9FCN | pdb_00009fcn

OPR3 loop swap variant L6(AchrOYE4) in complex with NADPH4

• PDB DOI: https://doi.org/10.2210/pdb9FCN/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Solanum lycopersicum, Achromobacter sp. JA81
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-05-15 Released: 2025-05-28 
• Deposition Author(s): Bijelic, A., Kerschbaumer, B., Macheroux, P.
• Funding Organization(s): Austrian Science Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.235 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Insights into the complexity of coenzyme specificity in ene-reductases

Kerschaumer, B., Macheroux, P., Bijelic, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 90.74 kDa 
• Atom Count: 6,142 
• Modeled Residue Count: 720 
• Deposited Residue Count: 800 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
12-oxophytodienoate reductase 3,Old yellow enzyme OYE4	A, B	400	Solanum lycopersicum, Achromobacter sp. JA81	Mutation(s): 0  Gene Names: OPR3 EC: 1.3.1.42 (PDB Primary Data), 1.6.99.1 (PDB Primary Data)
UniProt
Find proteins for I3V5V6 (Achromobacter sp. JA81) Explore I3V5V6  Go to UniProtKB:  I3V5V6
Find proteins for Q9FEW9 (Solanum lycopersicum) Explore Q9FEW9  Go to UniProtKB:  Q9FEW9
UniProt Groups	I3V5V6Q9FEW9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TXP (Subject of Investigation/LOI)	D [auth A], F [auth B]	1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE C21 H32 N7 O17 P3 MGWIKFWDIJJFDG-ILTSWSAWSA-N
FMN	C [auth A], E [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.235 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.322	α = 90
b = 93.996	β = 97.601
c = 89.275	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-28 
Deposition Author(s): Bijelic, A., Kerschbaumer, B., Macheroux, P.

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Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	--

Revision History  

• Version 1.0: 2025-05-28
  Type: Initial release