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Yorodumi- PDB-6y48: Baeyer-Villiger monooxygenase BVMOAFL210 from Aspergillus flavus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6y48 | ||||||
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Title | Baeyer-Villiger monooxygenase BVMOAFL210 from Aspergillus flavus in complex with NADP | ||||||
Components | Baeyer-Villiger monooxygenaseBaeyer–Villiger oxidation | ||||||
Keywords | FLAVOPROTEIN / Baeyer-Villiger monooxygenase | ||||||
Function / homology | Function and homology information N,N-dimethylaniline monooxygenase activity / NADP binding / flavin adenine dinucleotide binding Similarity search - Function | ||||||
Biological species | Aspergillus flavus NRRL3357 (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.087 Å | ||||||
Authors | Opperman, D.J. / Tolmie, C. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Catalysts / Year: 2020 Title: Natural Variation in the ‘Control Loop’ of BVMOAFL210 and Its Influence on Regioselectivity and Sulfoxidation Authors: Tolmie, C. / Aido-Machado, R.D. / Ferroni, F.M. / Smit, M.S. / Opperman, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6y48.cif.gz | 440.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y48.ent.gz | 360.5 KB | Display | PDB format |
PDBx/mmJSON format | 6y48.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y4/6y48 ftp://data.pdbj.org/pub/pdb/validation_reports/y4/6y48 | HTTPS FTP |
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-Related structure data
Related structure data | 5j7xS S: Starting model for refinement |
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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: 64313.363 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus flavus NRRL3357 (mold) / Gene: AFLA_013230 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B8N5I0 #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-NAP / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.6 Å3/Da / Density % sol: 52.66 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 0.5 M ammonium citrate tribasic pH 9; 27.5% (v/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 6, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 |
Reflection | Resolution: 2.087→129.643 Å / Num. obs: 72127 / % possible obs: 87.5 % / Redundancy: 3.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.077 / Rrim(I) all: 0.143 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.087→2.361 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3606 / CC1/2: 0.62 / Rpim(I) all: 0.42 / Rrim(I) all: 0.772 / % possible all: 73.7 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5J7X Resolution: 2.087→129.64 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.877 / SU B: 8.009 / SU ML: 0.204 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.367 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 122.74 Å2 / Biso mean: 34.89 Å2 / Biso min: 4.15 Å2
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Refinement step | Cycle: final / Resolution: 2.087→129.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.087→2.141 Å / Rfactor Rfree error: 0
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