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- PDB-8qne: OPR3 variant with redesigned loop 6 (9aa) -

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Basic information

Entry
Database: PDB / ID: 8qne
TitleOPR3 variant with redesigned loop 6 (9aa)
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 / 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 26, 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)44,9147
Polymers43,7691
Non-polymers1,1456
Water6,503361
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)87.360, 90.100, 49.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 12-oxophytodienoate reductase 3 / 12-oxophytodienoate-10 / 11-reductase 3 / OPDA-reductase 3 / LeOPR3


Mass: 43768.520 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, 12-oxophytodienoate reductase

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Non-polymers , 5 types, 367 molecules

#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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.38 Å3/Da / Density % sol: 48.35 %
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 II, DESY / Beamline: PETRA1 / Wavelength: 1.03323 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: 1.03323 Å / Relative weight: 1
ReflectionResolution: 1.4→43.68 Å / Num. obs: 907508 / % possible obs: 97.17 % / Redundancy: 12.1 % / CC1/2: 0.999 / Net I/σ(I): 18.31
Reflection shellResolution: 1.4→1.42 Å / Num. unique obs: 75301 / CC1/2: 0.38

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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→43.68 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1823 3766 5 %
Rwork0.1586 --
obs0.1598 75302 97.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→43.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2801 0 76 362 3239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0222981
X-RAY DIFFRACTIONf_angle_d1.4934062
X-RAY DIFFRACTIONf_dihedral_angle_d11.607433
X-RAY DIFFRACTIONf_chiral_restr0.112444
X-RAY DIFFRACTIONf_plane_restr0.018523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.3211060.30942015X-RAY DIFFRACTION75
1.42-1.440.28181150.28052191X-RAY DIFFRACTION81
1.44-1.460.33211200.26482277X-RAY DIFFRACTION84
1.46-1.480.24351290.26372443X-RAY DIFFRACTION92
1.48-1.50.26641370.24872605X-RAY DIFFRACTION96
1.5-1.520.25351380.22052630X-RAY DIFFRACTION99
1.52-1.550.25691430.20852706X-RAY DIFFRACTION99
1.55-1.570.21561400.18522654X-RAY DIFFRACTION100
1.57-1.60.19351420.17792702X-RAY DIFFRACTION100
1.6-1.630.20611420.1672694X-RAY DIFFRACTION100
1.63-1.670.19121420.16372698X-RAY DIFFRACTION100
1.67-1.70.20361440.16032733X-RAY DIFFRACTION100
1.7-1.740.19431410.15962688X-RAY DIFFRACTION100
1.74-1.790.18261420.162699X-RAY DIFFRACTION100
1.79-1.830.20171430.16182721X-RAY DIFFRACTION100
1.83-1.890.21061420.16832687X-RAY DIFFRACTION100
1.89-1.950.18321430.16052718X-RAY DIFFRACTION100
1.95-2.020.1941430.15472714X-RAY DIFFRACTION100
2.02-2.10.18161430.15572726X-RAY DIFFRACTION100
2.1-2.20.19031440.15462729X-RAY DIFFRACTION100
2.2-2.310.18221440.1552732X-RAY DIFFRACTION100
2.31-2.460.17671450.15672754X-RAY DIFFRACTION100
2.46-2.650.18981430.16772726X-RAY DIFFRACTION100
2.65-2.910.19321460.15842770X-RAY DIFFRACTION100
2.91-3.330.17511460.15292785X-RAY DIFFRACTION100
3.33-4.20.15281480.1362807X-RAY DIFFRACTION100
4.2-43.680.16161550.1472932X-RAY DIFFRACTION99

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