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Yorodumi- PDB-1w1m: STRUCTURE OF THE OCTAMERIC FLAVOENZYME VANILLYL-ALCOHOL OXIDASE: ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w1m | ||||||
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Title | STRUCTURE OF THE OCTAMERIC FLAVOENZYME VANILLYL-ALCOHOL OXIDASE: Glu502Gly Mutant | ||||||
Components | VANILLYL-ALCOHOL OXIDASE | ||||||
Keywords | OXIDOREDUCTASE / FLAVOENZYME / CATALYSIS / FAD | ||||||
Function / homology | Function and homology information vanillyl-alcohol oxidase / vanillyl-alcohol oxidase activity / methanol metabolic process / : / D-lactate dehydrogenase (cytochrome) activity / lactate catabolic process / D-lactate dehydrogenase activity / FAD binding / peroxisome / mitochondrion Similarity search - Function | ||||||
Biological species | PENICILLIUM SIMPLICISSIMUM (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Van Den Heuvel, R.H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Laboratory-Evolved Vanillyl-Alcohol Oxidase Produces Natural Vanillin Authors: Van Den Heuvel, R.H. / Van Den Berg, W.A. / Rovida, S. / Van Berkel, W.J. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w1m.cif.gz | 224.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w1m.ent.gz | 180 KB | Display | PDB format |
PDBx/mmJSON format | 1w1m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1w1m_validation.pdf.gz | 989.5 KB | Display | wwPDB validaton report |
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Full document | 1w1m_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1w1m_validation.xml.gz | 43.7 KB | Display | |
Data in CIF | 1w1m_validation.cif.gz | 58.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w1/1w1m ftp://data.pdbj.org/pub/pdb/validation_reports/w1/1w1m | HTTPS FTP |
-Related structure data
Related structure data | 1w1jC 1w1kC 1w1lC 2vaoS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 63035.059 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Details: COVALENT BOND BETWEEN FAD AND HIS 422 / Source: (gene. exp.) PENICILLIUM SIMPLICISSIMUM (fungus) / Description: FUNGUS / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P56216, alcohol oxidase #2: Chemical | #3: Chemical | Compound details | ENGINEERED | |
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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: 2.3 Å3/Da / Density % sol: 40 % / Description: BINDING STUDIES |
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Crystal grow | pH: 4.6 / Details: FROM 6% PEG4000, 100 MM ACETATE BUFFER PH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 2002 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→30 Å / Num. obs: 20676 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.127 |
Reflection shell | Resolution: 3→3.15 Å / Redundancy: 2 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VAO Resolution: 3→40 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.801 / SU B: 29.535 / SU ML: 0.542 / Cross valid method: THROUGHOUT / ESU R Free: 0.617 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.5 Å2
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Refinement step | Cycle: LAST / Resolution: 3→40 Å
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Refine LS restraints |
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