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Yorodumi- PDB-5dt5: Crystal structure of the GH1 beta-glucosidase from Exiguobacteriu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dt5 | |||||||||
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Title | Crystal structure of the GH1 beta-glucosidase from Exiguobacterium antarcticum B7 in space group P21 | |||||||||
Components | Beta-glucosidase | |||||||||
Keywords | HYDROLASE / GH1 family / beta-glucosidase / cold-active / tetramer | |||||||||
Function / homology | Function and homology information scopolin beta-glucosidase activity / beta-glucosidase / beta-glucosidase activity / cellulose catabolic process Similarity search - Function | |||||||||
Biological species | Exiguobacterium antarcticum | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.24 Å | |||||||||
Authors | Zanphorlin, L.M. / Giuseppe, P.O. / Tonoli, C.C.C. / Murakami, M.T. | |||||||||
Funding support | Brazil, 2items
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Citation | Journal: Sci Rep / Year: 2016 Title: Oligomerization as a strategy for cold adaptation: Structure and dynamics of the GH1 beta-glucosidase from Exiguobacterium antarcticum B7. Authors: Zanphorlin, L.M. / de Giuseppe, P.O. / Honorato, R.V. / Tonoli, C.C. / Fattori, J. / Crespim, E. / de Oliveira, P.S. / Ruller, R. / Murakami, M.T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dt5.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5dt5.ent.gz | 839.1 KB | Display | PDB format |
PDBx/mmJSON format | 5dt5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dt5_validation.pdf.gz | 504.1 KB | Display | wwPDB validaton report |
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Full document | 5dt5_full_validation.pdf.gz | 514.5 KB | Display | |
Data in XML | 5dt5_validation.xml.gz | 108.8 KB | Display | |
Data in CIF | 5dt5_validation.cif.gz | 148.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/5dt5 ftp://data.pdbj.org/pub/pdb/validation_reports/dt/5dt5 | HTTPS FTP |
-Related structure data
Related structure data | 5dt7C 4ptvS 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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Unit cell |
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-Components
#1: Protein | Mass: 53992.887 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Exiguobacterium antarcticum (strain B7) (bacteria) Strain: B7 / Gene: bglA, Eab7_0297 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: K0A8J9, beta-glucosidase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.04 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M TRIS (pH 8.5), 2% (v/v) PEG400 and 1.45 M lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 19, 2015 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.24→49.11 Å / Num. obs: 203452 / % possible obs: 97.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 9.54 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PTV Resolution: 2.24→49.11 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.2203 / WRfactor Rwork: 0.2005 / FOM work R set: 0.8185 / SU B: 10.96 / SU ML: 0.135 / SU R Cruickshank DPI: 0.0635 / SU Rfree: 0.0435 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.044 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.01 Å2 / Biso mean: 44.132 Å2 / Biso min: 18.05 Å2
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Refinement step | Cycle: final / Resolution: 2.24→49.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.238→2.296 Å / Total num. of bins used: 20
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Refinement TLS params. | L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: -0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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