+Open data
-Basic information
Entry | Database: PDB / ID: 5xdb | ||||||
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Title | Crystal structure of FMN-bound TdsC from Paenibacillus sp. A11-2 | ||||||
Components | Thermophilic dibenzothiophene desulfurization enzyme C | ||||||
Keywords | OXIDOREDUCTASE / Monooxygenase / FMN binding protein / tetramer | ||||||
Function / homology | Function and homology information dibenzothiophene monooxygenase / oxidoreductase activity, acting on the CH-CH group of donors / monooxygenase activity / flavin adenine dinucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | Paenibacillus sp. A11-2 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.811 Å | ||||||
Authors | Hino, T. / Hamamoto, H. / Ohshiro, T. / Nagano, S. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xdb.cif.gz | 359.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xdb.ent.gz | 287.9 KB | Display | PDB format |
PDBx/mmJSON format | 5xdb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xd/5xdb ftp://data.pdbj.org/pub/pdb/validation_reports/xd/5xdb | HTTPS FTP |
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-Related structure data
Related structure data | 5xb8SC 5xdcC 5xddC 5xdeC 5xdgC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Paenibacillus sp. A11-2 (bacteria) / Gene: tdsC / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LBX2 #2: Chemical | ChemComp-FMN / #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: 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: 2.94 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: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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