+Open data
-Basic information
Entry | Database: PDB / ID: 9em5 | ||||||
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Title | OPR3 variant Y364P in its monomeric form | ||||||
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 / FMN binding / peroxisome / 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 | 9em5.cif.gz | 114.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9em5.ent.gz | 68 KB | Display | PDB format |
PDBx/mmJSON format | 9em5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9em5_validation.pdf.gz | 791.5 KB | Display | wwPDB validaton report |
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Full document | 9em5_full_validation.pdf.gz | 792.4 KB | Display | |
Data in XML | 9em5_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 9em5_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/9em5 ftp://data.pdbj.org/pub/pdb/validation_reports/em/9em5 | HTTPS FTP |
-Related structure data
Related structure data | 8qn1C 8qn9C 8s8vC 8s8yC 9em0C 9em2C 9em3C 9em4C 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: 44335.145 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-FMN / |
#3: Chemical | ChemComp-MPD / ( |
#4: Chemical | ChemComp-CL / |
#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: 2.22 Å3/Da / Density % sol: 44.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M Tris-HCl (7.5), 50 mM sodium tartrate, 8-16% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.87 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: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→49.39 Å / Num. obs: 54069 / % possible obs: 98.84 % / Redundancy: 3 % / Biso Wilson estimate: 19.57 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.06 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 1.57→1.6 Å / Num. unique obs: 14664 / CC1/2: 0.35 / Rpim(I) all: 1.26 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→49.39 Å / SU ML: 0.2405 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.0772 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→49.39 Å
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Refine LS restraints |
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LS refinement shell |
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