+Open data
-Basic information
Entry | Database: PDB / ID: 6ed1 | |||||||||
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Title | Bacteroides dorei Beta-glucuronidase | |||||||||
Components | Glycosyl hydrolase family 2, sugar binding domain protein | |||||||||
Keywords | HYDROLASE / Glycosyl hydrolase | |||||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | Bacteroides dorei (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Biernat, K.A. / Redinbo, M.R. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Sci Rep / Year: 2019 Title: Structure, function, and inhibition of drug reactivating human gut microbial beta-glucuronidases. Authors: Biernat, K.A. / Pellock, S.J. / Bhatt, A.P. / Bivins, M.M. / Walton, W.G. / Tran, B.N.T. / Wei, L. / Snider, M.C. / Cesmat, A.P. / Tripathy, A. / Erie, D.A. / 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 | 6ed1.cif.gz | 686.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ed1.ent.gz | 559.1 KB | Display | PDB format |
PDBx/mmJSON format | 6ed1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ed1_validation.pdf.gz | 478.6 KB | Display | wwPDB validaton report |
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Full document | 6ed1_full_validation.pdf.gz | 538.1 KB | Display | |
Data in XML | 6ed1_validation.xml.gz | 120 KB | Display | |
Data in CIF | 6ed1_validation.cif.gz | 164.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/6ed1 ftp://data.pdbj.org/pub/pdb/validation_reports/ed/6ed1 | HTTPS FTP |
-Related structure data
Related structure data | 6ec6C 6ecaC 6ed2C 5uj6S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 100613.109 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides dorei (bacteria) / Gene: BSEG_01974 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: C3R9X4 #2: Chemical | ChemComp-NA / #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: 2.49 Å3/Da / Density % sol: 50.56 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.35 M sodium citrate, 16% PEG3350 |
-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 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→29.54 Å / Num. obs: 90006 / % possible obs: 99.35 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.1181 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.9→2.95 Å / Rmerge(I) obs: 0.4171 / Num. measured obs: 29812 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5UJ6 Resolution: 2.9→29.536 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.09
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→29.536 Å
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Refine LS restraints |
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LS refinement shell |
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