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- PDB-9fcn: OPR3 loop swap variant L6(AchrOYE4) in complex with NADPH4 -

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Basic information

Entry
Database: PDB / ID: 9fcn
TitleOPR3 loop swap variant L6(AchrOYE4) in complex with NADPH4
Components12-oxophytodienoate reductase 3,Old yellow enzyme OYE4
KeywordsFLAVOPROTEIN / Flavoenzymes / ene-reductases / old yellow enzymes / coenzymes
Function / homology
Function and homology information


NADPH dehydrogenase / 12-oxophytodienoate reductase / 12-oxophytodienoate reductase activity / oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / jasmonic acid biosynthetic process / oxylipin biosynthetic process / NADPH dehydrogenase activity / peroxisome / FMN binding / identical protein binding / cytosol
Similarity search - Function
Oxidoreductase Oye-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase-type TIM barrel
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Chem-TXP / Old yellow enzyme OYE4 / 12-oxophytodienoate reductase 3
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
Achromobacter sp. JA81 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsBijelic, A. / Kerschbaumer, B. / Macheroux, P.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science Fund Austria
CitationJournal: To Be Published
Title: Insights into the complexity of coenzyme specificity in ene-reductases
Authors: Kerschaumer, B. / Macheroux, P. / Bijelic, A.
History
DepositionMay 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 12-oxophytodienoate reductase 3,Old yellow enzyme OYE4
B: 12-oxophytodienoate reductase 3,Old yellow enzyme OYE4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7436
Polymers88,3362
Non-polymers2,4084
Water8,629479
1
A: 12-oxophytodienoate reductase 3,Old yellow enzyme OYE4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3723
Polymers44,1681
Non-polymers1,2042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 12-oxophytodienoate reductase 3,Old yellow enzyme OYE4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3723
Polymers44,1681
Non-polymers1,2042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.322, 93.996, 89.275
Angle α, β, γ (deg.)90.000, 97.601, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein 12-oxophytodienoate reductase 3,Old yellow enzyme OYE4 / 12-oxophytodienoate-10 / 11-reductase 3 / OPDA-reductase 3 / LeOPR3


Mass: 44167.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato), (gene. exp.) Achromobacter sp. JA81 (bacteria)
Gene: OPR3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9FEW9, UniProt: I3V5V6, 12-oxophytodienoate reductase, NADPH dehydrogenase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-TXP / 1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE


Mass: 747.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H32N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Tris-HCl, 50 mM sodium tartrate, 16-20% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.25→45.41 Å / Num. obs: 50345 / % possible obs: 98.19 % / Redundancy: 7.1 % / Biso Wilson estimate: 32.09 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.2212 / Net I/σ(I): 6.35
Reflection shellResolution: 2.25→2.31 Å / Rmerge(I) obs: 4.257 / Num. unique obs: 3357 / CC1/2: 0.21

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→45.41 Å / SU ML: 0.3418 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.9104
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2348 1922 5.1 %
Rwork0.1837 35788 -
obs0.1863 37710 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.09 Å2
Refinement stepCycle: LAST / Resolution: 2.25→45.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5525 0 138 485 6148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00785800
X-RAY DIFFRACTIONf_angle_d0.62817913
X-RAY DIFFRACTIONf_chiral_restr0.0457876
X-RAY DIFFRACTIONf_plane_restr0.00371006
X-RAY DIFFRACTIONf_dihedral_angle_d16.16042081
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.310.43321470.40342374X-RAY DIFFRACTION92.07
2.31-2.370.38661300.27572596X-RAY DIFFRACTION99.56
2.37-2.440.27641300.24142578X-RAY DIFFRACTION99.67
2.44-2.520.24891380.20692561X-RAY DIFFRACTION99.52
2.52-2.610.27581530.21022618X-RAY DIFFRACTION99.89
2.61-2.710.27111290.2142567X-RAY DIFFRACTION99.41
2.71-2.830.25571390.19062529X-RAY DIFFRACTION98.27
2.83-2.980.24671370.18732517X-RAY DIFFRACTION96.76
2.98-3.170.27691410.18682492X-RAY DIFFRACTION96.02
3.17-3.420.25151230.18342469X-RAY DIFFRACTION94.53
3.42-3.760.23241300.17012601X-RAY DIFFRACTION99.56
3.76-4.30.20031320.14922613X-RAY DIFFRACTION99.96
4.3-5.420.16361430.14072629X-RAY DIFFRACTION99.96
5.42-45.410.17411500.16632644X-RAY DIFFRACTION99.5

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