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- PDB-8qnp: OPR3 with redesigned loop 6 (9aa) in complex with NADH4 -

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Basic information

Entry
Database: PDB / ID: 8qnp
TitleOPR3 with redesigned loop 6 (9aa) in complex with NADH4
Components12-oxophytodienoate reductase 3
KeywordsFLAVOPROTEIN / Oly yellow enzyme / flavoenzyme / ene-reductase
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: 2 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,30911
Polymers87,5372
Non-polymers2,7729
Water6,810378
1
A: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2036
Polymers43,7691
Non-polymers1,4345
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1075
Polymers43,7691
Non-polymers1,3384
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.270, 91.790, 89.450
Angle α, β, γ (deg.)90.00, 98.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 12-oxophytodienoate reductase 3


Mass: 43768.520 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

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Non-polymers , 5 types, 387 molecules

#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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.29 Å3/Da / Density % sol: 46.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM MES/Tris, 50 mM ammonium sulfate, 12% 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: 2→45.9 Å / Num. obs: 365496 / % possible obs: 98.6 % / Redundancy: 7 % / CC1/2: 0.994 / Net I/σ(I): 6.09
Reflection shellResolution: 2→2.04 Å / Num. unique obs: 2756 / CC1/2: 0.462

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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: 2→45.9 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2393 2624 5 %
Rwork0.2128 --
obs0.2141 52479 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→45.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5532 0 145 381 6058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0175810
X-RAY DIFFRACTIONf_angle_d0.9797923
X-RAY DIFFRACTIONf_dihedral_angle_d16.632069
X-RAY DIFFRACTIONf_chiral_restr0.045876
X-RAY DIFFRACTIONf_plane_restr0.0051011
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.34681380.32732618X-RAY DIFFRACTION99
2.04-2.080.35141380.3252619X-RAY DIFFRACTION99
2.08-2.120.33581360.30512597X-RAY DIFFRACTION99
2.12-2.160.31551380.28822618X-RAY DIFFRACTION99
2.16-2.210.34911370.27892626X-RAY DIFFRACTION99
2.21-2.270.30241330.27012517X-RAY DIFFRACTION96
2.27-2.330.281380.25622618X-RAY DIFFRACTION98
2.33-2.40.26941370.25322608X-RAY DIFFRACTION99
2.4-2.480.29911400.23462664X-RAY DIFFRACTION99
2.48-2.570.30581380.23422627X-RAY DIFFRACTION99
2.57-2.670.27211380.2362613X-RAY DIFFRACTION99
2.67-2.790.28631410.22182678X-RAY DIFFRACTION99
2.79-2.940.26431370.20992614X-RAY DIFFRACTION99
2.94-3.120.23671390.20452630X-RAY DIFFRACTION99
3.12-3.360.25511350.20532551X-RAY DIFFRACTION95
3.36-3.70.23041390.18292658X-RAY DIFFRACTION100
3.7-4.230.17131400.17492665X-RAY DIFFRACTION100
4.23-5.330.20251410.16842676X-RAY DIFFRACTION100
5.33-45.90.17481410.19692658X-RAY DIFFRACTION97

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