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Open data
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Basic information
Entry | Database: PDB / ID: 5xdb | ||||||
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Title | Crystal structure of FMN-bound TdsC from Paenibacillus sp. A11-2 | ||||||
![]() | Thermophilic dibenzothiophene desulfurization enzyme C | ||||||
![]() | OXIDOREDUCTASE / Monooxygenase / FMN binding protein / tetramer | ||||||
Function / homology | ![]() dibenzothiophene monooxygenase / 3-methylbutanoyl-CoA dehydrogenase activity / L-leucine catabolic process / monooxygenase activity / flavin adenine dinucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hino, T. / Hamamoto, H. / Ohshiro, T. / Nagano, S. | ||||||
![]() | ![]() Title: Crystal structures of TdsC, a dibenzothiophene monooxygenase from the thermophile Paenibacillus sp. A11-2, reveal potential for expanding its substrate selectivity. Authors: Hino, T. / Hamamoto, H. / Suzuki, H. / Yagi, H. / Ohshiro, T. / Nagano, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 359.7 KB | Display | ![]() |
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PDB format | ![]() | 287.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 73.3 KB | Display | |
Data in CIF | ![]() | 108.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xb8SC ![]() 5xdcC ![]() 5xddC ![]() 5xdeC ![]() 5xdgC C: citing same article ( S: Starting model for refinement |
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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: 45814.242 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-FMN / #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.2 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 1.4 M ammonium sulfate, 0.1 M Tris-HCl, 12% (v/v) Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 10, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.811→35.51 Å / Num. obs: 527346 / % possible obs: 100 % / Redundancy: 7.3 % / Net I/σ(I): 8.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5XB8 Resolution: 1.811→35.5 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.13 / Phase error: 24 Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.811→35.5 Å
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Refine LS restraints |
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LS refinement shell |
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