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- PDB-8qna: OPR3 variant - R366A -

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Basic information

Entry
Database: PDB / ID: 8qna
TitleOPR3 variant - R366A
Components12-oxophytodienoate reductase 3
KeywordsFLAVOPROTEIN / Old Yellow Enzyme / ene-reductase / flavoenzyme / oxidoreductase
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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 12-oxophytodienoate reductase 3
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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)45,6114
Polymers44,3151
Non-polymers1,2963
Water7,638424
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)88.250, 90.330, 49.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein 12-oxophytodienoate reductase 3


Mass: 44315.086 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-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#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.: 424 / Source method: isolated from a natural source / Formula: H2O
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: 2.21 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, 18% 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: Mar 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.5→49.17 Å / Num. obs: 62151 / % possible obs: 97.54 % / Redundancy: 8.9 % / Biso Wilson estimate: 18.74 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.41
Reflection shellResolution: 1.5→1.52 Å / Num. unique obs: 62149 / CC1/2: 0.281

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Processing

Software
NameVersionClassification
PHENIXdev_4761refinement
PHENIXdev_4761refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→49.17 Å / SU ML: 0.2031 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.9783
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1938 3108 5 %
Rwork0.1539 59043 -
obs0.1559 62151 97.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.56 Å2
Refinement stepCycle: LAST / Resolution: 1.5→49.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2772 0 67 426 3265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00782922
X-RAY DIFFRACTIONf_angle_d1.03983990
X-RAY DIFFRACTIONf_chiral_restr0.0579440
X-RAY DIFFRACTIONf_plane_restr0.0104509
X-RAY DIFFRACTIONf_dihedral_angle_d14.69591038
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.33911190.3122269X-RAY DIFFRACTION83.55
1.52-1.550.32681340.2892541X-RAY DIFFRACTION93.86
1.55-1.580.31891390.25892648X-RAY DIFFRACTION97.28
1.58-1.60.28421400.23782643X-RAY DIFFRACTION97.58
1.6-1.630.2841400.21292670X-RAY DIFFRACTION97.67
1.63-1.670.28081390.20522635X-RAY DIFFRACTION97.88
1.67-1.70.23481420.19132692X-RAY DIFFRACTION97.99
1.7-1.740.26851400.1782670X-RAY DIFFRACTION98.42
1.74-1.790.22721390.17792650X-RAY DIFFRACTION98.41
1.79-1.840.2261430.16872717X-RAY DIFFRACTION98.38
1.84-1.890.20011390.1742635X-RAY DIFFRACTION96.59
1.89-1.950.21571410.15412672X-RAY DIFFRACTION98.36
1.95-2.020.22521430.13962711X-RAY DIFFRACTION98.79
2.02-2.10.19971420.13092707X-RAY DIFFRACTION98.65
2.1-2.20.18911430.13052713X-RAY DIFFRACTION99.2
2.2-2.310.17651430.12322729X-RAY DIFFRACTION99.17
2.31-2.460.17611460.13032766X-RAY DIFFRACTION99.52
2.46-2.650.17591420.14232694X-RAY DIFFRACTION98.4
2.65-2.910.18691450.14712755X-RAY DIFFRACTION98.24
2.91-3.340.15751460.14462781X-RAY DIFFRACTION99.69
3.34-4.20.16311490.13642819X-RAY DIFFRACTION99.73
4.2-49.170.17281540.15612926X-RAY DIFFRACTION98.43

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