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- PDB-6y6s: Mouse Galactocerebrosidase complexed with galacto-noeurostegine G... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6y6s | ||||||
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Title | Mouse Galactocerebrosidase complexed with galacto-noeurostegine GNS at pH 6.8 | ||||||
![]() | Galactocerebrosidase | ||||||
![]() | HYDROLASE / Inhibitor | ||||||
Function / homology | ![]() Glycosphingolipid catabolism / galactosylceramide catabolic process / galactosylceramidase / galactosylceramidase activity / myelination / lysosome / mitochondrion Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Deane, J.E. / McLoughlin, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The Bicyclic Form of galacto -Noeurostegine Is a Potent Inhibitor of beta-Galactocerebrosidase. Authors: Viuff, A. / Salamone, S. / McLoughlin, J. / Deane, J.E. / Jensen, H.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 335.3 KB | Display | ![]() |
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PDB format | ![]() | 226.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 26.4 KB | Display | |
Data in CIF | ![]() | 38.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6y6tC ![]() 3zr5S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 74596.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Glycosylated protein / Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 2 types, 4 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / | |
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-Non-polymers , 4 types, 270 molecules ![](data/chem/img/ODW.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ODW / ( |
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#5: Chemical | ChemComp-CA / |
#6: Chemical | ChemComp-NI / |
#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M sodium acetate, 0.1 M sodium cacodylate (pH 6.8), and 34% wt/vol polyethylene glycol 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 21, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→124.36 Å / Num. obs: 53072 / % possible obs: 100 % / Redundancy: 10 % / Biso Wilson estimate: 40.97 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.153 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.1→2.14 Å / Num. unique obs: 2623 / CC1/2: 0.461 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3zr5 Resolution: 2.1→56.07 Å / SU ML: 0.2553 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.2062
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.75 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→56.07 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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