+Open data
-Basic information
Entry | Database: PDB / ID: 8qn9 | ||||||
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Title | OPR3 variant - R283E | ||||||
Components | 12-oxophytodienoate reductase 3 | ||||||
Keywords | FLAVOPROTEIN / 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 | ||||||
Biological species | Solanum lycopersicum (tomato) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Bijelic, A. / Macheroux, P. / Kerschbaumer, B. | ||||||
Funding support | Austria, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qn9.cif.gz | 153.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qn9.ent.gz | 118.7 KB | Display | PDB format |
PDBx/mmJSON format | 8qn9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qn9_validation.pdf.gz | 820.9 KB | Display | wwPDB validaton report |
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Full document | 8qn9_full_validation.pdf.gz | 821.1 KB | Display | |
Data in XML | 8qn9_validation.xml.gz | 18 KB | Display | |
Data in CIF | 8qn9_validation.cif.gz | 27.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qn/8qn9 ftp://data.pdbj.org/pub/pdb/validation_reports/qn/8qn9 | HTTPS FTP |
-Related structure data
Related structure data | 8qn1C 8s8vC 8s8yC 9em0C 9em2C 9em3C 9em4C 9em5C 9em6C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 44373.121 Da / Num. of mol.: 1 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 |
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#2: Chemical | ChemComp-MPD / ( |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-FMN / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM MES/Tris, 50 mM ammonium sufate, 14% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 19, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→43.84 Å / Num. obs: 48262 / % possible obs: 92.4 % / Redundancy: 6.5 % / Biso Wilson estimate: 23.13 Å2 / CC1/2: 0.998 / Net I/σ(I): 15.41 |
Reflection shell | Resolution: 1.6→1.63 Å / Num. unique obs: 1770 / CC1/2: 0.458 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→43.84 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.79 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→43.84 Å
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Refine LS restraints |
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LS refinement shell |
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