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- PDB-8aul: OPR3 Y190F in complex with 2-methoxyethyl (Z)-2-(hydroxyimino)-3-... -

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Basic information

Entry
Database: PDB / ID: 8aul
TitleOPR3 Y190F in complex with 2-methoxyethyl (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-O8R / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 12-oxophytodienoate reductase 3
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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)90,8028
Polymers89,2552
Non-polymers1,5476
Water10,070559
1
A: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3794
Polymers44,6271
Non-polymers7523
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4234
Polymers44,6271
Non-polymers7963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.370, 93.950, 89.510
Angle α, β, γ (deg.)90.000, 97.400, 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: 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

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Non-polymers , 5 types, 565 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-O8R / 2-methoxyethyl (2~{Z})-2-hydroxyimino-3-oxidanylidene-butanoate / 2-methoxyethyl (Z)-2-(hydroxyimino)-3-oxobutanoate


Mass: 189.166 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11NO5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 559 / 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: 2.22 Å3/Da / Density % sol: 44.66 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM (Imidazole; MES monohydrate (acid)) pH 6.5; 30 mM Magnesium chloride hexahydrate; 30 mM Calcium chloride dihydrate; 20% v/v Glycerol; 10% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03319 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 1.5→41.52 Å / Num. obs: 225197 / % possible obs: 97.89 % / Redundancy: 1.9 % / Biso Wilson estimate: 16.96 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.12
Reflection shellResolution: 1.5→1.554 Å / Num. unique obs: 12353 / CC1/2: 0.695

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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: 1.5→41.52 Å / SU ML: 0.1314 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.456
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1802 1550 1.22 %
Rwork0.1576 124982 -
obs0.1579 126532 97.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.27 Å2
Refinement stepCycle: LAST / Resolution: 1.5→41.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5679 0 105 559 6343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00556094
X-RAY DIFFRACTIONf_angle_d0.82658298
X-RAY DIFFRACTIONf_chiral_restr0.0542892
X-RAY DIFFRACTIONf_plane_restr0.00891092
X-RAY DIFFRACTIONf_dihedral_angle_d14.55662262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.550.25191370.235711063X-RAY DIFFRACTION95.71
1.55-1.60.22741400.205811225X-RAY DIFFRACTION96.92
1.6-1.670.2091400.183411352X-RAY DIFFRACTION98.5
1.67-1.740.21521420.172611459X-RAY DIFFRACTION98.81
1.74-1.840.19361430.163911471X-RAY DIFFRACTION98.91
1.84-1.950.18441410.158411416X-RAY DIFFRACTION98.67
1.95-2.10.16921410.152211340X-RAY DIFFRACTION97.82
2.1-2.310.17391400.151211296X-RAY DIFFRACTION97.33
2.31-2.650.17511420.157411465X-RAY DIFFRACTION98.56
2.65-3.340.20091420.160711450X-RAY DIFFRACTION98.3
3.34-41.520.15211420.141211445X-RAY DIFFRACTION97.21

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