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Open data
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Basic information
Entry | Database: PDB / ID: 6d6w | |||||||||
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Title | Bacteroides uniformis beta-glucuronidase 1 bound to glucuronate | |||||||||
![]() | Beta-galactosidase/beta-glucuronidase | |||||||||
![]() | HYDROLASE / glycosyl hydrolase / beta-glucuronidase | |||||||||
Function / homology | ![]() glucuronoside catabolic process / beta-glucuronidase / beta-glucuronidase activity / carbohydrate binding / carbohydrate metabolic process / signaling receptor binding / extracellular space Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Walton, W.G. / Pellock, S.J. / Redinbo, M.R. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 591.1 KB | Display | ![]() |
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PDB format | ![]() | 470.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 127.8 KB | Display | |
Data in CIF | ![]() | 198.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6d1nC ![]() 6d1pC ![]() 6d41C ![]() 6d50C ![]() 6d7fC ![]() 6d89C ![]() 6d8gC ![]() 6d8kC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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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.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Sugar | ChemComp-GCU / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.25 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.1M Sodium Citrate: Citrate Acid, pH 5.5, 20% PEG 3000, 20mM Glucuronic Acid |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03319 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→29.98 Å / Num. all: 261960 / Num. obs: 261936 / % possible obs: 100 % / Redundancy: 6.7 % / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.8→1.83 Å |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→29.793 Å
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Refine LS restraints |
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LS refinement shell |
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