+Open data
-Basic information
Entry | Database: PDB / ID: 3gxd | ||||||
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Title | Crystal structure of Apo acid-beta-glucosidase pH 4.5 | ||||||
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 / positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization / galactosylceramidase / termination of signal transduction / galactosylceramidase activity / 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 / positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization / galactosylceramidase / termination of signal transduction / galactosylceramidase activity / lymphocyte migration / glucosylceramidase / scavenger receptor binding / glucosylceramide catabolic process / regulation of lysosomal protein catabolic process / autophagosome organization / glucosylceramidase activity / microglial cell proliferation / sphingosine biosynthetic process / glucosyltransferase activity / regulation of TOR signaling / ceramide biosynthetic process / lipid storage / microglia differentiation / response to thyroid hormone / Glycosphingolipid catabolism / pyramidal neuron differentiation / lipid glycosylation / brain morphogenesis / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / response to pH / 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 / antigen processing and presentation / negative regulation of interleukin-6 production / homeostasis of number of cells / regulation of macroautophagy / establishment of skin barrier / negative regulation of protein-containing complex assembly / positive regulation of protein dephosphorylation / cell maturation / cellular response to starvation / respiratory electron transport chain / cholesterol metabolic process / lysosomal lumen / negative regulation of MAP kinase activity / determination of adult lifespan / trans-Golgi network / autophagy / negative regulation of inflammatory response / response to estrogen / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / cellular response to tumor necrosis factor / T cell differentiation in thymus / 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: 2.5 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 | 3gxd.cif.gz | 397.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gxd.ent.gz | 328.6 KB | Display | PDB format |
PDBx/mmJSON format | 3gxd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gxd_validation.pdf.gz | 516.6 KB | Display | wwPDB validaton report |
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Full document | 3gxd_full_validation.pdf.gz | 567.5 KB | Display | |
Data in XML | 3gxd_validation.xml.gz | 76 KB | Display | |
Data in CIF | 3gxd_validation.cif.gz | 103.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/3gxd ftp://data.pdbj.org/pub/pdb/validation_reports/gx/3gxd | HTTPS FTP |
-Related structure data
Related structure data | 3gxfC 3gxiC 3gxmC 3gxnC 3gxpC 3gxtC 2nt0S 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
#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 #2: Chemical | ChemComp-PO4 / #3: Sugar | ChemComp-NAG / #4: 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: 3.21 Å3/Da / Density % sol: 61.67 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 4.5 Details: 0.8 M Na H2PO4, 0.8 M K H2PO4, 0.1 M Citrate pH 5.5 soaked with acetate buffer pH 4.5 and 1.8 M Li2SO4 prior to freezing, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å |
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Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→142 Å / Num. obs: 81268 |
Reflection shell | Resolution: 2.5→2.56 Å / Mean I/σ(I) obs: 2.1 |
-Processing
Software |
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Refinement | Starting model: PDB entry 2NT0 Resolution: 2.5→42.14 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.901 / WRfactor Rfree: 0.255 / WRfactor Rwork: 0.19 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.773 / SU B: 10.774 / SU ML: 0.235 / SU R Cruickshank DPI: 0.545 / SU Rfree: 0.327 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.545 / ESU R Free: 0.327 / 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: 124.23 Å2 / Biso mean: 49.621 Å2 / Biso min: 19.78 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→42.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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