+Open data
-Basic information
Entry | Database: PDB / ID: 9em2 | ||||||
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Title | OPR3 wild type in its dimeric form obtained without sulfate | ||||||
Components | 12-oxophytodienoate reductase 3 | ||||||
Keywords | FLAVOPROTEIN / 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 | ||||||
Biological species | Solanum lycopersicum (tomato) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 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 | 9em2.cif.gz | 178.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9em2.ent.gz | 137.3 KB | Display | PDB format |
PDBx/mmJSON format | 9em2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9em2_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 9em2_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 9em2_validation.xml.gz | 36 KB | Display | |
Data in CIF | 9em2_validation.cif.gz | 55.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/9em2 ftp://data.pdbj.org/pub/pdb/validation_reports/em/9em2 | HTTPS FTP |
-Related structure data
Related structure data | 8qn1C 8qn9C 8s8vC 8s8yC 9em0C 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: 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 (E. coli) / References: UniProt: Q9FEW9, 12-oxophytodienoate reductase #2: Chemical | #3: Chemical | ChemComp-TLA / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.24 Å3/Da / Density % sol: 45.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris/HCl (7.5), 50 mM sodium tartrate, 8-18% PEG8000 PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8731 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 8, 2024 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8731 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→46.67 Å / Num. obs: 136455 / % possible obs: 99.46 % / Redundancy: 7 % / CC1/2: 0.99 / Rpim(I) all: 0.04 / Net I/σ(I): 9.17 |
Reflection shell | Resolution: 1.54→1.56 Å / Num. unique obs: 4107 / CC1/2: 0.13 / Rpim(I) all: 1.72 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→46.67 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.11 / 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: 1.54→46.67 Å
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Refine LS restraints |
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LS refinement shell |
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