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Yorodumi- PDB-6jdk: Crystal structure of Baeyer-Villiger monooxygenase from Parvibacu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jdk | ||||||
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Title | Crystal structure of Baeyer-Villiger monooxygenase from Parvibaculum lavamentivorans | ||||||
Components | Baeyer-Villiger monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / monooxygenase | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor / N,N-dimethylaniline monooxygenase activity / NADP binding / flavin adenine dinucleotide binding Similarity search - Function | ||||||
Biological species | Parvibaculum lavamentivorans | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.495 Å | ||||||
Authors | Kim, J.-S. / Nguyen, T.D. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2019 Title: Structural basis for the selective addition of an oxygen atom to cyclic ketones by Baeyer-Villiger monooxygenase from Parvibaculum lavamentivorans. Authors: Nguyen, T.D. / Choi, G.E. / Gu, D.H. / Seo, P.W. / Kim, J.W. / Park, J.B. / Kim, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jdk.cif.gz | 428.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jdk.ent.gz | 348.2 KB | Display | PDB format |
PDBx/mmJSON format | 6jdk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jdk_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6jdk_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6jdk_validation.xml.gz | 41 KB | Display | |
Data in CIF | 6jdk_validation.cif.gz | 56.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/6jdk ftp://data.pdbj.org/pub/pdb/validation_reports/jd/6jdk | HTTPS FTP |
-Related structure data
Related structure data | 1w4xS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 61850.676 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Parvibaculum lavamentivorans (strain DS-1 / DSM 13023 / NCIMB 13966) (bacteria) Strain: DS-1 / DSM 13023 / NCIMB 13966 / Gene: Plav_1781 / Production host: Escherichia (bacteria) References: UniProt: A7HU16, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.38 Å3/Da / Density % sol: 48.25 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion Details: 0.1 M 3-(N-morpholino)propanesulfonic acid (pH 7.5), 0.04 M calcium acetate, and 24% (w/v) PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 25, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.495→50 Å / Num. obs: 39987 / % possible obs: 98.1 % / Redundancy: 5.6 % / CC1/2: 0.977 / Rpim(I) all: 0.097 / Net I/σ(I): 2.8 |
Reflection shell | Resolution: 2.5→2.54 Å / Num. unique obs: 1830 / CC1/2: 0.638 / Rpim(I) all: 0.378 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1w4x Resolution: 2.495→19.88 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.58 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.495→19.88 Å
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Refine LS restraints |
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LS refinement shell |
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