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- PDB-9fcp: OPR3 loop swap variant L6(AchrOYE4) in complex with NADH4 -

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Basic information

Entry
Database: PDB / ID: 9fcp
TitleOPR3 loop swap variant L6(AchrOYE4) in complex with NADH4
Components12-oxophytodienoate reductase 3,Old yellow enzyme OYE4
KeywordsFLAVOPROTEIN / Flavoenzymes / ene-reductases / old yellow enzymes / coenzymes
Function / homology
Function and homology information


NADPH dehydrogenase / 12-oxophytodienoate reductase / 12-oxophytodienoate reductase activity / oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / jasmonic acid biosynthetic process / oxylipin biosynthetic process / NADPH dehydrogenase activity / peroxisome / FMN binding / identical protein binding / cytosol
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 / Old yellow enzyme OYE4 / 12-oxophytodienoate reductase 3
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
Achromobacter sp. JA81 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBijelic, A. / Kerschbaumer, B. / Macheroux, P.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science Fund Austria
CitationJournal: To Be Published
Title: Insights into the complexity of coenzyme specificity in ene-reductases
Authors: Kerschaumer, B. / Macheroux, P. / Bijelic, A.
History
DepositionMay 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 12-oxophytodienoate reductase 3,Old yellow enzyme OYE4
B: 12-oxophytodienoate reductase 3,Old yellow enzyme OYE4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,5836
Polymers88,3362
Non-polymers2,2484
Water7,981443
1
A: 12-oxophytodienoate reductase 3,Old yellow enzyme OYE4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2923
Polymers44,1681
Non-polymers1,1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 12-oxophytodienoate reductase 3,Old yellow enzyme OYE4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2923
Polymers44,1681
Non-polymers1,1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.190, 92.960, 89.710
Angle α, β, γ (deg.)90.000, 97.928, 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,Old yellow enzyme OYE4 / 12-oxophytodienoate-10 / 11-reductase 3 / OPDA-reductase 3 / LeOPR3


Mass: 44167.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato), (gene. exp.) Achromobacter sp. JA81 (bacteria)
Gene: OPR3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9FEW9, UniProt: I3V5V6, 12-oxophytodienoate reductase, NADPH dehydrogenase
#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-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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.3 Å3/Da / Density % sol: 46.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Tris-HCl, 50 mM sodium tartrate, 16-20% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2→45.44 Å / Num. obs: 52186 / % possible obs: 96.55 % / Redundancy: 4.7 % / Biso Wilson estimate: 35.59 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.1776 / Net I/σ(I): 5.55
Reflection shellResolution: 2→2.04 Å / Rmerge(I) obs: 1.829 / Num. unique obs: 2781 / CC1/2: 0.311

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→45.44 Å / SU ML: 0.3061 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.2779
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2289 2607 5 %
Rwork0.1932 49579 -
obs0.195 52186 96.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.09 Å2
Refinement stepCycle: LAST / Resolution: 2→45.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5449 0 105 449 6003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00235686
X-RAY DIFFRACTIONf_angle_d0.5467747
X-RAY DIFFRACTIONf_chiral_restr0.0432860
X-RAY DIFFRACTIONf_plane_restr0.0035993
X-RAY DIFFRACTIONf_dihedral_angle_d17.4852095
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.40111390.38162642X-RAY DIFFRACTION97.85
2.04-2.080.35351370.3312611X-RAY DIFFRACTION97.83
2.08-2.120.3421400.30332656X-RAY DIFFRACTION97.46
2.12-2.160.35731360.29282576X-RAY DIFFRACTION97.27
2.16-2.210.3141380.26662628X-RAY DIFFRACTION97.5
2.21-2.270.33241400.26112645X-RAY DIFFRACTION97.99
2.27-2.330.29651380.25192650X-RAY DIFFRACTION97.76
2.33-2.40.29281370.24332604X-RAY DIFFRACTION97.37
2.4-2.480.26391390.23682629X-RAY DIFFRACTION97.5
2.48-2.570.28591390.22582670X-RAY DIFFRACTION98.11
2.57-2.670.25451370.21772590X-RAY DIFFRACTION97.05
2.67-2.790.23921370.20632616X-RAY DIFFRACTION96.97
2.79-2.940.22611380.19522633X-RAY DIFFRACTION96.96
2.94-3.120.22351340.19442550X-RAY DIFFRACTION94.67
3.12-3.360.23061180.18372237X-RAY DIFFRACTION82.89
3.36-3.70.20371310.16312490X-RAY DIFFRACTION91.58
3.7-4.230.16121410.14692692X-RAY DIFFRACTION99.37
4.23-5.330.17341430.13962721X-RAY DIFFRACTION99.38
5.33-45.440.19951450.16972739X-RAY DIFFRACTION98.97

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