[English] 日本語
Yorodumi- PDB-7bbs: Structure of Bg10: an alcohol-tolerant and glucose-stimulated B-g... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bbs | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of Bg10: an alcohol-tolerant and glucose-stimulated B-glucosidase | |||||||||
Components | Beta-glucosidase Bg10 | |||||||||
Keywords | HYDROLASE / Glucose-stimulated / GH1 family / metagenomics | |||||||||
Function / homology | Function and homology information scopolin beta-glucosidase activity / beta-glucosidase activity / beta-glucosidase / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | uncultured bacterium (environmental samples) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Maldaner Pereira, P.A. / Gomes-Pepe, E.S. / Silva, S.T.N. / Matias, P.M. / Lemos, E.G.M. | |||||||||
Funding support | Brazil, Portugal, 2items
| |||||||||
Citation | Journal: TO BE PUBLISHED Title: Structure of Bg10: an alcohol-tolerant and glucose-stimulated beta-glucosidase Authors: Maldaner Pereira, P.A. / Gomes-Pepe, E.S. / Silva, S.T.N. / Matias, P.M. / Lemos, E.G.M. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7bbs.cif.gz | 420.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7bbs.ent.gz | 288.1 KB | Display | PDB format |
PDBx/mmJSON format | 7bbs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bb/7bbs ftp://data.pdbj.org/pub/pdb/validation_reports/bb/7bbs | HTTPS FTP |
---|
-Related structure data
Related structure data | 1gnxS S: Starting model for refinement |
---|---|
Similar structure data | |
Experimental dataset #1 | Data reference: 10.5281/zenodo.4327001 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||
Components on special symmetry positions |
| |||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
|
-Components
#1: Protein | Mass: 54233.020 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Production host: Escherichia coli (E. coli) / References: UniProt: A0A1L3HS62, beta-glucosidase #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.9 % / Description: diamond-shaped plates |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 12% (v/v) PEG 3550, 250 mM potassium citrate, 4% (v/v) 1,5-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 13, 2019 |
Radiation | Monochromator: Si 111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→112.13 Å / Num. obs: 33702 / % possible obs: 54.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 27.94 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.193 / Rpim(I) all: 0.124 / Rrim(I) all: 0.23 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 2.3→2.604 Å / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1686 / CC1/2: 0.584 / Rpim(I) all: 0.486 / Rrim(I) all: 0.809 / % possible all: 8.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GNX Resolution: 2.3→112.13 Å / SU ML: 0.336 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.498 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.35 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→112.13 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 1.42353283856 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 17 - 484
|