3RND | pdb_00003rnd

W116I-OYE1 complexed with 2-(Hydroxymethyl)-cyclopent-2-enone

• PDB DOI: https://doi.org/10.2210/pdb3RND/pdb

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


• Deposited: 2011-04-22 Released: 2011-08-03 
• Deposition Author(s): Pompeu, Y.A., Stewart, J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.168 (Depositor), 0.172 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

Literature

Biocatalytic Reductions of Baylis-Hillman Adducts

Walton, A.Z., Conerly, W.C., Pompeu, Y.A., Sullivan, B.T., Stewart, J.D.

(2011) ACS Catal 

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: 45.48 kDa 
• Atom Count: 3,684 
• Modeled Residue Count: 399 
• Deposited Residue Count: 399 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADPH dehydrogenase 1	A	399	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
3RN	C [auth A]	2-(hydroxymethyl)cyclopent-2-en-1-one C6 H8 O2 DQTFESRTIZHRRO-UHFFFAOYSA-N
MG	D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.168 (Depositor), 0.172 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.18	α = 90
b = 141.18	β = 90
c = 42.789	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
PHENIX	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-03 
Deposition Author(s): Pompeu, Y.A., Stewart, J.D.

Revision History  

• Version 1.0: 2011-08-03
  Type: Initial release
  
• Version 1.1: 2011-08-17
  Changes: Derived calculations
• Version 1.2: 2011-11-16
  Changes: Atomic model
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description