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- PDB-5dt7: Crystal structure of the GH1 beta-glucosidase from Exiguobacteriu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5dt7 | |||||||||
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Title | Crystal structure of the GH1 beta-glucosidase from Exiguobacterium antarcticum B7 in space group C2221 | |||||||||
![]() | Beta-glucosidase | |||||||||
![]() | HYDROLASE / GH1 family / beta-glucosidase / cold-active / tetramer | |||||||||
Function / homology | ![]() scopolin beta-glucosidase activity / beta-glucosidase / beta-glucosidase activity / cellulose catabolic process Similarity search - Function | |||||||||
Biological species | Exiguobacterium antarcticum | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zanphorlin, L.M. / Giuseppe, P.O. / Tonoli, C.C.C. / Murakami, M.T. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 555.7 KB | Display | ![]() |
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PDB format | ![]() | 438.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5dt5C ![]() 4ptvS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 53992.887 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: B7 / Gene: bglA, Eab7_0297 / Plasmid: pET28a / Production host: ![]() ![]() #2: Chemical | ChemComp-CXS / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.8 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M CAPS (pH 10.5), 0.2 M lithium sulfate and 2 M ammonium sulfate using in situ proteolysis (1:1000 (w/w) ratio of trypsin:protein |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 12, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.459 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.15→50 Å / Num. obs: 123301 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 42.751 Å2 / Rmerge F obs: 0.996 / Rmerge(I) obs: 0.086 / Rrim(I) all: 0.103 / Χ2: 1.094 / Net I/σ(I): 8.19 / Num. measured all: 776096 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4PTV Resolution: 2.15→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 12.892 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.167 / 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: 98.9 Å2 / Biso mean: 44.182 Å2 / Biso min: 27.55 Å2
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Refinement step | Cycle: final / Resolution: 2.15→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.147→2.202 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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