+Open data
-Basic information
Entry | Database: PDB / ID: 6d1n | |||||||||
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Title | Apo structure of Bacteroides uniformis Beta-glucuronidase 1 | |||||||||
Components | Beta-galactosidase/beta-glucuronidase | |||||||||
Keywords | HYDROLASE / glycoside hydrolase | |||||||||
Function / homology | Function and homology information : / beta-glucuronidase / beta-glucuronidase activity / carbohydrate binding / carbohydrate metabolic process / signaling receptor binding / extracellular space Similarity search - Function | |||||||||
Biological species | Bacteroides uniformis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 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 | 6d1n.cif.gz | 273.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6d1n.ent.gz | 216.7 KB | Display | PDB format |
PDBx/mmJSON format | 6d1n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6d1n_validation.pdf.gz | 447.9 KB | Display | wwPDB validaton report |
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Full document | 6d1n_full_validation.pdf.gz | 454.4 KB | Display | |
Data in XML | 6d1n_validation.xml.gz | 51.1 KB | Display | |
Data in CIF | 6d1n_validation.cif.gz | 76.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/6d1n ftp://data.pdbj.org/pub/pdb/validation_reports/d1/6d1n | HTTPS FTP |
-Related structure data
Related structure data | 6d1pC 6d41C 6d50C 6d6wC 6d7fC 6d89C 6d8gC 6d8kC 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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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 70098.500 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides uniformis (bacteria) / Gene: uidA_4, ERS417307_01040 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A174CQK8, beta-glucuronidase #2: Chemical | ChemComp-GOL / #3: Chemical | #4: 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: 2.71 Å3/Da / Density % sol: 54.6 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 1000, 0.1M Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03322 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03322 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→29.605 Å / Num. obs: 75592 / % possible obs: 99.9 % / Redundancy: 6.8 % / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 2.2→2.25 Å |
-Processing
Software |
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Refinement | Resolution: 2.2→29.605 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.81
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→29.605 Å
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Refine LS restraints |
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LS refinement shell |
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