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- PDB-9em4: OPR3 variant Y364P in its dimeric form obtained with ammonium sulfate -

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Basic information

Entry
Database: PDB / ID: 9em4
TitleOPR3 variant Y364P in its dimeric form obtained with ammonium sulfate
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 / 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 / 12-oxophytodienoate reductase 3
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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
Revision 1.1Aug 21, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 12-oxophytodienoate reductase 3
A: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,8746
Polymers88,6702
Non-polymers1,2044
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-26 kcal/mol
Surface area25680 Å2
Unit cell
Length a, b, c (Å)57.531, 89.640, 80.943
Angle α, β, γ (deg.)90.00, 109.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 12-oxophytodienoate reductase 3 / 12-oxophytodienoate-10 / 11-reductase 3 / OPDA-reductase 3 / LeOPR3


Mass: 44335.145 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.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
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: 2.23 Å3/Da / Density % sol: 44.73 %
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: 2.01→46.5 Å / Num. obs: 51254 / % possible obs: 99.26 % / Redundancy: 6.9 % / CC1/2: 0.99 / Rpim(I) all: 0.05 / Net I/σ(I): 9.09
Reflection shellResolution: 2.01→2.05 Å / Num. unique obs: 2515 / CC1/2: 0.53 / Rpim(I) all: 0.63

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→46.5 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2438 2470 4.82 %
Rwork0.2064 --
obs0.2081 51234 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.01→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5618 0 79 158 5855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145854
X-RAY DIFFRACTIONf_angle_d0.7427993
X-RAY DIFFRACTIONf_dihedral_angle_d13.1432068
X-RAY DIFFRACTIONf_chiral_restr0.048887
X-RAY DIFFRACTIONf_plane_restr0.0081042
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.050.35171190.32452392X-RAY DIFFRACTION88
2.05-2.090.32431540.3152670X-RAY DIFFRACTION100
2.09-2.140.33121520.29762738X-RAY DIFFRACTION100
2.14-2.190.33561240.28622710X-RAY DIFFRACTION100
2.19-2.240.30371340.27882728X-RAY DIFFRACTION100
2.24-2.30.3211220.28332734X-RAY DIFFRACTION100
2.3-2.370.33231260.26212743X-RAY DIFFRACTION100
2.37-2.450.29221090.25712696X-RAY DIFFRACTION100
2.45-2.530.29051640.23472728X-RAY DIFFRACTION100
2.53-2.640.2831740.242670X-RAY DIFFRACTION100
2.64-2.760.25641460.23782718X-RAY DIFFRACTION100
2.76-2.90.30151540.23722726X-RAY DIFFRACTION100
2.9-3.080.27211570.22492696X-RAY DIFFRACTION100
3.08-3.320.25031000.21122754X-RAY DIFFRACTION100
3.32-3.650.24231230.19122766X-RAY DIFFRACTION100
3.66-4.180.19981310.16492756X-RAY DIFFRACTION100
4.18-5.270.17681490.15752737X-RAY DIFFRACTION100
5.27-46.50.21320.17012802X-RAY DIFFRACTION100
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)
12.6215-0.3195-0.05950.7225-0.35883.9455-0.09920.22510.2972-0.33020.23320.1672-0.6373-0.5017-0.11491.118-0.04450.0530.68960.07660.602817.477111.3572-4.8974
21.7511-0.30160.02390.9911-1.17484.2314-0.16330.09240.1842-0.40020.1066-0.3887-0.4240.81760.05151.0546-0.15470.23490.6244-0.03080.566332.1657.58660.3289
30.44350.1422-1.0450.0444-0.33482.45890.2470.04160.05630.39550.17490.42630.02490.4519-0.40480.89770.01890.14590.6173-0.02490.572130.6597-2.7398-14.6368
43.0431-0.41920.57062.00560.00532.41320.02230.4956-0.4194-0.6464-0.0120.38870.5387-0.28550.01661.1681-0.14670.10650.7175-0.00070.673816.1152-3.4456-11.7203
51.4531-0.10930.23342.4681-0.42740.82460.00570.1234-0.0049-0.06290.0261-0.2070.06330.1029-0.03670.2950.00170.0490.2675-0.0150.243545.4614-3.5804-43.7417
62.39480.13421.01183.96660.72182.3752-0.0248-0.05610.40160.21340.0763-0.0588-0.25520.0259-0.04490.2827-0.00540.02330.2489-0.00950.324645.972611.3046-41.1935
73.5202-0.474-2.76841.53071.20367.6330.1992-0.27940.11490.4763-0.2090.2014-0.1688-0.3912-0.07550.4922-0.03270.08740.3933-0.0260.426832.2679.5287-34.0785
81.78590.35480.2492.7615-0.40290.8229-0.01040.00420.1952-0.01550.06530.4405-0.122-0.1153-0.04790.27780.00930.05420.28910.00750.35427.27072.0964-41.3487
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 11 through 156 )
2X-RAY DIFFRACTION2chain 'B' and (resid 157 through 270 )
3X-RAY DIFFRACTION3chain 'B' and (resid 271 through 296 )
4X-RAY DIFFRACTION4chain 'B' and (resid 297 through 384 )
5X-RAY DIFFRACTION5chain 'A' and (resid 10 through 229 )
6X-RAY DIFFRACTION6chain 'A' and (resid 230 through 270 )
7X-RAY DIFFRACTION7chain 'A' and (resid 271 through 298 )
8X-RAY DIFFRACTION8chain 'A' and (resid 299 through 385 )

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