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Open data
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Basic information
Entry | Database: PDB / ID: 6d1p | |||||||||
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Title | Apo structure of Bacteroides uniformis beta-glucuronidase 3 | |||||||||
![]() | Glycosyl hydrolases family 2, sugar binding domain protein | |||||||||
![]() | HYDROLASE / beta-glucuronidase | |||||||||
Function / homology | ![]() hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process 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 | ![]() | 342.3 KB | Display | ![]() |
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PDB format | ![]() | 274.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6d1nC ![]() 6d41C ![]() 6d50C ![]() 6d6wC ![]() 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 93185.133 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: M094_3281 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 831 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SCN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SCN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | ChemComp-K / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.57 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 8% PEG 3350, 0.2 M Potassium Thiocyanate and 0.1M Hepes pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 5, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03316 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→29.48 Å / Num. obs: 83426 / % possible obs: 99.9 % / Redundancy: 6.8 % / Net I/σ(I): 21 |
Reflection shell | Resolution: 2.35→2.39 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 / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→29.095 Å
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Refine LS restraints |
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LS refinement shell |
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