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- PDB-4ufj: Mouse Galactocerebrosidase complexed with iso-galacto-fagomine la... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ufj | |||||||||
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Title | Mouse Galactocerebrosidase complexed with iso-galacto-fagomine lactam IGL | |||||||||
![]() | GALACTOCEREBROSIDASE![]() | |||||||||
![]() | ![]() ![]() ![]() ![]() | |||||||||
Function / homology | ![]() Glycosphingolipid catabolism / galactosylceramide catabolic process / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Hill, C.H. / Viuff, A.H. / Spratley, S.J. / Salamone, S. / Christensen, S.H. / Read, R.J. / Moriarty, N.W. / Jensen, H.H. / Deane, J.E. | |||||||||
![]() | ![]() Title: Azasugar Inhibitors as Pharmacological Chaperones for Krabbe Disease. Authors: Hill, C.H. / Viuff, A.H. / Spratley, S.J. / Salamone, S. / Christensen, S.H. / Read, R.J. / Moriarty, N.W. / Jensen, H.H. / Deane, J.E. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 278.4 KB | Display | ![]() |
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PDB format | ![]() | 224.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4ufhC ![]() 4ufiC ![]() 4ufkC ![]() 4uflC ![]() 4ufmC ![]() 3zr5S 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
-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: COMPLEX WITH IGL / 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 , 3 types, 198 molecules ![](data/chem/img/IF7.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-IF7 / ( |
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#5: Chemical | ChemComp-CA / |
#6: Water | ChemComp-HOH / ![]() |
-Details
Sequence details | NUMBERING IS FROM SECOND START SITE AS USED IN THE LITERATURE |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.78 % / Description: NONE |
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Crystal grow![]() | pH: 6.8 Details: 0.2 M SODIUM ACETATE, 0.1 M SODIUM CACODYLATE (PH 6.8), 34% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 28, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.2→63.2 Å / Num. obs: 46932 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 8.6 % / Biso Wilson estimate: 38.64 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 8.5 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 2 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 3ZR5 Resolution: 2.2→63.212 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 20.32 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→63.212 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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