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- PDB-8auj: OPR3 Y190F variant in complex with ethyl (Z)-2-(hydroxyimino)-3-o... -

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Basic information

Entry
Database: PDB / ID: 8auj
TitleOPR3 Y190F variant in complex with ethyl (Z)-2-(hydroxyimino)-3-oxobutanoate
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-L9I / 12-oxophytodienoate reductase 3
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 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)90,6108
Polymers89,2552
Non-polymers1,3556
Water10,575587
1
A: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3054
Polymers44,6271
Non-polymers6783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3054
Polymers44,6271
Non-polymers6783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.456, 92.724, 90.343
Angle α, β, γ (deg.)90.000, 99.314, 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: 44627.465 Da / Num. of mol.: 2 / Mutation: Y190F
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
#3: Chemical ChemComp-L9I / ethyl (2Z)-2-hydroxyimino-3-oxidanylidene-butanoate


Mass: 159.140 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H9NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 587 / 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: 2.35 Å3/Da / Density % sol: 47.58 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM (Tris (base); BICINE) pH 8.5; 20 mM Sodium formate; 20 mM Ammonium acetate; 20 mM Sodium citrate tribasic dihydrate; 20 mM Potassium sodium tartrate tetrahydrate; 20 mM Sodium oxamate; ...Details: 100 mM (Tris (base); BICINE) pH 8.5; 20 mM Sodium formate; 20 mM Ammonium acetate; 20 mM Sodium citrate tribasic dihydrate; 20 mM Potassium sodium tartrate tetrahydrate; 20 mM Sodium oxamate; 20% v/v Ethylene glycol; 10 % w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.57→40.17 Å / Num. obs: 210187 / % possible obs: 94.97 % / Redundancy: 1.8 % / Biso Wilson estimate: 17.43 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.31
Reflection shellResolution: 1.57→1.626 Å / Num. unique obs: 21511 / CC1/2: 0.862

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction
AutoProcessdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3hgs

3hgs


Resolution: 1.57→40.17 Å / SU ML: 0.1225 / Cross valid method: FREE R-VALUE / σ(F): 1.06 / Phase error: 16.6599
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1634 1155 1.05 %
Rwork0.1546 108842 -
obs0.1547 109997 97.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.95 Å2
Refinement stepCycle: LAST / Resolution: 1.57→40.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5728 0 92 587 6407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00546237
X-RAY DIFFRACTIONf_angle_d0.78148513
X-RAY DIFFRACTIONf_chiral_restr0.0541909
X-RAY DIFFRACTIONf_plane_restr0.00861132
X-RAY DIFFRACTIONf_dihedral_angle_d13.49632333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.640.22891400.19213160X-RAY DIFFRACTION94.28
1.64-1.720.17951460.176413759X-RAY DIFFRACTION98.89
1.72-1.830.19421460.16413785X-RAY DIFFRACTION98.6
1.83-1.970.17831460.156413730X-RAY DIFFRACTION98.38
1.97-2.170.18261460.156813753X-RAY DIFFRACTION98.64
2.17-2.480.17341400.159313163X-RAY DIFFRACTION93.99
2.48-3.130.16211460.160913803X-RAY DIFFRACTION98.57
3.13-40.170.13741450.139513689X-RAY DIFFRACTION96.63

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