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- PDB-8qny: OPR3 variant with redesigned loop 6 (8aa) in complex with NADPH4 -

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Basic information

Entry
Database: PDB / ID: 8qny
TitleOPR3 variant with redesigned loop 6 (8aa) 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: 1.65 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 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6266
Polymers87,2192
Non-polymers2,4084
Water9,638535
1
A: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8133
Polymers43,6091
Non-polymers1,2042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8133
Polymers43,6091
Non-polymers1,2042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.736, 91.727, 89.770
Angle α, β, γ (deg.)90.00, 98.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 12-oxophytodienoate reductase 3


Mass: 43609.312 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-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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 535 / 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: 46.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM MES/Tris, 50 mM ammonium sulfate, 14% 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 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.65→49.13 Å / Num. obs: 632860 / % possible obs: 87 % / Redundancy: 7.6 % / CC1/2: 0.995 / Net I/σ(I): 8.5
Reflection shellResolution: 1.65→1.67 Å / Num. unique obs: 10981 / CC1/2: 0.483

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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: 1.65→49.13 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2162 4225 5.08 %
Rwork0.1818 --
obs0.1835 83146 87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→49.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5556 0 114 545 6215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135839
X-RAY DIFFRACTIONf_angle_d1.2547966
X-RAY DIFFRACTIONf_dihedral_angle_d17.0932098
X-RAY DIFFRACTIONf_chiral_restr0.076879
X-RAY DIFFRACTIONf_plane_restr0.0131025
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.344730.33651373X-RAY DIFFRACTION45
1.67-1.690.305810.30041488X-RAY DIFFRACTION50
1.69-1.710.3448890.28881630X-RAY DIFFRACTION54
1.71-1.730.3047960.27711817X-RAY DIFFRACTION61
1.73-1.750.2856960.25812067X-RAY DIFFRACTION69
1.75-1.780.29761280.24992329X-RAY DIFFRACTION77
1.78-1.80.26331440.24312749X-RAY DIFFRACTION91
1.8-1.830.28291610.2372840X-RAY DIFFRACTION94
1.83-1.860.26141560.22162874X-RAY DIFFRACTION96
1.86-1.890.26311500.21482873X-RAY DIFFRACTION96
1.89-1.920.26321620.20032927X-RAY DIFFRACTION96
1.92-1.960.24351480.20632851X-RAY DIFFRACTION96
1.96-1.990.23541640.2082929X-RAY DIFFRACTION96
1.99-2.030.25881550.2112841X-RAY DIFFRACTION96
2.03-2.080.2531780.20062881X-RAY DIFFRACTION96
2.08-2.130.22211380.18052882X-RAY DIFFRACTION95
2.13-2.180.21031540.17912874X-RAY DIFFRACTION95
2.18-2.240.23151560.1862856X-RAY DIFFRACTION95
2.24-2.310.22951400.18692871X-RAY DIFFRACTION95
2.31-2.380.23661500.18362902X-RAY DIFFRACTION95
2.38-2.460.24191530.17932816X-RAY DIFFRACTION94
2.46-2.560.20871550.17922811X-RAY DIFFRACTION93
2.56-2.680.21281720.18042811X-RAY DIFFRACTION93
2.68-2.820.21341330.18232749X-RAY DIFFRACTION90
2.82-30.23791280.18472667X-RAY DIFFRACTION87
3-3.230.21531180.17782244X-RAY DIFFRACTION74
3.23-3.550.19081630.16712856X-RAY DIFFRACTION94
3.55-4.070.17061570.14593000X-RAY DIFFRACTION99
4.07-5.120.15961810.13483026X-RAY DIFFRACTION99
5.13-49.130.20291460.17663087X-RAY DIFFRACTION99

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