+Open data
-Basic information
Entry | Database: PDB / ID: 6d8k | |||||||||
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Title | Bacteroides multiple species beta-glucuronidase | |||||||||
Components | Glycosyl hydrolase family 2, sugar binding domain protein | |||||||||
Keywords | HYDROLASE / glycosyl hydrolase / beta-glucuronidase | |||||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | Bacteroides ovatus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | |||||||||
Authors | Walton, W.G. / Pellock, S.J. / Redinbo, M.R. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Three structurally and functionally distinct beta-glucuronidases from the human gut microbeBacteroides uniformis. Authors: Pellock, S.J. / Walton, W.G. / Biernat, K.A. / Torres-Rivera, D. / Creekmore, B.C. / Xu, Y. / Liu, J. / Tripathy, A. / Stewart, L.J. / 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 | 6d8k.cif.gz | 427.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6d8k.ent.gz | 350.2 KB | Display | PDB format |
PDBx/mmJSON format | 6d8k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/6d8k ftp://data.pdbj.org/pub/pdb/validation_reports/d8/6d8k | HTTPS FTP |
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-Related structure data
Related structure data | 6d1nC 6d1pC 6d41C 6d50C 6d6wC 6d7fC 6d89C 6d8gC 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: 69348.617 Da / Num. of mol.: 4 / Fragment: residues 27-567 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides ovatus (bacteria) / Gene: HMPREF2532_04191 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A139KTC9 #2: 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: 2.61 Å3/Da / Density % sol: 52.88 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.2 M Magnesium Chloride, 0.1 M MES: NaOH, pH 6.5, 10 % (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03321 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03321 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→29.435 Å / Num. obs: 73250 / % possible obs: 99.7 % / Redundancy: 4.2 % / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.65→2.71 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→29.435 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.16 / 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: 2.65→29.435 Å
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Refine LS restraints |
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LS refinement shell |
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