[English] 日本語
Yorodumi- PDB-8bap: Eugenol Oxidase (EUGO) from Rhodococcus jostii RHA1, eightfold mu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bap | ||||||
---|---|---|---|---|---|---|---|
Title | Eugenol Oxidase (EUGO) from Rhodococcus jostii RHA1, eightfold mutant active on propanol syringol | ||||||
Components | Probable vanillyl-alcohol oxidase | ||||||
Keywords | OXIDOREDUCTASE / Biocatalysis / lignin / FAD / flavoenzyme | ||||||
Function / homology | Function and homology information 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 | Rhodococcus jostii RHA1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Alvigini, L. / Mattevi, A. | ||||||
Funding support | European Union, 1items
| ||||||
Citation | Journal: Acs Catalysis / Year: 2023 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8bap.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8bap.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 8bap.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bap_validation.pdf.gz | 7.8 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8bap_full_validation.pdf.gz | 8 MB | Display | |
Data in XML | 8bap_validation.xml.gz | 293.3 KB | Display | |
Data in CIF | 8bap_validation.cif.gz | 396.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ba/8bap ftp://data.pdbj.org/pub/pdb/validation_reports/ba/8bap | HTTPS FTP |
-Related structure data
Related structure data | 8bamC 5fxdS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
5 |
| ||||||||
6 |
| ||||||||
7 |
| ||||||||
8 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 58899.574 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus jostii RHA1 (bacteria) / Strain: RHA1 / Gene: RHA1_ro03282 / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 / References: UniProt: Q0SBK1, vanillyl-alcohol oxidase #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-55B / #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.45 % |
---|---|
Crystal grow | Temperature: 293 K / Method: batch mode / Details: Morpheus screening, condition A6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000002 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|