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- PDB-9em5: OPR3 variant Y364P in its monomeric form -

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Basic information

Entry
Database: PDB / ID: 9em5
TitleOPR3 variant Y364P in its monomeric form
Components12-oxophytodienoate reductase 3
KeywordsFLAVOPROTEIN / ene-reductase / Old Yellow Enzyme
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: 1.6 Å
AuthorsBijelic, A. / Macheroux, P. / Kerschbaumer, B.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science Fund Austria
CitationJournal: Sci Rep / Year: 2024
Title: Analysis of homodimer formation in 12-oxophytodienoate reductase 3 in solutio and crystallo challenges the physiological role of the dimer.
Authors: Kerschbaumer, B. / Macheroux, P. / Bijelic, A.
History
DepositionMar 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9454
Polymers44,3351
Non-polymers6103
Water5,909328
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-27 kcal/mol
Surface area13460 Å2
Unit cell
Length a, b, c (Å)44.338, 89.941, 51.284
Angle α, β, γ (deg.)90.000, 105.634, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 44335.145 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
#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.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.22 Å3/Da / Density % sol: 44.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Tris-HCl (7.5), 50 mM sodium tartrate, 8-16% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.87 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.57→49.39 Å / Num. obs: 54069 / % possible obs: 98.84 % / Redundancy: 3 % / Biso Wilson estimate: 19.57 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.06 / Net I/σ(I): 5.8
Reflection shellResolution: 1.57→1.6 Å / Num. unique obs: 14664 / CC1/2: 0.35 / Rpim(I) all: 1.26

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→49.39 Å / SU ML: 0.2405 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.0772
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2075 2534 4.98 %
Rwork0.1838 48363 -
obs0.185 50897 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25 Å2
Refinement stepCycle: LAST / Resolution: 1.6→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2788 0 40 330 3158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01622897
X-RAY DIFFRACTIONf_angle_d1.39413944
X-RAY DIFFRACTIONf_chiral_restr0.0906435
X-RAY DIFFRACTIONf_plane_restr0.0133509
X-RAY DIFFRACTIONf_dihedral_angle_d16.29411051
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.630.39281140.43262618X-RAY DIFFRACTION97.5
1.63-1.660.44381640.38692660X-RAY DIFFRACTION99.58
1.66-1.70.36291590.33512700X-RAY DIFFRACTION99.69
1.7-1.740.28391430.27852584X-RAY DIFFRACTION99.89
1.74-1.780.27141520.25272715X-RAY DIFFRACTION99.72
1.78-1.830.24511440.21772683X-RAY DIFFRACTION99.96
1.83-1.890.25651350.20762666X-RAY DIFFRACTION99.93
1.89-1.950.24011240.20222730X-RAY DIFFRACTION99.96
1.95-2.020.21191210.2152712X-RAY DIFFRACTION99.89
2.02-2.10.23611400.18032665X-RAY DIFFRACTION100
2.1-2.190.21111640.17312676X-RAY DIFFRACTION99.93
2.19-2.310.21711400.17042699X-RAY DIFFRACTION99.89
2.31-2.450.20771370.1712698X-RAY DIFFRACTION100
2.45-2.640.21821220.17242716X-RAY DIFFRACTION99.96
2.64-2.910.17781470.16912678X-RAY DIFFRACTION100
2.91-3.330.18021470.16652695X-RAY DIFFRACTION99.96
3.33-4.190.17081360.14932718X-RAY DIFFRACTION99.96
4.19-49.390.16031450.1542750X-RAY DIFFRACTION99.9

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