[English] 日本語
Yorodumi- PDB-6d41: Bacteriodes uniformis beta-glucuronidase 1 bound to D-glucaro-1,5... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6d41 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Bacteriodes uniformis beta-glucuronidase 1 bound to D-glucaro-1,5-lactone | |||||||||
Components | Beta-galactosidase/beta-glucuronidase | |||||||||
Keywords | HYDROLASE | |||||||||
Function / homology | Function and homology information beta-glucuronidase / beta-glucuronidase activity / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | Bacteroides uniformis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Walton, W.G. / Pellock, S.J. / Redinbo, M.R. | |||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6d41.cif.gz | 286.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6d41.ent.gz | 226.5 KB | Display | PDB format |
PDBx/mmJSON format | 6d41.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/6d41 ftp://data.pdbj.org/pub/pdb/validation_reports/d4/6d41 | HTTPS FTP |
---|
-Related structure data
Related structure data | 6d1nSC 6d1pC 6d50C 6d6wC 6d7fC 6d89C 6d8gC 6d8kC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
3 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-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: Sugar | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.79 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 16% PEG 1000, Tris pH 8.5, 2mM Saccharolactone |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03322 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 16, 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: 1.9→29.934 Å / Num. obs: 114979 / % possible obs: 97.7 % / Redundancy: 6.9 % / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.9→1.93 Å |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6D1N Resolution: 1.9→29.934 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.05
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→29.934 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|