8QO7 | pdb_00008qo7

OPR3 variant R283E in complex with NADPH4

• PDB DOI: https://doi.org/10.2210/pdb8QO7/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Solanum lycopersicum
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-09-28 Released: 2025-04-09 
• Deposition Author(s): Bijelic, A., Macheroux, P., Kerschbaumer, B.
• Funding Organization(s): Austrian Science Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of OPR3 wildtype and variants in complex with NAD(P)H

Kerschbaumer, B., Bijelic, A., Macheroux, P.

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

Macromolecule Content 

• Total Structure Weight: 46.42 kDa 
• Atom Count: 3,380 
• Modeled Residue Count: 355 
• Deposited Residue Count: 402 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
12-oxophytodienoate reductase 3	A	402	Solanum lycopersicum	Mutation(s): 1  Gene Names: OPR3 EC: 1.3.1.42
UniProt
Find proteins for Q9FEW9 (Solanum lycopersicum) Explore Q9FEW9  Go to UniProtKB:  Q9FEW9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5J8 (Subject of Investigation/LOI)	C [auth A], D [auth A]	[[(2R,3S,4R,5R)-5-(5-aminocarbonyl-3,4-dihydro-2H-pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methyl hydrogen phosphate C21 H32 N7 O17 P3 XBYZUJOLVDCGQT-NNYOXOHSSA-N
FMN	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.4	α = 90
b = 90.27	β = 90
c = 49.48	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-09 
Deposition Author(s): Bijelic, A., Macheroux, P., Kerschbaumer, B.

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Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	--

Revision History  

• Version 1.0: 2025-04-09
  Type: Initial release