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Yorodumi- PDB-3gxf: Crystal structure of acid-beta-glucosidase with isofagomine at ne... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gxf | ||||||
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Title | Crystal structure of acid-beta-glucosidase with isofagomine at neutral pH | ||||||
Components | Glucosylceramidase | ||||||
Keywords | HYDROLASE / Alternative initiation / Disease mutation / Disulfide bond / Gaucher disease / Glycoprotein / Glycosidase / Ichthyosis / Lipid metabolism / Lysosome / Membrane / Sphingolipid metabolism | ||||||
Function / homology | Function and homology information positive regulation of protein lipidation / steryl-beta-glucosidase activity / beta-glucoside catabolic process / positive regulation of neuronal action potential / cerebellar Purkinje cell layer formation / galactosylceramidase / termination of signal transduction / galactosylceramidase activity / positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization / lymphocyte migration ...positive regulation of protein lipidation / steryl-beta-glucosidase activity / beta-glucoside catabolic process / positive regulation of neuronal action potential / cerebellar Purkinje cell layer formation / galactosylceramidase / termination of signal transduction / galactosylceramidase activity / positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization / lymphocyte migration / glucosylceramidase / glucosylceramide catabolic process / scavenger receptor binding / regulation of lysosomal protein catabolic process / sphingosine biosynthetic process / autophagosome organization / glucosylceramidase activity / microglial cell proliferation / regulation of TOR signaling / glucosyltransferase activity / ceramide biosynthetic process / lipid storage / response to thyroid hormone / microglia differentiation / Glycosphingolipid catabolism / pyramidal neuron differentiation / lipid glycosylation / brain morphogenesis / response to pH / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / positive regulation of protein-containing complex disassembly / motor behavior / neuromuscular process / Transferases; Glycosyltransferases; Hexosyltransferases / hematopoietic stem cell proliferation / lysosome organization / response to testosterone / response to dexamethasone / Association of TriC/CCT with target proteins during biosynthesis / negative regulation of interleukin-6 production / homeostasis of number of cells / antigen processing and presentation / regulation of macroautophagy / establishment of skin barrier / negative regulation of protein-containing complex assembly / positive regulation of protein dephosphorylation / cell maturation / cholesterol metabolic process / respiratory electron transport chain / cellular response to starvation / lysosomal lumen / negative regulation of MAP kinase activity / determination of adult lifespan / trans-Golgi network / negative regulation of inflammatory response / autophagy / response to estrogen / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / T cell differentiation in thymus / cellular response to tumor necrosis factor / proteasome-mediated ubiquitin-dependent protein catabolic process / neuron apoptotic process / negative regulation of neuron apoptotic process / lysosome / lysosomal membrane / signaling receptor binding / Golgi apparatus / endoplasmic reticulum / extracellular exosome Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å | ||||||
Authors | Lieberman, R.L. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Effects of pH and iminosugar pharmacological chaperones on lysosomal glycosidase structure and stability. Authors: Lieberman, R.L. / D'aquino, J.A. / Ringe, D. / Petsko, G.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gxf.cif.gz | 417.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gxf.ent.gz | 343.5 KB | Display | PDB format |
PDBx/mmJSON format | 3gxf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/3gxf ftp://data.pdbj.org/pub/pdb/validation_reports/gx/3gxf | HTTPS FTP |
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-Related structure data
Related structure data | 3gxdC 3gxiC 3gxmC 3gxnC 3gxpC 3gxtC 2nsxS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 4 / Auth seq-ID: 1 - 497 / Label seq-ID: 1 - 497
NCS ensembles :
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-Components
-Protein / Sugars , 2 types, 8 molecules ABCD
#1: Protein | Mass: 55640.168 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GBA, GC, GLUC / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P04062, glucosylceramidase #3: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 976 molecules
#2: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Water | ChemComp-HOH / | |
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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: 3.24 Å3/Da / Density % sol: 62.02 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.5 Details: 0.8 M NaH2PO4, 0.8 M KH2PO4, 0.1 M Hepes pH 7.5, SOAK with 500uM isofagomine for 10 min, glycerol in cryo, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.4→32.12 Å / Num. obs: 103572 |
-Processing
Software |
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Refinement | Starting model: PDB entry '2NSX Resolution: 2.4→32.12 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.216 / WRfactor Rwork: 0.157 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.825 / SU B: 7.687 / SU ML: 0.178 / SU R Cruickshank DPI: 0.336 / SU Rfree: 0.255 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.336 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.29 Å2 / Biso mean: 27.274 Å2 / Biso min: 6.12 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→32.12 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Number: 3930 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.4→2.463 Å / Total num. of bins used: 20
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