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- PDB-2ylr: SNAPSHOTS OF ENZYMATIC BAEYER-VILLIGER CATALYSIS: OXYGEN ACTIVATI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ylr | ||||||
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Title | SNAPSHOTS OF ENZYMATIC BAEYER-VILLIGER CATALYSIS: OXYGEN ACTIVATION AND INTERMEDIATE STABILIZATION: COMPLEX WITH NADP | ||||||
![]() | PHENYLACETONE MONOOXYGENASE | ||||||
![]() | OXIDOREDUCTASE / BAEYER-VILLIGER REACTION / FAD / 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 | ![]() | 128.7 KB | Display | ![]() |
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PDB format | ![]() | 97.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2ylsC ![]() 2yltC ![]() 2ylwC ![]() 2ylxC ![]() 2ylzC ![]() 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: 61191.449 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-NAP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 40 % / Description: NONE |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 6.5 Details: BY VAPOR-DIFFUSION AT 4 DEGREES C USING 1-3 MICROL OF PROTEIN SOLUTIONS (18 MG/ML IN 0.5 MICROM FAD AND 4 MM NADP, 50 MM TRIS/HCL PH 7.5) MIXED WITH EQUAL VOLUMES OF RESERVOIR CONTAINING 40% ...Details: BY VAPOR-DIFFUSION AT 4 DEGREES C USING 1-3 MICROL OF PROTEIN SOLUTIONS (18 MG/ML IN 0.5 MICROM FAD AND 4 MM NADP, 50 MM TRIS/HCL PH 7.5) MIXED WITH EQUAL VOLUMES OF RESERVOIR CONTAINING 40% W/V PEG4000, 100 MM MES/HCL PH 6.5, AND 100 MM NACL. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / 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: 2.26→30 Å / Num. obs: 34179 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.26→2.4 Å / Redundancy: 4 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.7 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1W4X Resolution: 2.26→42.78 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.907 / SU B: 5.756 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.207 / 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: 25.185 Å2
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Refinement step | Cycle: LAST / Resolution: 2.26→42.78 Å
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Refine LS restraints |
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