[English] 日本語
Yorodumi- PDB-8ht0: Improved thermostability of a glucose-tolerant glycosidase based ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ht0 | ||||||
---|---|---|---|---|---|---|---|
Title | Improved thermostability of a glucose-tolerant glycosidase based on its X-ray crystal structure | ||||||
Components | Beta-glucosidase | ||||||
Keywords | HYDROLASE / glycosidase / crystal / thermostability | ||||||
Function / homology | Function and homology information scopolin beta-glucosidase activity / beta-glucosidase activity / beta-glucosidase / cellulose catabolic process Similarity search - Function | ||||||
Biological species | Caldibacillus thermoamylovorans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Dong, P.P. / Wu, Y.K. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: To Be Published Title: Improved thermostability of a glucose-tolerant glycosidase based on its X-ray crystal structure Authors: Dong, P.P. / Wu, Y.K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8ht0.cif.gz | 112.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8ht0.ent.gz | 84.8 KB | Display | PDB format |
PDBx/mmJSON format | 8ht0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ht/8ht0 ftp://data.pdbj.org/pub/pdb/validation_reports/ht/8ht0 | HTTPS FTP |
---|
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 51936.414 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caldibacillus thermoamylovorans (bacteria) Gene: CQJ30_16875 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2U8EHQ1, beta-glucosidase |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.07 Å3/Da / Density % sol: 69.81 % |
---|---|
Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop Details: 0.1M Citric acid pH 4.0,1.4M Ammonium sulfate pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 6, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→43.16 Å / Num. obs: 61362 / % possible obs: 100 % / Redundancy: 26.4 % / CC1/2: 1 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 1.96→2.01 Å / Num. unique obs: 4500 / CC1/2: 0.671 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→39.197 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.79 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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→39.197 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|