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Yorodumi- PDB-5xkd: Crystal structure of dibenzothiophene sulfone monooxygenase BdsA ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xkd | ||||||
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Title | Crystal structure of dibenzothiophene sulfone monooxygenase BdsA in complex with FMN at 2.4 angstrom | ||||||
Components | Dibenzothiophene desulfurization enzyme A | ||||||
Keywords | OXIDOREDUCTASE / dibenzothiophene desulfurization enzyme / monooxygenase / flavin mononucleotide | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / nucleotide binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.393 Å | ||||||
Authors | Gu, L. / Su, T. / Liu, S. / Su, J. | ||||||
Citation | Journal: Front Microbiol / Year: 2018 Title: Structural and Biochemical Characterization of BdsA fromBacillus subtilisWU-S2B, a Key Enzyme in the "4S" Desulfurization Pathway. Authors: Su, T. / Su, J. / Liu, S. / Zhang, C. / He, J. / Huang, Y. / Xu, S. / Gu, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xkd.cif.gz | 352.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xkd.ent.gz | 287.5 KB | Display | PDB format |
PDBx/mmJSON format | 5xkd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xk/5xkd ftp://data.pdbj.org/pub/pdb/validation_reports/xk/5xkd | HTTPS FTP |
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-Related structure data
Related structure data | 5xkcSC S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 49709.730 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: bdsA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8GRC7, EC: 1.14.14.22 #2: Chemical | ChemComp-FMN / #3: 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: 2.47 Å3/Da / Density % sol: 50.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: soaked in the solution containing 0.1M Sodium citrate pH 5.5, 35% PEG 200, 1mM FMN for 30 min |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.985 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.985 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 78295 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rsym value: 0.105 / Net I/σ(I): 29.05 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 4.21 / Rsym value: 0.569 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XKC Resolution: 2.393→48.25 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.49 / 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: 2.393→48.25 Å
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Refine LS restraints |
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LS refinement shell |
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