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Yorodumi- PDB-4ufk: Mouse Galactocerebrosidase complexed with dideoxy-imino-lyxitol DIL -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ufk | |||||||||
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Title | Mouse Galactocerebrosidase complexed with dideoxy-imino-lyxitol DIL | |||||||||
Components | GALACTOCEREBROSIDASE | |||||||||
Keywords | HYDROLASE / GLYCOSYL HYDROLASE / LYSOSOME | |||||||||
Function / homology | Function and homology information Glycosphingolipid catabolism / galactosylceramide catabolic process / galactosylceramidase / galactosylceramidase activity / myelination / lysosome / mitochondrion Similarity search - Function | |||||||||
Biological species | MUS MUSCULUS (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.402 Å | |||||||||
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. | |||||||||
Citation | Journal: Chem.Sci. / Year: 2015 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ufk.cif.gz | 278.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ufk.ent.gz | 225.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ufk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uf/4ufk ftp://data.pdbj.org/pub/pdb/validation_reports/uf/4ufk | HTTPS FTP |
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-Related structure data
Related structure data | 4ufhC 4ufiC 4ufjC 4uflC 4ufmC 3zr5S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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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 DIL / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line (production host): HEK293 T / Production host: HOMO SAPIENS (human) / References: UniProt: P54818, galactosylceramidase |
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-Sugars , 2 types, 5 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | |
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-Non-polymers , 3 types, 183 molecules
#3: Chemical | ChemComp-LDU / |
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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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.43 % / 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: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.98 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 28, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→73.22 Å / Num. obs: 35733 / % possible obs: 99.7 % / Observed criterion σ(I): 2.1 / Redundancy: 10.4 % / Biso Wilson estimate: 43.47 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 10.4 % / Rmerge(I) obs: 1.18 / Mean I/σ(I) obs: 2.1 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZR5 Resolution: 2.402→73.218 Å / SU ML: 0.25 / σ(F): 1.34 / Phase error: 18.96 / 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: 2.402→73.218 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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