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Yorodumi- PDB-8aui: Xenobiotic reductase A Y27F variant in complex with 2-methoxyethy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8aui | ||||||
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Title | Xenobiotic reductase A Y27F variant in complex with 2-methoxyethyl (Z)-2-(hydroxyimino)-3-oxobutanoate | ||||||
Components | NADH:flavin oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / Ene-reductase / FMN / oxime / TIM-barrel | ||||||
Function / homology | Function and homology information NADPH dehydrogenase activity / FMN binding / NADP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å | ||||||
Authors | Polidori, N. / Gruber, K. | ||||||
Funding support | Austria, 1items
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Citation | Journal: Acs Catalysis / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8aui.cif.gz | 215.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8aui.ent.gz | 137.9 KB | Display | PDB format |
PDBx/mmJSON format | 8aui.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/8aui ftp://data.pdbj.org/pub/pdb/validation_reports/au/8aui | HTTPS FTP |
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-Related structure data
Related structure data | 8a8iC 8au8C 8au9C 8auaC 8aubC 8aueC 8aufC 8augC 8auhC 8aujC 8aulC 8aumC 8aunC 8auoC 8auqC 3n19S S: Starting model for refinement 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: 40936.043 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: xenA, HB4184_21910 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9R9V9 #2: Chemical | #3: Chemical | ChemComp-O8R / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.54 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100 mM (Sodium HEPES; MOPS (acid)) pH 7.5; 30 mM Magnesium chloride hexahydrate; 30 mM Calcium chloride dihydrate; 12,5% v/v MPD; 12,5% PEG 1000; 12,5% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03319 Å |
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: 1.54→45.6 Å / Num. obs: 217359 / % possible obs: 99.41 % / Redundancy: 3.5 % / Biso Wilson estimate: 17.04 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.71 |
Reflection shell | Resolution: 1.54→1.595 Å / Num. unique obs: 11124 / CC1/2: 0.775 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3n19 Resolution: 1.54→45.6 Å / SU ML: 0.1438 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.7416 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: 22.42 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.54→45.6 Å
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Refine LS restraints |
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LS refinement shell |
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