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- PDB-2ylz: SNAPSHOTS OF ENZYMATIC BAEYER-VILLIGER CATALYSIS: OXYGEN ACTIVATI... -
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Open data
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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 | ||||||
![]() | PHENYLACETONE MONOOXYGENASE | ||||||
![]() | OXIDOREDUCTASE / OXYGENASE | ||||||
Function / homology | ![]() phenylacetone monooxygenase / phenylacetone monooxygenase activity / N,N-dimethylaniline monooxygenase activity / NADP binding / flavin adenine dinucleotide binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Orru, R. / Dudek, H.M. / Martinoli, C. / Torres Pazmino, D.E. / Royant, A. / Weik, M. / Fraaije, M.W. / Mattevi, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 129.3 KB | Display | ![]() |
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PDB format | ![]() | 98.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 719.8 KB | Display | ![]() |
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Full document | ![]() | 724.1 KB | Display | |
Data in XML | ![]() | 24.7 KB | Display | |
Data in CIF | ![]() | 36.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ylrC ![]() 2ylsC ![]() 2yltC ![]() 2ylwC ![]() 2ylxC ![]() 2ym1C ![]() 2ym2C ![]() 1w4xS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-FAD / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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