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- PDB-8kap: Glycoside hydrolase family 1 beta-glucosidase from Streptomyces g... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8kap | ||||||
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Title | Glycoside hydrolase family 1 beta-glucosidase from Streptomyces griseus (ligand-free) | ||||||
![]() | SGR_2426 | ||||||
![]() | HYDROLASE / beta-Glucosidase | ||||||
Function / homology | DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kumakura, H. / Motouchi, S. / Nakai, H. / Nakajima, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Identification of beta-1,2-glucan-associated glycoside hydrolase family 1 beta-glucosidase from Streptomyces griseus Authors: Kumakura, H. / Motouchi, S. / Nakai, H. / Nakajima, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 317.5 KB | Display | ![]() |
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PDB format | ![]() | 249.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 497.6 KB | Display | ![]() |
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Full document | ![]() | 508.5 KB | Display | |
Data in XML | ![]() | 55.9 KB | Display | |
Data in CIF | ![]() | 76.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8kaqC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 45762.668 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
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-Non-polymers , 5 types, 311 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/BTB.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BTB.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PEG / | ||||||
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#3: Chemical | ChemComp-BTB / #4: Chemical | #5: Chemical | ChemComp-1PE / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Bis-Tris (pH 5.5), 0.2 M ammonium acetate, 15% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Nov 7, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→48.43 Å / Num. obs: 89749 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.991 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.2→2.24 Å / Num. unique obs: 4548 / CC1/2: 0.685 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.474 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→46.261 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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