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- PDB-8aun: OPR3 Y370F variant in complex with ethyl (Z)-2-(hydroxyimino)-3-o... -

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Basic information

Entry
Database: PDB / ID: 8aun
TitleOPR3 Y370F 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 / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 12-oxophytodienoate reductase 3
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 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

Downloads & links

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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)91,17715
Polymers89,2552
Non-polymers1,92213
Water11,494638
1
A: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5797
Polymers44,6271
Non-polymers9526
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5978
Polymers44,6271
Non-polymers9707
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.312, 92.833, 90.151
Angle α, β, γ (deg.)90.000, 99.322, 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

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Protein , 1 types, 2 molecules AB

#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: Y370F
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

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Non-polymers , 6 types, 651 molecules

#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-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.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 638 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM (Imidazole; MES monohydrate (acid)) pH 6.5; 20 mM Sodium formate; 20 mM Ammonium acetate; 20 mM Sodium citrate tribasic dihydrate; 20 mM Potassium sodium tartrate tetrahydrate; 20 mM ...Details: 100 mM (Imidazole; MES monohydrate (acid)) pH 6.5; 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: 1.49→40.11 Å / Num. obs: 241139 / % possible obs: 93.85 % / Redundancy: 1.9 % / Biso Wilson estimate: 15.84 Å2 / CC1/2: 0.994 / Net I/σ(I): 9.49
Reflection shellResolution: 1.49→1.545 Å / Num. unique obs: 20980 / CC1/2: 0.874

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Processing

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

3hgs


Resolution: 1.49→40.11 Å / SU ML: 0.1078 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 17.1763
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1756 1328 1.05 %
Rwork0.1576 125193 -
obs0.1578 126521 97.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.03 Å2
Refinement stepCycle: LAST / Resolution: 1.49→40.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5727 0 129 638 6494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00556248
X-RAY DIFFRACTIONf_angle_d0.85768504
X-RAY DIFFRACTIONf_chiral_restr0.0808907
X-RAY DIFFRACTIONf_plane_restr0.00561127
X-RAY DIFFRACTIONf_dihedral_angle_d21.23132313
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.550.23381330.188512528X-RAY DIFFRACTION88.12
1.55-1.620.17741500.166514164X-RAY DIFFRACTION99.83
1.62-1.710.19521520.155914267X-RAY DIFFRACTION99.79
1.71-1.810.16111500.154314183X-RAY DIFFRACTION99.44
1.81-1.950.19581500.158314084X-RAY DIFFRACTION98.79
1.95-2.150.17941480.157513990X-RAY DIFFRACTION97.69
2.15-2.460.1721440.160313546X-RAY DIFFRACTION94.79
2.46-3.10.15651510.164914240X-RAY DIFFRACTION99.39
3.1-40.110.17591500.148914191X-RAY DIFFRACTION98.08

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