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Yorodumi- PDB-6uss: Catalytic S88C mutant of gut microbial sulfatase from Bacteroides... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6uss | ||||||
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Title | Catalytic S88C mutant of gut microbial sulfatase from Bacteroides fragilis CAG:558 | ||||||
Components | Sulfatase | ||||||
Keywords | HYDROLASE / microbiome / arylsulfatase | ||||||
Function / homology | Sulfatases signature 1. / Sulfatase, conserved site / sulfuric ester hydrolase activity / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / Sulfatase / Sulfatase domain-containing protein Function and homology information | ||||||
Biological species | Bacteroides fragilis CAG:558 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Ervin, S.M. / Redinbo, M.R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2020 Title: Structural Insights into Endobiotic Reactivation by Human Gut Microbiome-Encoded Sulfatases. Authors: Ervin, S.M. / Simpson, J.B. / Gibbs, M.E. / Creekmore, B.C. / Lim, L. / Walton, W.G. / Gharaibeh, R.Z. / Redinbo, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6uss.cif.gz | 254.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uss.ent.gz | 163.6 KB | Display | PDB format |
PDBx/mmJSON format | 6uss.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6uss_validation.pdf.gz | 248.7 KB | Display | wwPDB validaton report |
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Full document | 6uss_full_validation.pdf.gz | 248.7 KB | Display | |
Data in XML | 6uss_validation.xml.gz | 1002 B | Display | |
Data in CIF | 6uss_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/us/6uss ftp://data.pdbj.org/pub/pdb/validation_reports/us/6uss | HTTPS FTP |
-Related structure data
Related structure data | 6ustC 6biaS 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
#1: Protein | Mass: 57872.117 Da / Num. of mol.: 2 / Mutation: S88C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides fragilis CAG:558 (bacteria) Production host: Escherichia coli (E. coli) / References: UniProt: A0A081TVR9, UniProt: R5RYH7*PLUS #2: Chemical | #3: 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: 2.95 Å3/Da / Density % sol: 58.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 9mg/mL protein 10% (w/v) PEG 8000, 100 mM Potassium phosphate monobasic/ Sodium phosphate dibasic pH 6.2 200 mM Sodium Chloride. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→49.48 Å / Num. obs: 47324 / % possible obs: 99.1 % / Redundancy: 4.2 % / Biso Wilson estimate: 21.17 Å2 / CC1/2: 0.971 / Net I/σ(I): 5.01 |
Reflection shell | Resolution: 2.5→2.589 Å / Num. unique obs: 4698 / CC1/2: 0.708 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6BIA Resolution: 2.5→49.48 Å / SU ML: 0.2981 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.3352 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: 22.19 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→49.48 Å
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Refine LS restraints |
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LS refinement shell |
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