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

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Basic information

Entry
Database: PDB / ID: 8aum
TitleOPR3 Y190F variant 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: 1.35 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)91,20711
Polymers89,2552
Non-polymers1,9529
Water11,620645
1
A: 12-oxophytodienoate reductase 3
hetero molecules


  • defined by author
  • 45.9 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)45,9508
Polymers44,6271
Non-polymers1,3227
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2573
Polymers44,6271
Non-polymers6302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.380, 92.100, 89.960
Angle α, β, γ (deg.)90.000, 99.110, 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 , 6 types, 654 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-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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 645 / 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: 2.26 Å3/Da / Density % sol: 45.65 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM (Sodium HEPES; MOPS (acid)) pH 7.5; 30 mM Sodium nitrate; 30 mM Sodium phosphate dibasic; 30 mM Ammonium sulphate; 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: 1.35→45.92 Å / Num. obs: 317534 / % possible obs: 95.14 % / Redundancy: 1.8 % / Biso Wilson estimate: 14.42 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.19
Reflection shellResolution: 1.35→1.398 Å / Num. unique obs: 15988 / CC1/2: 0.967

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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: 1.35→45.92 Å / SU ML: 0.1147 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.5068
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1836 2099 1.27 %
Rwork0.1645 163483 -
obs0.1647 165582 95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.38 Å2
Refinement stepCycle: LAST / Resolution: 1.35→45.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5718 0 126 645 6489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00526496
X-RAY DIFFRACTIONf_angle_d0.82768882
X-RAY DIFFRACTIONf_chiral_restr0.0796938
X-RAY DIFFRACTIONf_plane_restr0.00861194
X-RAY DIFFRACTIONf_dihedral_angle_d13.86132456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.380.27111320.222710235X-RAY DIFFRACTION89.57
1.38-1.410.23621370.202710722X-RAY DIFFRACTION93.23
1.41-1.450.23111370.193310627X-RAY DIFFRACTION93.02
1.45-1.50.23291390.196110818X-RAY DIFFRACTION94.72
1.5-1.540.21911400.187710847X-RAY DIFFRACTION94.9
1.54-1.60.22551350.181810629X-RAY DIFFRACTION93.05
1.6-1.660.16711420.174211060X-RAY DIFFRACTION96.57
1.66-1.740.1941420.172411078X-RAY DIFFRACTION96.65
1.74-1.830.19651430.174711119X-RAY DIFFRACTION96.74
1.83-1.950.17721420.168911000X-RAY DIFFRACTION96.36
1.95-2.10.19131400.167110943X-RAY DIFFRACTION95.51
2.1-2.310.19271390.162110805X-RAY DIFFRACTION93.94
2.31-2.640.16311440.166911235X-RAY DIFFRACTION97.72
2.64-3.330.18661450.161211254X-RAY DIFFRACTION97.64
3.33-45.920.15771420.143111111X-RAY DIFFRACTION95.28

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