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- PDB-8qn3: OPR3 wildtype in complex with NADH4 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8qn3
TitleOPR3 wildtype in complex with NADH4
Components12-oxophytodienoate reductase 3
KeywordsFLAVOPROTEIN / Old yellow enzyme / ene-reductase / flavoenzyme / oxidoreductase
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-WI6 / 12-oxophytodienoate reductase 3
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBijelic, A. / Macheroux, P. / Keschbaumer, B.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science Fund Austria
CitationJournal: Febs J. / Year: 2024
Title: Loop 6 and the beta-hairpin flap are structural hotspots that determine cofactor specificity in the FMN-dependent family of ene-reductases.
Authors: Kerschbaumer, B. / Totaro, M.G. / Friess, M. / Breinbauer, R. / Bijelic, A. / Macheroux, P.
History
DepositionSep 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)91,2428
Polymers88,8022
Non-polymers2,4406
Water5,098283
1
A: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7175
Polymers44,4011
Non-polymers1,3164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5253
Polymers44,4011
Non-polymers1,1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.740, 89.460, 81.020
Angle α, β, γ (deg.)90.000, 107.401, 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: 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 (E. coli) / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-WI6 / 1,4,5,6-Tetrahydronicotinamide adenine dinucleotide / [[(2R,3S,4R,5R)-5-[(3S)-3-aminocarbonyl-3,6-dihydro-2H-pyridin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2S,3R,4S,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate


Mass: 667.457 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H31N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 45.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM MES/Tris, 10 mM ammonium sulfate, 12% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.75→46.91 Å / Num. obs: 1468942 / % possible obs: 99.9 % / Redundancy: 18.6 % / Biso Wilson estimate: 34.37 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.51
Reflection shellResolution: 1.75→1.77 Å / Num. unique obs: 2748 / CC1/2: 0.742

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Processing

Software
NameVersionClassification
PHENIXdev_4761refinement
PHENIXdev_4761refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→46.91 Å / SU ML: 0.2539 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.4204
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2249 3953 5 %
Rwork0.2004 75121 -
obs0.2016 79074 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.88 Å2
Refinement stepCycle: LAST / Resolution: 1.75→46.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5414 0 124 283 5821
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00545671
X-RAY DIFFRACTIONf_angle_d0.73887750
X-RAY DIFFRACTIONf_chiral_restr0.0495865
X-RAY DIFFRACTIONf_plane_restr0.0065993
X-RAY DIFFRACTIONf_dihedral_angle_d16.00121978
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.770.50091370.45272613X-RAY DIFFRACTION99.57
1.77-1.790.40241420.38632688X-RAY DIFFRACTION99.93
1.79-1.820.34451390.34682659X-RAY DIFFRACTION99.68
1.82-1.840.28461410.29622678X-RAY DIFFRACTION99.86
1.84-1.870.28111430.27022714X-RAY DIFFRACTION99.9
1.87-1.90.33081380.25612616X-RAY DIFFRACTION99.96
1.9-1.930.2821430.23272712X-RAY DIFFRACTION99.93
1.93-1.960.23291390.21512644X-RAY DIFFRACTION99.93
1.96-1.990.22451420.21272706X-RAY DIFFRACTION99.89
1.99-2.030.26821400.21792649X-RAY DIFFRACTION99.96
2.03-2.070.25741410.22332684X-RAY DIFFRACTION99.93
2.07-2.110.24791400.22842668X-RAY DIFFRACTION99.96
2.11-2.150.25481420.2182698X-RAY DIFFRACTION99.86
2.15-2.20.22191400.21672659X-RAY DIFFRACTION99.82
2.2-2.260.26091410.2162674X-RAY DIFFRACTION99.96
2.26-2.320.25171430.20492714X-RAY DIFFRACTION99.76
2.32-2.390.21451380.20712631X-RAY DIFFRACTION99.89
2.39-2.470.22381420.20862695X-RAY DIFFRACTION100
2.47-2.550.23021420.19952691X-RAY DIFFRACTION100
2.55-2.660.23271410.21252685X-RAY DIFFRACTION100
2.66-2.780.23471410.21292681X-RAY DIFFRACTION99.96
2.78-2.920.24121420.20942700X-RAY DIFFRACTION99.89
2.92-3.110.20961420.20412693X-RAY DIFFRACTION99.96
3.11-3.350.24011420.2012690X-RAY DIFFRACTION100
3.35-3.680.18651420.18972699X-RAY DIFFRACTION100
3.68-4.220.19411420.17342703X-RAY DIFFRACTION100
4.22-5.310.21841430.17192718X-RAY DIFFRACTION99.97
5.31-46.910.20311450.18292759X-RAY DIFFRACTION99.83

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