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Yorodumi- PDB-5fxe: Crystal structure of eugenol oxidase in complex with coniferyl alcohol -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fxe | ||||||
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Title | Crystal structure of eugenol oxidase in complex with coniferyl alcohol | ||||||
Components | EUGENOL OXIDASE | ||||||
Keywords | OXIDOREDUCTASE / BIOCATALYSIS / SELECTIVE OXIDATION / KINETIC RESOLUTION / OXIDASES / EUGENOL | ||||||
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: 1.9 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fxe.cif.gz | 226.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fxe.ent.gz | 180.6 KB | Display | PDB format |
PDBx/mmJSON format | 5fxe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fxe_validation.pdf.gz | 1023.5 KB | Display | wwPDB validaton report |
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Full document | 5fxe_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5fxe_validation.xml.gz | 42.9 KB | Display | |
Data in CIF | 5fxe_validation.cif.gz | 61.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fx/5fxe ftp://data.pdbj.org/pub/pdb/validation_reports/fx/5fxe | HTTPS FTP |
-Related structure data
Related structure data | 5fxdC 5fxfC 5fxpC 2vaoS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9991, 0.02749, -0.03227), 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, vanillyl-alcohol oxidase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Nonpolymer details | FLAVIN-ADENINE DINUCLEOTI | |
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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: 2.12 Å3/Da / Density % sol: 41.97 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 24% PEG6000, 0.1 M TRIS/HCL PH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 10, 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: 1.9→85.4 Å / Num. obs: 77427 / % possible obs: 97.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.7 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VAO Resolution: 1.9→89.53 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.027 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 18.332 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→89.53 Å
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Refine LS restraints |
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