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Yorodumi- PDB-8aub: 12-oxophytodienoate reductase 3 (OPR3) from Solanum lycopersicum ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8aub | ||||||
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Title | 12-oxophytodienoate reductase 3 (OPR3) from Solanum lycopersicum in complex with ethyl (Z)-2-(hydroxyimino)-3-oxopentanoate | ||||||
Components | 12-oxophytodienoate reductase 3 | ||||||
Keywords | OXIDOREDUCTASE / Ene-reductase / oxime / FMN / complex | ||||||
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: 1.62 Å | ||||||
Authors | Polidori, N. / Gruber, K. | ||||||
Funding support | Austria, 1items
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Citation | Journal: Acs Catalysis / Year: 2023 Title: Mechanistic Insights into the Ene-Reductase-Catalyzed Promiscuous Reduction of Oximes to Amines. Authors: Breukelaar, W.B. / Polidori, N. / Singh, A. / Daniel, B. / Glueck, S.M. / Gruber, K. / Kroutil, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8aub.cif.gz | 210.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8aub.ent.gz | 132.4 KB | Display | PDB format |
PDBx/mmJSON format | 8aub.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/8aub ftp://data.pdbj.org/pub/pdb/validation_reports/au/8aub | HTTPS FTP |
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-Related structure data
Related structure data | 8a8iC 8au8C 8au9C 8auaC 8aueC 8aufC 8augC 8auhC 8auiC 8aujC 8aulC 8aumC 8aunC 8auoC 8auqC 3hgsS S: Starting model for refinement 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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2 |
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Unit cell |
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-Components
#1: Protein | 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 BL21(DE3) (bacteria) / References: UniProt: Q9FEW9, 12-oxophytodienoate reductase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PEG / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.97 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100 mM CaCl2,10 % w/v PEG 8000, 100 mM Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.965459 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→44.2 Å / Num. obs: 176405 / % possible obs: 91.63 % / Redundancy: 1.6 % / Biso Wilson estimate: 17.69 Å2 / CC1/2: 0.987 / Net I/σ(I): 5.06 |
Reflection shell | Resolution: 1.62→1.678 Å / Num. unique obs: 18096 / CC1/2: 0.619 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HGS Resolution: 1.62→44.2 Å / SU ML: 0.1965 / Cross valid method: FREE R-VALUE / σ(F): 0.92 / Phase error: 22.8987 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.62→44.2 Å
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Refine LS restraints |
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LS refinement shell |
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