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Yorodumi- PDB-6d8g: D341A D367A calcium binding mutant of Bacteroides uniformis beta-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6d8g | |||||||||
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Title | D341A D367A calcium binding mutant of Bacteroides uniformis beta-glucuronidase 2 | |||||||||
Components | Glycosyl hydrolases family 2, sugar binding domain protein | |||||||||
Keywords | HYDROLASE / beta-glucuronidase | |||||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | Bacteroides uniformis str. 3978 T3 ii (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 | 6d8g.cif.gz | 340.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6d8g.ent.gz | 272 KB | Display | PDB format |
PDBx/mmJSON format | 6d8g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6d8g_validation.pdf.gz | 445.1 KB | Display | wwPDB validaton report |
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Full document | 6d8g_full_validation.pdf.gz | 466.7 KB | Display | |
Data in XML | 6d8g_validation.xml.gz | 56 KB | Display | |
Data in CIF | 6d8g_validation.cif.gz | 76.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/6d8g ftp://data.pdbj.org/pub/pdb/validation_reports/d8/6d8g | HTTPS FTP |
-Related structure data
Related structure data | 6d1nC 6d1pC 6d41C 6d50C 6d6wC 6d7fC 6d89C 6d8kC 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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Unit cell |
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-Components
#1: Protein | Mass: 101348.812 Da / Num. of mol.: 2 / Mutation: D341A, D367A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides uniformis str. 3978 T3 ii (bacteria) Gene: M094_3283 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A078SUX9 #2: Chemical | |
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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: 2.38 Å3/Da / Density % sol: 48.33 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Potassium Chloride, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.98618 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98618 Å / Relative weight: 1 |
Reflection | Resolution: 3→29.55 Å / Num. obs: 39566 / % possible obs: 99.9 % / Redundancy: 13.3 % / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 3→3.12 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5UJ6 Resolution: 3→29.546 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.21 / 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: 3→29.546 Å
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Refine LS restraints |
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LS refinement shell |
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