+Open data
-Basic information
Entry | Database: PDB / ID: 4hz6 | |||||||||
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Title | crystal structure of BglB | |||||||||
Components | Beta-glucosidase | |||||||||
Keywords | HYDROLASE / glucosidase / beta-glucosidase / bglB / Bgl / Glycosidase / TIM barrel / Carbohydrate/Sugar Binding | |||||||||
Function / homology | Function and homology information scopolin beta-glucosidase activity / beta-glucosidase / beta-glucosidase activity / cellulose catabolic process / cytosol Similarity search - Function | |||||||||
Biological species | uncultured bacterium (environmental samples) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | |||||||||
Authors | Hwang, K.Y. / Nam, K.H. | |||||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2010 Title: Structural insights into the substrate recognition properties of beta-glucosidase. Authors: Nam, K.H. / Sung, M.W. / Hwang, K.Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hz6.cif.gz | 204 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hz6.ent.gz | 159.5 KB | Display | PDB format |
PDBx/mmJSON format | 4hz6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hz/4hz6 ftp://data.pdbj.org/pub/pdb/validation_reports/hz/4hz6 | HTTPS FTP |
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-Related structure data
Related structure data | 4hz7C 4hz8C 3cmjS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 50294.273 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 39-482 / Mutation: E39N, L40V, Q41K, P42K, K45E, R477N, A481E, A482D Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Gene: bglA / Production host: Escherichia coli (E. coli) / References: UniProt: Q0GMU3 |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.69 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M Tris, pH 7.0-7.4, 0.8M Na/K tartaric acid, VAPOR DIFFUSION, HANGING DROP, temperature 295K, temperature 295.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.23 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 14, 2008 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.23 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→20.03 Å / Num. all: 82773 / Num. obs: 82773 / % possible obs: 95.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.4→1.45 Å / % possible all: 88.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CMJ Resolution: 1.4→20.03 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / Occupancy max: 1 / Occupancy min: 1 / SU B: 1.74 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 57.35 Å2 / Biso mean: 13.9182 Å2 / Biso min: 4.98 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→20.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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