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- PDB-8aul: OPR3 Y190F in complex with 2-methoxyethyl (Z)-2-(hydroxyimino)-3-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8aul | ||||||
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Title | OPR3 Y190F in complex with 2-methoxyethyl (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 | ![]() | 212 KB | Display | ![]() |
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PDB format | ![]() | 133.4 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 ![]() 8aumC ![]() 8aunC ![]() 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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1 | ![]()
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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: Y190F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 565 molecules ![](data/chem/img/FMN.gif)
![](data/chem/img/O8R.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/O8R.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-PGE / | #6: 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: 2.22 Å3/Da / Density % sol: 44.66 % |
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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; 30 mM Magnesium chloride hexahydrate; 30 mM Calcium chloride dihydrate; 20% v/v Glycerol; 10% w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 26, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03319 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→41.52 Å / Num. obs: 225197 / % possible obs: 97.89 % / Redundancy: 1.9 % / Biso Wilson estimate: 16.96 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.12 |
Reflection shell | Resolution: 1.5→1.554 Å / Num. unique obs: 12353 / CC1/2: 0.695 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3hgs Resolution: 1.5→41.52 Å / SU ML: 0.1314 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.456 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: 21.27 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→41.52 Å
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Refine LS restraints |
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LS refinement shell |
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