+Open data
-Basic information
Entry | Database: PDB / ID: 6l8a | ||||||
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Title | Tetrathionate hydrolase from Acidithiobacillus ferrooxidans | ||||||
Components | Tetrathionate hydrolase | ||||||
Keywords | HYDROLASE / Tetrathionate | ||||||
Function / homology | Function and homology information Hydrolases; Acting on sulfur-sulfur bonds / hydrolase activity / plasma membrane Similarity search - Function | ||||||
Biological species | Acidithiobacillus ferrooxidans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95004814203 Å | ||||||
Authors | Tamada, T. / Hirano, Y. | ||||||
Citation | Journal: Protein Sci. / Year: 2020 Title: Reaction mechanism of tetrathionate hydrolysis based on the crystal structure of tetrathionate hydrolase from Acidithiobacillus ferrooxidans. Authors: Kanao, T. / Hase, N. / Nakayama, H. / Yoshida, K. / Nishiura, K. / Kosaka, M. / Kamimura, K. / Hirano, Y. / Tamada, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l8a.cif.gz | 642.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l8a.ent.gz | 423.3 KB | Display | PDB format |
PDBx/mmJSON format | 6l8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6l8a_validation.pdf.gz | 517.8 KB | Display | wwPDB validaton report |
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Full document | 6l8a_full_validation.pdf.gz | 536.8 KB | Display | |
Data in XML | 6l8a_validation.xml.gz | 94 KB | Display | |
Data in CIF | 6l8a_validation.cif.gz | 133.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l8/6l8a ftp://data.pdbj.org/pub/pdb/validation_reports/l8/6l8a | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 50047.230 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acidithiobacillus ferrooxidans (bacteria) Production host: Escherichia coli (E. coli) References: UniProt: B7J3C9, Hydrolases; Acting on sulfur-sulfur bonds #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 1.93 Å3/Da / Density % sol: 36.42 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: sodium chloride, glycine, PEG 1000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 27, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→42.4 Å / Num. obs: 156219 / % possible obs: 99.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 25.7759592713 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.109 / Net I/av σ(I): 10.3 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.9 / Num. unique obs: 15660 / CC1/2: 0.875 / Rrim(I) all: 0.563 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.95004814203→42.3647721231 Å / SU ML: 0.227474103365 / Cross valid method: FREE R-VALUE / σ(F): 1.96795806727 / Phase error: 23.0146924341 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 25.7975605035 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95004814203→42.3647721231 Å
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Refine LS restraints |
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LS refinement shell |
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