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- PDB-7z98: Crystal structure of F191M variant Variovorax paradoxus indole mo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7z98 | ||||||
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Title | Crystal structure of F191M variant Variovorax paradoxus indole monooxygenase (VpIndA1) in complex with methyl phenyl sulfide | ||||||
![]() | Putative dehydrogenase/oxygenase subunit (Flavoprotein) | ||||||
![]() | 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 / (methylsulfanyl)benzene / FLAVIN-ADENINE DINUCLEOTIDE / Putative dehydrogenase/oxygenase subunit (Flavoprotein)![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kratky, J. / Weisse, R. / Strater, N. | ||||||
Funding support | 1items
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 174.6 KB | Display | ![]() |
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PDB format | ![]() | 136.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 20.2 KB | Display | |
Data in CIF | ![]() | 30.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7z4xSC ![]() 7z94C ![]() 7z97C ![]() 7z99C ![]() 7zcaC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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.) ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-FAD / | ||||||
#3: Chemical | #4: Chemical | ChemComp-16R / ( | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.32 % |
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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 methyl phenyl sulfide, cryo: 15 % (v/v) ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 23, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.73→47.24 Å / Num. obs: 59530 / % possible obs: 98.2 % / Redundancy: 8.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.03 / Rrim(I) all: 0.09 / Net I/σ(I): 12.4 / Num. measured all: 514810 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7z4x Resolution: 1.73→45.93 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.11 / 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: 118.52 Å2 / Biso mean: 37.6668 Å2 / Biso min: 18.01 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.73→45.93 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22
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