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- PDB-8qo8: OPR3 variant R283E in complex with NADH4 -

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Basic information

Entry
Database: PDB / ID: 8qo8
TitleOPR3 variant R283E in complex with NADH4
Components12-oxophytodienoate reductase 3
KeywordsFLAVOPROTEIN / Old Yellow Enzyme / ene-reductase / flavoenzyme
Function / homology
Function and homology information


12-oxophytodienoate reductase / 12-oxophytodienoate reductase activity / jasmonic acid biosynthetic process / oxylipin biosynthetic process / peroxisome / FMN binding / identical protein binding
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-WI6 / 12-oxophytodienoate reductase 3
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsBijelic, A. / Macheroux, P. / Kerschbaumer, B.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science Fund Austria
CitationJournal: To Be Published
Title: Crystal structures of OPR3 wildtype and variants in complex with NAD(P)H
Authors: Kerschbaumer, B. / Bijelic, A. / Macheroux, P.
History
DepositionSep 28, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 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
B: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9946
Polymers88,7462
Non-polymers2,2484
Water13,385743
1
A: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4973
Polymers44,3731
Non-polymers1,1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4973
Polymers44,3731
Non-polymers1,1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.470, 93.320, 89.400
Angle α, β, γ (deg.)90.00, 97.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 12-oxophytodienoate reductase 3


Mass: 44373.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: OPR3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FEW9
#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-WI6 / 1,4,5,6-Tetrahydronicotinamide adenine dinucleotide / [[(2R,3S,4R,5R)-5-[(3S)-3-aminocarbonyl-3,6-dihydro-2H-pyridin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2S,3R,4S,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate


Mass: 667.457 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H31N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 743 / 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: 2.3 Å3/Da / Density % sol: 46.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM MES/Tris, 10 mM ammonium sulfate, 14% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.47→46.66 Å / Num. obs: 905053 / % possible obs: 97.17 % / Redundancy: 6.8 % / CC1/2: 0.998 / Net I/σ(I): 9.88
Reflection shellResolution: 1.47→1.51 Å / Num. unique obs: 44830 / CC1/2: 0.62

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Processing

Software
NameVersionClassification
PHENIX(dev_4761)refinement
XDSdata reduction
XSCALEdata scaling
PHASER(dev_4761)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→46.66 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2036 1874 1.41 %
Rwork0.1868 --
obs0.187 132568 97.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.47→46.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5484 0 114 743 6341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015757
X-RAY DIFFRACTIONf_angle_d1.0937851
X-RAY DIFFRACTIONf_dihedral_angle_d15.8792078
X-RAY DIFFRACTIONf_chiral_restr0.085868
X-RAY DIFFRACTIONf_plane_restr0.0151007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.510.49871210.43438381X-RAY DIFFRACTION81
1.51-1.550.39731400.36189803X-RAY DIFFRACTION95
1.55-1.60.36621460.305110219X-RAY DIFFRACTION99
1.6-1.660.28981450.277310169X-RAY DIFFRACTION99
1.66-1.730.27521470.251910185X-RAY DIFFRACTION99
1.73-1.810.26971460.218610134X-RAY DIFFRACTION98
1.81-1.90.21351430.197610045X-RAY DIFFRACTION97
1.9-2.020.17941470.178310252X-RAY DIFFRACTION100
2.02-2.180.18461490.17810318X-RAY DIFFRACTION100
2.18-2.40.19451460.173410307X-RAY DIFFRACTION100
2.4-2.740.20581460.178510140X-RAY DIFFRACTION98
2.74-3.460.17921480.17410349X-RAY DIFFRACTION100
3.46-46.660.16681500.152910392X-RAY DIFFRACTION99

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