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Yorodumi- PDB-2ylz: SNAPSHOTS OF ENZYMATIC BAEYER-VILLIGER CATALYSIS: OXYGEN ACTIVATI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ylz | ||||||
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Title | SNAPSHOTS OF ENZYMATIC BAEYER-VILLIGER CATALYSIS: OXYGEN ACTIVATION AND INTERMEDIATE STABILIZATION: Met446Gly MUTANT | ||||||
Components | PHENYLACETONE MONOOXYGENASE | ||||||
Keywords | OXIDOREDUCTASE / OXYGENASE | ||||||
Function / homology | Function and homology information phenylacetone monooxygenase / phenylacetone monooxygenase activity / N,N-dimethylaniline monooxygenase activity / NADP binding / flavin adenine dinucleotide binding Similarity search - Function | ||||||
Biological species | THERMOBIFIDA FUSCA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Orru, R. / Dudek, H.M. / Martinoli, C. / Torres Pazmino, D.E. / Royant, A. / Weik, M. / Fraaije, M.W. / Mattevi, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Snapshots of Enzymatic Baeyer-Villiger Catalysis: Oxygen Activation and Intermediate Stabilization. Authors: Orru, R. / Dudek, H.M. / Martinoli, C. / Torres Pazmino, D.E. / Royant, A. / Weik, M. / Fraaije, M.W. / Mattevi, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ylz.cif.gz | 129.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ylz.ent.gz | 98.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ylz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yl/2ylz ftp://data.pdbj.org/pub/pdb/validation_reports/yl/2ylz | HTTPS FTP |
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-Related structure data
Related structure data | 2ylrC 2ylsC 2yltC 2ylwC 2ylxC 2ym1C 2ym2C 1w4xS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 61117.309 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOBIFIDA FUSCA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): TOP10 / References: UniProt: Q47PU3, phenylacetone monooxygenase | ||||
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#2: Chemical | ChemComp-FAD / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.43 Å3/Da / Density % sol: 50 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: CRYSTALS WERE GROWN AT 293 K BY THE VAPOUR DIFFUSION METHOD. HANGING DROPS WERE FORMED BY MIXING EQUAL VOLUMES OF 18 MG PROTEIN/ML IN 5 MM FAD AND 50 MM SODIUM PHOSPHATE PH 7.0, AND OF A ...Details: CRYSTALS WERE GROWN AT 293 K BY THE VAPOUR DIFFUSION METHOD. HANGING DROPS WERE FORMED BY MIXING EQUAL VOLUMES OF 18 MG PROTEIN/ML IN 5 MM FAD AND 50 MM SODIUM PHOSPHATE PH 7.0, AND OF A WELL SOLUTION CONSISTING OF 1.5 M AMMONIUM SULPHATE AND 0.5 M LITHIUM CHLORIDE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 56991 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 4 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1W4X Resolution: 2→36.4 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.363 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.185 Å2
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Refinement step | Cycle: LAST / Resolution: 2→36.4 Å
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Refine LS restraints |
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