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- PDB-8aun: OPR3 Y370F variant in complex with ethyl (Z)-2-(hydroxyimino)-3-o... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8aun | ||||||
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Title | OPR3 Y370F variant in complex with ethyl (Z)-2-(hydroxyimino)-3-oxobutanoate | ||||||
![]() | 12-oxophytodienoate reductase 3 | ||||||
![]() | OXIDOREDUCTASE / Ene-reductase / oxime / FMN / complex | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Polidori, N. / Gruber, K. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 219.3 KB | Display | ![]() |
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PDB format | ![]() | 138.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8a8iC ![]() 8au8C ![]() 8au9C ![]() 8auaC ![]() 8aubC ![]() 8aueC ![]() 8aufC ![]() 8augC ![]() 8auhC ![]() 8auiC ![]() 8aujC ![]() 8aulC ![]() 8aumC ![]() 8auoC ![]() 8auqC ![]() 3hgsS S: Starting model for refinement 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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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 44627.465 Da / Num. of mol.: 2 / Mutation: Y370F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 651 molecules ![](data/chem/img/FMN.gif)
![](data/chem/img/L9I.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/L9I.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-PGE / | #6: Chemical | ChemComp-PEG / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.67 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100 mM (Imidazole; MES monohydrate (acid)) pH 6.5; 20 mM Sodium formate; 20 mM Ammonium acetate; 20 mM Sodium citrate tribasic dihydrate; 20 mM Potassium sodium tartrate tetrahydrate; 20 mM ...Details: 100 mM (Imidazole; MES monohydrate (acid)) pH 6.5; 20 mM Sodium formate; 20 mM Ammonium acetate; 20 mM Sodium citrate tribasic dihydrate; 20 mM Potassium sodium tartrate tetrahydrate; 20 mM Sodium oxamate; 20% v/v Ethylene glycol; 10 % w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 6, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→40.11 Å / Num. obs: 241139 / % possible obs: 93.85 % / Redundancy: 1.9 % / Biso Wilson estimate: 15.84 Å2 / CC1/2: 0.994 / Net I/σ(I): 9.49 |
Reflection shell | Resolution: 1.49→1.545 Å / Num. unique obs: 20980 / CC1/2: 0.874 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3hgs Resolution: 1.49→40.11 Å / SU ML: 0.1078 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 17.1763 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: 20.03 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.49→40.11 Å
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Refine LS restraints |
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LS refinement shell |
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