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- PDB-8qn9: OPR3 variant - R283E -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8qn9
TitleOPR3 variant - R283E
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 / 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
DepositionSep 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0444
Polymers44,3731
Non-polymers6713
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-28 kcal/mol
Surface area13600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.680, 89.780, 49.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
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 / 12-oxophytodienoate-10 / 11-reductase 3 / OPDA-reductase 3 / LeOPR3


Mass: 44373.121 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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.19 Å3/Da / Density % sol: 43.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM MES/Tris, 50 mM ammonium sufate, 14% 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: 1.6→43.84 Å / Num. obs: 48262 / % possible obs: 92.4 % / Redundancy: 6.5 % / Biso Wilson estimate: 23.13 Å2 / CC1/2: 0.998 / Net I/σ(I): 15.41
Reflection shellResolution: 1.6→1.63 Å / Num. unique obs: 1770 / CC1/2: 0.458

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Processing

Software
NameVersionClassification
PHENIX(dev_4761: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→43.84 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1818 2414 5 %
Rwork0.1524 --
obs0.1539 48262 92.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→43.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2807 0 13 317 3137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122903
X-RAY DIFFRACTIONf_angle_d1.1543956
X-RAY DIFFRACTIONf_dihedral_angle_d13.8561049
X-RAY DIFFRACTIONf_chiral_restr0.058435
X-RAY DIFFRACTIONf_plane_restr0.013508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.630.3362890.28931681X-RAY DIFFRACTION59
1.63-1.670.26531000.25711909X-RAY DIFFRACTION67
1.67-1.710.2591190.22052250X-RAY DIFFRACTION77
1.71-1.750.23961410.20052680X-RAY DIFFRACTION94
1.75-1.80.19981480.1812810X-RAY DIFFRACTION97
1.8-1.850.21171460.17112774X-RAY DIFFRACTION97
1.85-1.910.20261490.16542841X-RAY DIFFRACTION98
1.91-1.980.20161500.15442854X-RAY DIFFRACTION98
1.98-2.060.18591500.14472841X-RAY DIFFRACTION98
2.06-2.150.17351460.14542781X-RAY DIFFRACTION96
2.15-2.260.18861500.13412853X-RAY DIFFRACTION98
2.26-2.410.17491510.13112864X-RAY DIFFRACTION99
2.41-2.590.15121530.1392911X-RAY DIFFRACTION99
2.59-2.850.18071530.14442907X-RAY DIFFRACTION99
2.85-3.260.17021500.14992846X-RAY DIFFRACTION97
3.27-4.110.15451570.14012972X-RAY DIFFRACTION99
4.11-43.840.19261620.15893074X-RAY DIFFRACTION98

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