+Open data
-Basic information
Entry | Database: PDB / ID: 6u7j | ||||||
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Title | Uncultured Clostridium sp. Beta-glucuronidase | ||||||
Components | Beta-glucuronidase | ||||||
Keywords | HYDROLASE / microbiome / Glycosyl hydrolase | ||||||
Function / homology | Function and homology information beta-galactosidase / beta-galactosidase activity / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | uncultured Clostridium sp. (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Ervin, S.M. / Redinbo, M.R. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Gut microbial beta-glucuronidases reactivate estrogens as components of the estrobolome that reactivate estrogens. Authors: Ervin, S.M. / Li, H. / Lim, L. / Roberts, L.R. / Liang, X. / Mani, S. / 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 | 6u7j.cif.gz | 606.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6u7j.ent.gz | 398.9 KB | Display | PDB format |
PDBx/mmJSON format | 6u7j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u7/6u7j ftp://data.pdbj.org/pub/pdb/validation_reports/u7/6u7j | HTTPS FTP |
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-Related structure data
Related structure data | 6u7iC 4jkmS 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: 69930.359 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured Clostridium sp. (environmental samples) Gene: uidA_2, SAMEA3545339_03359 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1C5YG41, beta-glucuronidase #2: Chemical | ChemComp-CA / #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: 2.79 Å3/Da / Density % sol: 55.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Calcium Chloride, 0.1 M Tris: HCl, pH 8.5 and 20 % (w/v) PEG 4000 |
-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 PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→29.31 Å / Num. obs: 146335 / % possible obs: 97.94 % / Redundancy: 2.7 % / Biso Wilson estimate: 34.1 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.89 |
Reflection shell | Resolution: 2.2→2.279 Å / Num. unique obs: 14633 / CC1/2: 0.834 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JKM Resolution: 2.2→29.31 Å / SU ML: 0.2121 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.781 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: 37.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→29.31 Å
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Refine LS restraints |
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LS refinement shell |
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