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- PDB-8aub: 12-oxophytodienoate reductase 3 (OPR3) from Solanum lycopersicum ... -

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Basic information

Entry
Database: PDB / ID: 8aub
Title12-oxophytodienoate reductase 3 (OPR3) from Solanum lycopersicum in complex with ethyl (Z)-2-(hydroxyimino)-3-oxopentanoate
Components12-oxophytodienoate reductase 3
KeywordsOXIDOREDUCTASE / Ene-reductase / oxime / FMN / complex
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-O8I / DI(HYDROXYETHYL)ETHER / 12-oxophytodienoate reductase 3
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsPolidori, N. / Gruber, K.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science Fund Austria
CitationJournal: Acs Catalysis / Year: 2023
Title: Mechanistic Insights into the Ene-Reductase-Catalyzed Promiscuous Reduction of Oximes to Amines.
Authors: Breukelaar, W.B. / Polidori, N. / Singh, A. / Daniel, B. / Glueck, S.M. / Gruber, K. / Kroutil, W.
History
DepositionAug 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: 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
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)90,59211
Polymers88,8022
Non-polymers1,7909
Water7,260403
1
A: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3496
Polymers44,4011
Non-polymers9485
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2435
Polymers44,4011
Non-polymers8424
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.794, 88.397, 89.921
Angle α, β, γ (deg.)90.000, 99.904, 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: 44401.203 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 BL21(DE3) (bacteria) / References: UniProt: Q9FEW9, 12-oxophytodienoate reductase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-O8I / ethyl (2~{Z})-2-hydroxyimino-3-oxidanylidene-pentanoate / ethyl (Z)-2-(hydroxyimino)-3-oxopentanoate


Mass: 173.167 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.2 Å3/Da / Density % sol: 43.97 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100 mM CaCl2,10 % w/v PEG 8000, 100 mM Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 1.62→44.2 Å / Num. obs: 176405 / % possible obs: 91.63 % / Redundancy: 1.6 % / Biso Wilson estimate: 17.69 Å2 / CC1/2: 0.987 / Net I/σ(I): 5.06
Reflection shellResolution: 1.62→1.678 Å / Num. unique obs: 18096 / CC1/2: 0.619

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
AutoProcessdata processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HGS

3hgs


Resolution: 1.62→44.2 Å / SU ML: 0.1965 / Cross valid method: FREE R-VALUE / σ(F): 0.92 / Phase error: 22.8987
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2145 1852 1.05 %
Rwork0.1921 174168 -
obs0.1924 176020 91.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.33 Å2
Refinement stepCycle: LAST / Resolution: 1.62→44.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5794 0 121 403 6318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00576197
X-RAY DIFFRACTIONf_angle_d0.82078422
X-RAY DIFFRACTIONf_chiral_restr0.0535904
X-RAY DIFFRACTIONf_plane_restr0.00511102
X-RAY DIFFRACTIONf_dihedral_angle_d14.18252283
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.660.32651480.288313935X-RAY DIFFRACTION94.51
1.66-1.710.32751390.265713532X-RAY DIFFRACTION93.28
1.71-1.770.27011420.249613371X-RAY DIFFRACTION91.42
1.77-1.830.27871360.233313008X-RAY DIFFRACTION88.68
1.83-1.90.24261410.233913360X-RAY DIFFRACTION91.53
1.9-1.990.24941480.208613902X-RAY DIFFRACTION94.71
1.99-2.10.24521470.200913686X-RAY DIFFRACTION94.01
2.1-2.230.19421500.188513674X-RAY DIFFRACTION93.82
2.23-2.40.23471430.192913390X-RAY DIFFRACTION91.59
2.4-2.640.21191430.187513362X-RAY DIFFRACTION91.24
2.64-3.020.18711360.190112904X-RAY DIFFRACTION88.32
3.02-3.810.22821310.177312737X-RAY DIFFRACTION86.96
3.81-44.20.1561480.155913307X-RAY DIFFRACTION91.14

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