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- PDB-8s8v: OPR3 variant R283D in its monomeric form -

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Basic information

Entry
Database: PDB / ID: 8s8v
TitleOPR3 variant R283D in its monomeric form
Components12-oxophytodienoate reductase 3
KeywordsFLAVOPROTEIN / ene-reductase / Old Yellow Enzyme
Function / homology
Function and homology information


12-oxophytodienoate reductase / 12-oxophytodienoate reductase activity / jasmonic acid biosynthetic process / oxylipin biosynthetic process / FMN binding / peroxisome / 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 / 12-oxophytodienoate reductase 3
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBijelic, A. / Macheroux, P. / Kerschbaumer, B.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science Fund Austria
CitationJournal: Sci Rep / Year: 2024
Title: Analysis of homodimer formation in 12-oxophytodienoate reductase 3 in solutio and crystallo challenges the physiological role of the dimer
Authors: Kerschbaumer, B. / Macheroux, P. / Bijelic, A.
History
DepositionMar 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release

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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)89,6314
Polymers88,7182
Non-polymers9132
Water00
1
A: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8152
Polymers44,3591
Non-polymers4561
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8152
Polymers44,3591
Non-polymers4561
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.390, 89.314, 95.528
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 12-oxophytodienoate reductase 3


Mass: 44359.094 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
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
Has ligand of interestN

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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: 2.08 Å3/Da / Density % sol: 40.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES/Tris (6.5), 10 mM ammonium sulfate, 8-16% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.87 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.69→44.66 Å / Num. obs: 133610 / % possible obs: 94.4 % / Redundancy: 3.6 % / CC1/2: 0.9 / Rpim(I) all: 0.29 / Net I/σ(I): 1.71
Reflection shellResolution: 2.69→2.76 Å / Num. unique obs: 37427 / CC1/2: 0.18 / Rpim(I) all: 0.89

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→44.66 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2966 1445 10.03 %
Rwork0.2497 --
obs0.2545 14404 93.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→44.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5451 0 62 0 5513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055647
X-RAY DIFFRACTIONf_angle_d1.0347706
X-RAY DIFFRACTIONf_dihedral_angle_d14.3851996
X-RAY DIFFRACTIONf_chiral_restr0.061858
X-RAY DIFFRACTIONf_plane_restr0.012999
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.110.33861360.29971226X-RAY DIFFRACTION91
3.11-3.230.33161340.28811284X-RAY DIFFRACTION94
3.23-3.380.3011500.28031301X-RAY DIFFRACTION96
3.38-3.560.32131490.25611307X-RAY DIFFRACTION96
3.56-3.780.34491420.2491283X-RAY DIFFRACTION95
3.78-4.070.26661490.23241304X-RAY DIFFRACTION95
4.07-4.480.2751480.22971298X-RAY DIFFRACTION94
4.48-5.130.25491430.22821309X-RAY DIFFRACTION94
5.13-6.460.33011400.25531301X-RAY DIFFRACTION92
6.46-44.660.27621540.23911346X-RAY DIFFRACTION91
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1651-0.0831-0.02060.4887-0.36470.42430.0357-0.2546-0.11120.2372-0.07060.00520.0780.02060.09130.320.00460.01820.28310.0290.32793.378317.739914.7122
20.9753-0.50790.85951.0287-0.61510.7922-0.02690.07970.13550.1522-0.02550.0458-0.10030.0767-0.09810.3226-0.04480.07390.219-0.03910.32057.737928.607428.0175
30.4441-0.2206-0.33370.91260.1630.68980.05350.1254-0.24030.0822-0.27850.09350.02710.1389-0.08970.2741-0.0339-0.02930.39550.09690.324-8.539526.586512.9854
40.0938-0.08760.29840.0767-0.22391.241-0.02530.08290.13-0.1134-0.01070.19450.21010.2270.13240.3232-0.06740.04410.19750.05950.352146.459928.645633.8855
51.1012-0.33250.69411.16770.03171.90080.17620.1390.0845-0.1623-0.1768-0.3789-0.1920.4008-0.16730.2476-0.04210.03980.1701-0.02630.317451.814227.201216.4951
60.51120.3634-0.1152.11820.21810.24570.06010.0536-0.4428-0.60760.1508-0.1961-0.25730.17220.23530.37640.0676-0.0420.273-0.00450.298852.977415.72620.5914
71.2854-0.42971.04580.8098-0.03032.04210.14950.28880.07240.0255-0.0369-0.11540.13790.20630.11380.358-0.0505-0.0190.13510.00040.302445.18369.65626.1903
81.4403-0.0361-0.40591.16090.19810.89880.20570.27040.1376-0.1178-0.31760.17110.1625-0.3574-0.06580.3741-0.0728-0.0450.28330.02520.275232.424123.721636.389
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 122 )
2X-RAY DIFFRACTION2chain 'A' and (resid 123 through 270 )
3X-RAY DIFFRACTION3chain 'A' and (resid 271 through 384 )
4X-RAY DIFFRACTION4chain 'B' and (resid 10 through 122 )
5X-RAY DIFFRACTION5chain 'B' and (resid 123 through 176 )
6X-RAY DIFFRACTION6chain 'B' and (resid 177 through 229 )
7X-RAY DIFFRACTION7chain 'B' and (resid 230 through 311 )
8X-RAY DIFFRACTION8chain 'B' and (resid 312 through 384 )

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