+Open data
-Basic information
Entry | Database: PDB / ID: 3ta9 | ||||||
---|---|---|---|---|---|---|---|
Title | beta-Glucosidase A from the halothermophile H. orenii | ||||||
Components | Glycoside hydrolase family 1 | ||||||
Keywords | HYDROLASE / TIM barrel / glucosidase | ||||||
Function / homology | Function and homology information scopolin beta-glucosidase activity / beta-glucosidase / beta-glucosidase activity / cellulose catabolic process Similarity search - Function | ||||||
Biological species | Halothermothrix orenii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Hofmann, A. / Wang, C.K. / Kori, L.D. / Patel, B.K. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2011 Title: Expression, purification and preliminary crystallographic analysis of the recombinant (beta)-glucosidase (BglA) from the halothermophile Halothermothrix orenii Authors: Kori, L.D. / Hofmann, A. / Patel, B.K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ta9.cif.gz | 190.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ta9.ent.gz | 150 KB | Display | PDB format |
PDBx/mmJSON format | 3ta9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ta/3ta9 ftp://data.pdbj.org/pub/pdb/validation_reports/ta/3ta9 | HTTPS FTP |
---|
-Related structure data
Related structure data | 3fj0 S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
2 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
|
-Components
#1: Protein | Mass: 53158.531 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halothermothrix orenii (bacteria) / Strain: H 168 / OCM 544 / DSM 9562 / Gene: Hore_15280 / Production host: Escherichia coli (E. coli) / References: UniProt: B8CYA8, beta-glucosidase #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.76 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M magnesium acetate, 20% PEG8000, 0.1 M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95375 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 29, 2011 |
Radiation | Monochromator: Double Si with sagittally bent second crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95375 Å / Relative weight: 1 |
Reflection | Resolution: 3→74 Å / Num. all: 19974 / Num. obs: 19515 / % possible obs: 98.4 % / Redundancy: 7.9 % / Rsym value: 0.14 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 6 % / Num. unique all: 2747 / Rsym value: 0.262 / % possible all: 96 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3FJ0 3fj0 Resolution: 3→24.894 Å / SU ML: 0.44 / σ(F): 1.34 / Phase error: 24.87 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 15.003 Å2 / ksol: 0.338 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→24.894 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|