+Open data
-Basic information
Entry | Database: PDB / ID: 5fxd | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of eugenol oxidase in complex with isoeugenol | ||||||
Components | PROBABLE VANILLYL-ALCOHOL OXIDASE | ||||||
Keywords | OXIDOREDUCTASE / BIOCATALYSIS / SELECTIVE OXIDATION / KINETIC RESOLUTION / OXIDASES / EUGENOL | ||||||
Function / homology | Function and homology information vanillyl-alcohol oxidase / vanillyl-alcohol oxidase activity / FAD binding Similarity search - Function | ||||||
Biological species | RHODOCOCCUS JOSTII RHA1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Nguyen, Q.-T. / de Gonzalo, G. / Binda, C. / Martinez, A.R. / Mattevi, A. / Fraaije, M.W. | ||||||
Citation | Journal: Chembiochem / Year: 2016 Title: Biocatalytic Properties and Structural Analysis of Eugenol Oxidase from Rhodococcus Jostii Rha1: A Versatile Oxidative Biocatalyst. Authors: Nguyen, Q. / De Gonzalo, G. / Binda, C. / Rioz-Martinez, A. / Mattevi, A. / Fraaije, M.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5fxd.cif.gz | 229.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5fxd.ent.gz | 182.8 KB | Display | PDB format |
PDBx/mmJSON format | 5fxd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fx/5fxd ftp://data.pdbj.org/pub/pdb/validation_reports/fx/5fxd | HTTPS FTP |
---|
-Related structure data
Related structure data | 5fxeC 5fxfC 5fxpC 2vaoS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.999, 0.02864, -0.03305), Vector: |
-Components
#1: Protein | Mass: 58738.395 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: COVALENT BOND BETWEEN THE FAD AND HIS390 / Source: (gene. exp.) RHODOCOCCUS JOSTII RHA1 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q0SBK1 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Nonpolymer details | FLAVIN-ADENINE DINUCLEOTI | Sequence details | OTHER DETAILS THIS RESEARCH WAS SUPPORTED THE EUROPEAN UNION (EU) PROJECT ROBOX (GRANT AGREEMENT NO. ...OTHER DETAILS THIS RESEARCH WAS SUPPORTED THE EUROPEAN UNION (EU) PROJECT ROBOX (GRANT AGREEMENT NO. 635734) UNDER EU'S HORIZON 2020 PROGRAMME RESEARCH AND INNOVATION | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42 % / Description: NONE |
---|---|
Crystal grow | pH: 8 / Details: 24% PEG6000, 0.1 M TRIS/HCL PH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98 |
Detector | Type: PILATUS / Detector: PIXEL / Date: Aug 31, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→85 Å / Num. obs: 109694 / % possible obs: 98.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 1.8 / % possible all: 98 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VAO Resolution: 1.7→89.86 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.405 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.35 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→89.86 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|