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- PDB-8qnk: OPR3 variant R283D in complex with NADPH4 -

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Basic information

Entry
Database: PDB / ID: 8qnk
TitleOPR3 variant R283D in complex with NADPH4
Components12-oxophytodienoate reductase 3
KeywordsFLAVOPROTEIN / Old yellow enzyme / flavoenzyme / ene-reductase / 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: 1.91 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 with NAD(P)H
Authors: Kerschbaumer, B. / Bijelic, A. / Macheroux, P.
History
DepositionSep 27, 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
B: 12-oxophytodienoate reductase 3
C: 12-oxophytodienoate reductase 3
D: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,87511
Polymers177,4364
Non-polymers3,4387
Water16,664925
1
A: 12-oxophytodienoate reductase 3
B: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4966
Polymers88,7182
Non-polymers1,7784
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-24 kcal/mol
Surface area26000 Å2
2
C: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5633
Polymers44,3591
Non-polymers1,2042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-4 kcal/mol
Surface area13270 Å2
3
D: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8152
Polymers44,3591
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-4 kcal/mol
Surface area12780 Å2
Unit cell
Length a, b, c (Å)80.576, 90.483, 114.632
Angle α, β, γ (deg.)90.00, 110.02, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
12-oxophytodienoate reductase 3


Mass: 44359.094 Da / Num. of mol.: 4
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.: 4 / 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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 925 / 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: 2.21 Å3/Da / Density % sol: 44.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM Tris-HCl, 50 mM sodium tartrate, 10% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.91→35.9 Å / Num. obs: 114489 / % possible obs: 95.49 % / Redundancy: 4 % / Biso Wilson estimate: 27.59 Å2 / CC1/2: 0.998 / Net I/σ(I): 8.56
Reflection shellResolution: 1.91→1.93 Å / Num. unique obs: 3915 / CC1/2: 0.417

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Processing

Software
NameVersionClassification
PHENIX(dev_4761)refinement
XDSdata reduction
XSCALEdata scaling
PHASER0.8856phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→35.9 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2218 5510 4.81 %
Rwork0.1948 --
obs0.1962 114489 95.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.91→35.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11242 0 228 925 12395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911756
X-RAY DIFFRACTIONf_angle_d1.0516029
X-RAY DIFFRACTIONf_dihedral_angle_d16.4364204
X-RAY DIFFRACTIONf_chiral_restr0.0541765
X-RAY DIFFRACTIONf_plane_restr0.0112062
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.930.38321750.34043740X-RAY DIFFRACTION98
1.93-1.950.36491880.32433749X-RAY DIFFRACTION98
1.95-1.980.34562090.3143674X-RAY DIFFRACTION98
1.98-20.34831750.31393701X-RAY DIFFRACTION98
2-2.030.31011900.29883699X-RAY DIFFRACTION98
2.03-2.060.3111750.27623727X-RAY DIFFRACTION98
2.06-2.090.2911870.26923686X-RAY DIFFRACTION97
2.09-2.120.31711890.25443677X-RAY DIFFRACTION97
2.12-2.150.29221760.24373617X-RAY DIFFRACTION96
2.15-2.190.27331860.24613631X-RAY DIFFRACTION96
2.19-2.220.27751940.23213553X-RAY DIFFRACTION94
2.22-2.260.25091550.21943204X-RAY DIFFRACTION84
2.26-2.310.23881590.19682736X-RAY DIFFRACTION73
2.31-2.360.22911480.19573002X-RAY DIFFRACTION79
2.36-2.410.21521770.19723234X-RAY DIFFRACTION86
2.41-2.460.22321710.20383620X-RAY DIFFRACTION96
2.46-2.520.24851960.20573836X-RAY DIFFRACTION100
2.52-2.590.26141680.2043763X-RAY DIFFRACTION100
2.59-2.670.23322020.20093776X-RAY DIFFRACTION99
2.67-2.750.2191950.20083782X-RAY DIFFRACTION99
2.75-2.850.22281710.19643746X-RAY DIFFRACTION99
2.85-2.970.22671630.19163813X-RAY DIFFRACTION99
2.97-3.10.18852130.18833731X-RAY DIFFRACTION98
3.1-3.270.21282030.1823681X-RAY DIFFRACTION98
3.27-3.470.21880.17623753X-RAY DIFFRACTION98
3.47-3.740.18721800.16473682X-RAY DIFFRACTION97
3.74-4.110.18121570.15533735X-RAY DIFFRACTION97
4.11-4.710.1692110.15163753X-RAY DIFFRACTION99
4.71-5.930.18752200.16863809X-RAY DIFFRACTION100
5.93-35.90.21611890.17383869X-RAY DIFFRACTION98

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