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- PDB-6jz8: b-glucuronidase from Ruminococcus gnavus in complex with D-glucar... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6jz8 | |||||||||
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Title | b-glucuronidase from Ruminococcus gnavus in complex with D-glucaro 1,5-lactone | |||||||||
![]() | Beta-glucuronidase | |||||||||
![]() | HYDROLASE / b-glucuronidase | |||||||||
Function / homology | ![]() glucuronoside catabolic process / beta-glucuronidase / beta-glucuronidase activity / beta-galactosidase activity / carbohydrate binding / carbohydrate metabolic process / signaling receptor binding / extracellular space Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Dashnyam, P. / Lin, H.Y. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Substituent Position of Iminocyclitols Determines the Potency and Selectivity for Gut Microbial Xenobiotic-Reactivating Enzymes. Authors: Dashnyam, P. / Lin, H.Y. / Chen, C.Y. / Gao, S. / Yeh, L.F. / Hsieh, W.C. / Tu, Z. / Lin, C.H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 270.1 KB | Display | ![]() |
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PDB format | ![]() | 213.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.8 KB | Display | ![]() |
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Full document | ![]() | 468.6 KB | Display | |
Data in XML | ![]() | 51.3 KB | Display | |
Data in CIF | ![]() | 78.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jz1C ![]() 6jz2C ![]() 6jz3C ![]() 6jz4C ![]() 6jz5C ![]() 6jz6C ![]() 6jz7C ![]() 5z19S S: Starting model for refinement 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 70038.883 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Sugar | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 70% MPD, 0.1 M HEPES, pH 7.5, 0.2 M CaCl2 |
-Data collection
Diffraction | Mean temperature: 277 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 11, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.58→30 Å / Num. obs: 183679 / % possible obs: 97.1 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.023 / Rrim(I) all: 0.058 / Χ2: 0.889 / Net I/σ(I): 15.7 / Num. measured all: 1120545 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5Z19 Resolution: 1.583→29.95 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso max: 73.61 Å2 / Biso mean: 17.4162 Å2 / Biso min: 4.67 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.583→29.95 Å
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LS refinement shell | Resolution: 1.583→1.64 Å
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