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

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Basic information

Entry
Database: PDB / ID: 8aua
Title12-oxophytodienoate reductase 3 (OPR3) from Solanum lycopersicum 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: 1.9 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)90,0336
Polymers88,8022
Non-polymers1,2314
Water8,701483
1
A: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0173
Polymers44,4011
Non-polymers6152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0173
Polymers44,4011
Non-polymers6152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.521, 90.797, 89.945
Angle α, β, γ (deg.)90.000, 98.721, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 10 through 23 or resid 25...
d_2ens_1(chain "B" and (resid 10 through 23 or resid 25...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASNLEUA1 - 14
d_12ens_1HISTHRA16 - 61
d_13ens_1ALATHRA63 - 120
d_14ens_1PROSERA123 - 125
d_15ens_1ARGVALA127 - 213
d_16ens_1ALAVALA215 - 217
d_17ens_1ALALEUA219 - 244
d_18ens_1LEUHISA246 - 260
d_19ens_1GLYTHRA262 - 271
d_110ens_1PROASNA273 - 346
d_111ens_1LYSLEUA348 - 365
d_112ens_1FMNFMNB
d_113ens_1YYYYYYC
d_21ens_1ASNLEUD1 - 14
d_22ens_1HISTHRD16 - 61
d_23ens_1ALATHRD63 - 120
d_24ens_1PROSERD123 - 125
d_25ens_1ARGVALD127 - 213
d_26ens_1ALAVALD215 - 217
d_27ens_1ALALEUD219 - 244
d_28ens_1LEUHISD246 - 260
d_29ens_1GLYTHRD262 - 271
d_210ens_1PROASND273 - 346
d_211ens_1LYSLEUD348 - 365
d_212ens_1FMNFMNE
d_213ens_1YYYYYYF

NCS oper: (Code: givenMatrix: (-0.954337916474, 0.00102206977701, -0.298727461999), (-0.000789647794504, -0.999999284361, -0.000898739649914), (-0.298728166793, -0.000621811843427, 0.954338040589) ...NCS oper: (Code: given
Matrix: (-0.954337916474, 0.00102206977701, -0.298727461999), (-0.000789647794504, -0.999999284361, -0.000898739649914), (-0.298728166793, -0.000621811843427, 0.954338040589)
Vector: -6.79731971229, -21.3208729202, 44.4451777117)

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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-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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / 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: 2.25 Å3/Da / Density % sol: 45.35 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM carboxylic acid mix (0.02M Sodium formate; 0.02M Ammonium acetate; 0.02M Sodium citrate tribasic dihydrate; 0.02M Potassium sodium tartrate tetrahydrate; 0.02M Sodium oxamate), 20% ...Details: 100 mM carboxylic acid mix (0.02M Sodium formate; 0.02M Ammonium acetate; 0.02M Sodium citrate tribasic dihydrate; 0.02M Potassium sodium tartrate tetrahydrate; 0.02M Sodium oxamate), 20% v/v Ethylene glycol; 10 % w/v PEG 8000, 100 mM Tris (base), BICINE pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.978564 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978564 Å / Relative weight: 1
ReflectionResolution: 1.9→48.95 Å / Num. obs: 102290 / % possible obs: 93.04 % / Redundancy: 1.8 % / Biso Wilson estimate: 20.15 Å2 / CC1/2: 0.988 / Net I/σ(I): 6.2
Reflection shellResolution: 1.9→1.968 Å / Num. unique obs: 4029 / CC1/2: 0.584

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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: 1.9→48.95 Å / SU ML: 0.2768 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.0419
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2683 2753 4.77 %
Rwork0.2094 54941 -
obs0.2122 57694 93.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.34 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5704 0 84 483 6271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076038
X-RAY DIFFRACTIONf_angle_d0.98219
X-RAY DIFFRACTIONf_chiral_restr0.0557888
X-RAY DIFFRACTIONf_plane_restr0.00941078
X-RAY DIFFRACTIONf_dihedral_angle_d13.75452229
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.369287507395 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.2942360.3223900X-RAY DIFFRACTION30.33
1.93-1.970.34591650.28752928X-RAY DIFFRACTION99.42
1.97-2.010.30271360.25842908X-RAY DIFFRACTION99.25
2.01-2.050.31471530.2632905X-RAY DIFFRACTION99.06
2.05-2.090.35591420.26592913X-RAY DIFFRACTION98.42
2.09-2.140.31881350.23862895X-RAY DIFFRACTION98.38
2.14-2.190.28351380.23652901X-RAY DIFFRACTION99.18
2.19-2.250.3187720.25791568X-RAY DIFFRACTION52.26
2.25-2.320.27731450.24122890X-RAY DIFFRACTION99.15
2.32-2.390.32791500.23022918X-RAY DIFFRACTION99.13
2.39-2.480.31051660.23662890X-RAY DIFFRACTION99.09
2.48-2.580.27171420.22842930X-RAY DIFFRACTION98.81
2.58-2.70.31011540.23982870X-RAY DIFFRACTION98.6
2.7-2.840.29181300.21622945X-RAY DIFFRACTION99.26
2.84-3.020.29011520.21332925X-RAY DIFFRACTION99.03
3.02-3.250.27561370.21022916X-RAY DIFFRACTION98.29
3.25-3.580.24061500.18862896X-RAY DIFFRACTION97.85
3.58-4.090.2621550.17292898X-RAY DIFFRACTION97.98
4.09-5.160.18261450.15622938X-RAY DIFFRACTION98.5
5.16-48.950.22191500.17793007X-RAY DIFFRACTION99.21

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