 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.395	α = 90
b = 141.395	β = 90
c = 42.82	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-20 
Deposition Author(s): Santangelo, S., Brenna, E., Stewart, J.D., Powell III, R.W.

Revision History  

• Version 1.0: 2016-01-20
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description