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- PDB-8au8: Xenobiotic reductase A from P. putida in complex with ethyl (Z)-2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8au8 | ||||||
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Title | Xenobiotic reductase A from P. putida in complex with ethyl (Z)-2-(hydroxyimino)-3-oxopentanoate | ||||||
![]() | Xenobiotic reductase | ||||||
![]() | OXIDOREDUCTASE / Ene-reductase / oxime / FMN / complex | ||||||
Function / homology | ![]() NADPH dehydrogenase activity / FMN binding / NADP binding / metal ion 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 | ![]() | 216 KB | Display | ![]() |
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PDB format | ![]() | 137.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 35.6 KB | Display | |
Data in CIF | ![]() | 54.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8a8iC ![]() 8au9C ![]() 8auaC ![]() 8aubC ![]() 8aueC ![]() 8aufC ![]() 8augC ![]() 8auhC ![]() 8auiC ![]() 8aujC ![]() 8aulC ![]() 8aumC ![]() 8aunC ![]() 8auoC ![]() 8auqC ![]() 3n19S 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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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 40964.086 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 7 types, 766 molecules ![](data/chem/img/FMN.gif)
![](data/chem/img/O8I.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/O8I.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-PG4 / | #8: 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: 2.43 Å3/Da / Density % sol: 49.35 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 90 mM halogen mix (30 mM NaF, 30 mM NaBr, 30 mM NaI), 25% MPD, 10% PEG 3350, 100 mM Tris pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Oct 13, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→46.55 Å / Num. obs: 196951 / % possible obs: 96.79 % / Redundancy: 2.5 % / Biso Wilson estimate: 17.79 Å2 / CC1/2: 0.965 / Net I/σ(I): 4.05 |
Reflection shell | Resolution: 1.58→1.636 Å / Num. unique obs: 19854 / CC1/2: 0.676 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3n19 Resolution: 1.58→45.52 Å / SU ML: 0.1955 / Cross valid method: FREE R-VALUE / σ(F): 1.05 / Phase error: 20.3068 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: 22.39 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.58→45.52 Å
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Refine LS restraints |
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LS refinement shell |
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