[English] 日本語
![](img/lk-miru.gif)
- PDB-6d89: Bacteroides uniformis beta-glucuronidase 1 with N-terminal loop d... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6d89 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Bacteroides uniformis beta-glucuronidase 1 with N-terminal loop deletion | |||||||||
![]() | Beta-galactosidase/beta-glucuronidase | |||||||||
![]() | HYDROLASE / glycosyl hydrolase 2 / beta-glucuronidase | |||||||||
Function / homology | ![]() : / 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 | ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 500.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 419.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 6d1nC ![]() 6d1pC ![]() 6d41C ![]() 6d50C ![]() 6d6wC ![]() 6d7fC ![]() 6d8gC ![]() 6d8kC C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 69107.555 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CIT / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.03 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.1 M Sodium Citrate: Citric Acid, pH 5.5, 20 % (w/v) PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
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: 2→29.345 Å / Num. obs: 163378 / % possible obs: 98.4 % / Redundancy: 6.1 % / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2→2.03 Å |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→29.345 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|