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Yorodumi- PDB-7z99: Crystal structure of F191M variant of Variovorax paradoxus indole... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7z99 | ||||||
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Title | Crystal structure of F191M variant of Variovorax paradoxus indole monooxygenase (VpIndA1) in complex with methyl phenyl sulfoxide | ||||||
Components | Putative dehydrogenase/oxygenase subunit (Flavoprotein) | ||||||
Keywords | OXIDOREDUCTASE / FAD-dependent monooxygenase / styrene monooxygenase / StyA1 / IMO | ||||||
Function / homology | Styrene monooxygenase StyA, putative substrate binding domain / Styrene monooxygenase A putative substrate binding domain / FAD/NAD(P)-binding domain superfamily / nucleotide binding / FLAVIN-ADENINE DINUCLEOTIDE / [(S)-methylsulfinyl]benzene / Putative dehydrogenase/oxygenase subunit (Flavoprotein) Function and homology information | ||||||
Biological species | Variovorax paradoxus EPS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.92 Å | ||||||
Authors | Kratky, J. / Weisse, R. / Strater, N. | ||||||
Funding support | 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2023 Title: Structural and Mechanistic Studies on Substrate and Stereoselectivity of the Indole Monooxygenase VpIndA1: New Avenues for Biocatalytic Epoxidations and Sulfoxidations. Authors: Kratky, J. / Eggerichs, D. / Heine, T. / Hofmann, S. / Sowa, P. / Weisse, R.H. / Tischler, D. / Strater, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z99.cif.gz | 169.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z99.ent.gz | 132.4 KB | Display | PDB format |
PDBx/mmJSON format | 7z99.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z99_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7z99_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7z99_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 7z99_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z9/7z99 ftp://data.pdbj.org/pub/pdb/validation_reports/z9/7z99 | HTTPS FTP |
-Related structure data
Related structure data | 7z4xSC 7z94C 7z97C 7z98C 7zcaC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 47308.590 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Variovorax paradoxus EPS (bacteria) / Strain: EPS / Gene: Varpa_4903 / Production host: Escherichia coli (E. coli) / References: UniProt: E6V140 | ||||||
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#2: Chemical | ChemComp-FAD / | ||||||
#3: Chemical | Mass: 140.203 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8OS Details: The crystals were incubated with a racemic mixture of methyl phenyl sulfoxide. only (s)-methyl phenyl sulfoxide is modelled in this coordinate file. Both configurations, (r) and (s), can be ...Details: The crystals were incubated with a racemic mixture of methyl phenyl sulfoxide. only (s)-methyl phenyl sulfoxide is modelled in this coordinate file. Both configurations, (r) and (s), can be modeled each in the three low-energy rotamers of the -S(=O)CH3 group into the electron density with comparable fit. Feature type: SUBJECT OF INVESTIGATION #4: Water | ChemComp-HOH / | Has ligand of interest | Y | Nonpolymer details | The crystals were incubated with a racemic mixture of methyl phenyl sulfoxide. only (s)-methyl ...The crystals were incubated with a racemic mixture of methyl phenyl sulfoxide. only (s)-methyl phenyl sulfoxide is modelled in this coordinate file. Both configurations, (r) and (s), can be modeled each in the three low-energy rotamers of the -S(=O)CH3 group into the electron density with comparable fit. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 100 mM Na-acetate pH 5, 1400 mM Na-malonate, 1 mM DTT, 3 mM FAD, 1 mM racemic methyl phenyl sulfoxide, cryo: 15 % (v/v) ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 2.101424 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 17, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 2.101424 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.92→46.73 Å / Num. obs: 38322 / % possible obs: 88.9 % / Redundancy: 16.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.019 / Rrim(I) all: 0.081 / Net I/σ(I): 23.4 / Num. measured all: 645788 / Scaling rejects: 23 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 7z4x Resolution: 1.92→45.58 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.87 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 216.73 Å2 / Biso mean: 36.3183 Å2 / Biso min: 20.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.92→45.58 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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