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- PDB-8bap: Eugenol Oxidase (EUGO) from Rhodococcus jostii RHA1, eightfold mu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8bap | ||||||
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Title | Eugenol Oxidase (EUGO) from Rhodococcus jostii RHA1, eightfold mutant active on propanol syringol | ||||||
![]() | Probable vanillyl-alcohol oxidase | ||||||
![]() | OXIDOREDUCTASE / Biocatalysis / lignin / FAD / flavoenzyme | ||||||
Function / homology | ![]() vanillyl-alcohol oxidase / vanillyl-alcohol oxidase activity / D-lactate dehydrogenase (cytochrome) activity / lactate catabolic process / D-lactate dehydrogenase activity / FAD binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Alvigini, L. / Mattevi, A. | ||||||
Funding support | European Union, 1items
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![]() | ![]() Title: One-Pot Biocatalytic Synthesis of rac -Syringaresinol from a Lignin-Derived Phenol. Authors: Guo, Y. / Alvigini, L. / Saifuddin, M. / Ashley, B. / Trajkovic, M. / Alonso-Cotchico, L. / Mattevi, A. / Fraaije, M.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 | ![]() | 1.6 MB | Display | ![]() |
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PDB format | ![]() | 1.3 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 7.8 MB | Display | ![]() |
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Full document | ![]() | 8 MB | Display | |
Data in XML | ![]() | 293.3 KB | Display | |
Data in CIF | ![]() | 396.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8bamC ![]() 5fxdS 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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Unit cell |
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Components
#1: Protein | Mass: 58899.574 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-55B / #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.45 % |
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Crystal grow | Temperature: 293 K / Method: batch mode / Details: Morpheus screening, condition A6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.000002 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 379398 / % possible obs: 98.2 % / Redundancy: 3.5 % / CC1/2: 0.987 / Rmerge(I) obs: 0.137 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 2.3→2.34 Å / Rmerge(I) obs: 0.707 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 18712 / CC1/2: 0.537 / % possible all: 97.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5FXD Resolution: 2.3→49.044 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 25.95 / Stereochemistry target values: ML
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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 max: 117.67 Å2 / Biso mean: 34.5075 Å2 / Biso min: 8.69 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→49.044 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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