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- PDB-8qo7: OPR3 variant R283E in complex with NADPH4 -

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Basic information

Entry
Database: PDB / ID: 8qo7
TitleOPR3 variant R283E in complex with NADPH4
Components12-oxophytodienoate reductase 3
KeywordsFLAVOPROTEIN / Old Yellow Enzyme / ene-reductase / flavoenzyme / NADPH
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
Chem-5J8 / FLAVIN MONONUCLEOTIDE / 12-oxophytodienoate reductase 3
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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

Downloads & links

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Assembly

Deposited unit
A: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4205
Polymers44,3731
Non-polymers2,0474
Water9,566531
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.400, 90.270, 49.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein 12-oxophytodienoate reductase 3


Mass: 44373.121 Da / Num. of mol.: 1
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.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-5J8 / [[(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


Mass: 747.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H32N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 531 / 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: 2.22 Å3/Da / Density % sol: 44.71 %
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: 1.033 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: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.4→45.13 Å / Num. obs: 78424 / % possible obs: 99.66 % / Redundancy: 24.2 % / CC1/2: 0.999 / Net I/σ(I): 31.68
Reflection shellResolution: 1.4→1.42 Å / Num. unique obs: 37199 / CC1/2: 0.812

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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: 1.4→45.13 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1708 3922 5 %
Rwork0.1514 --
obs0.1523 78424 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→45.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2749 0 89 531 3369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172920
X-RAY DIFFRACTIONf_angle_d1.6113985
X-RAY DIFFRACTIONf_dihedral_angle_d11.736414
X-RAY DIFFRACTIONf_chiral_restr0.11436
X-RAY DIFFRACTIONf_plane_restr0.021505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.23491320.20442496X-RAY DIFFRACTION95
1.42-1.440.24271360.19382592X-RAY DIFFRACTION99
1.44-1.450.20081380.17992618X-RAY DIFFRACTION99
1.45-1.470.22421370.17112615X-RAY DIFFRACTION99
1.47-1.490.23381390.16632634X-RAY DIFFRACTION100
1.49-1.520.17511380.15892611X-RAY DIFFRACTION100
1.52-1.540.18591390.15372654X-RAY DIFFRACTION100
1.54-1.570.21011370.14562604X-RAY DIFFRACTION100
1.57-1.590.16491410.14422669X-RAY DIFFRACTION100
1.59-1.620.16981380.14132635X-RAY DIFFRACTION100
1.62-1.650.17371420.14242681X-RAY DIFFRACTION100
1.65-1.690.17481370.13772619X-RAY DIFFRACTION100
1.69-1.720.16061400.14932650X-RAY DIFFRACTION100
1.72-1.760.16121400.14342672X-RAY DIFFRACTION100
1.76-1.810.1691400.14652642X-RAY DIFFRACTION100
1.81-1.860.1551380.15242639X-RAY DIFFRACTION100
1.86-1.910.20541420.16082695X-RAY DIFFRACTION100
1.91-1.970.20391390.15452645X-RAY DIFFRACTION100
1.97-2.040.20021400.15232642X-RAY DIFFRACTION100
2.04-2.130.15061400.14622660X-RAY DIFFRACTION100
2.13-2.220.15321410.14492687X-RAY DIFFRACTION100
2.22-2.340.16091420.14832690X-RAY DIFFRACTION100
2.34-2.490.1861400.152671X-RAY DIFFRACTION100
2.49-2.680.17421420.16162694X-RAY DIFFRACTION100
2.68-2.950.14521430.15472715X-RAY DIFFRACTION100
2.95-3.370.16931420.14712707X-RAY DIFFRACTION100
3.37-4.250.13681460.13792776X-RAY DIFFRACTION100
4.25-45.130.17611530.15672889X-RAY DIFFRACTION100

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