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- PDB-3vkk: Crystal Structure Of The Covalent Intermediate Of Human Cytosolic... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3vkk | ||||||
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Title | Crystal Structure Of The Covalent Intermediate Of Human Cytosolic Beta-Glucosidase-mannose complex | ||||||
![]() | Cytosolic beta-glucosidase | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Noguchi, J. / Hayashi, Y. / Okino, N. / Ito, M. / Kimura, M. / Kakuta, Y. | ||||||
![]() | ![]() Title: Structural basis for inhibition mechanism of human cytosolic beta-glucosidase by monnoside Authors: Noguchi, J. / Hayashi, Y. / Okino, N. / Ito, M. / Kimura, M. / Kakuta, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.7 KB | Display | ![]() |
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PDB format | ![]() | 86.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | |
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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
-Protein / Sugars , 2 types, 2 molecules A![](data/chem/img/MAN.gif)
![](data/chem/img/MAN.gif)
#1: Protein | Mass: 53750.402 Da / Num. of mol.: 1 / Mutation: E165Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#6: Sugar | ChemComp-MAN / ![]() |
-Non-polymers , 6 types, 169 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PLM.gif)
![](data/chem/img/OLA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PLM.gif)
![](data/chem/img/OLA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ![]() #3: Chemical | ![]() #4: Chemical | ChemComp-PLM / | ![]() #5: Chemical | ChemComp-OLA / | ![]() #7: Chemical | ChemComp-MG / | #8: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow![]() | Temperature: 293.4 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 27.5% PEG3350, 0.2M MgCl2, 0.1M Tris-HCl, 15% glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.4K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2→50 Å / Num. all: 34315 / Num. obs: 34315 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 43.6 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 8.8 / Num. unique all: 3355 / Rsym value: 0.342 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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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 mean: 28.963 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.001→2.053 Å / Total num. of bins used: 20
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