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- PDB-9em6: OPR3 variant Y364P in its dimeric form obtained without ammonium ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9em6 | ||||||
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Title | OPR3 variant Y364P in its dimeric form obtained without ammonium sulfate | ||||||
![]() | 12-oxophytodienoate reductase 3 | ||||||
![]() | FLAVOPROTEIN / ene-reductase / Old Yellow Enzyme | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bijelic, A. / Macheroux, P. / Kerschbaumer, B. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 207.9 KB | Display | ![]() |
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PDB format | ![]() | 130.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8qn1C ![]() 8qn9C ![]() 8s8vC ![]() 8s8yC ![]() 9em0C ![]() 9em2C ![]() 9em3C ![]() 9em4C ![]() 9em5C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 44335.145 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.59 % |
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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: ![]() ![]() ![]() |
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: 1.72→46.81 Å / Num. obs: 81190 / % possible obs: 96.87 % / Redundancy: 6.6 % / Biso Wilson estimate: 29.57 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.036 / Net I/σ(I): 10.14 |
Reflection shell | Resolution: 1.72→1.74 Å / Num. unique obs: 1595 / CC1/2: 0.29 / Rpim(I) all: 0.98 |
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Processing
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Refinement | Method to determine structure: ![]() 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: 37.02 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.72→46.81 Å
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Refine LS restraints |
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LS refinement shell |
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