+Open data
-Basic information
Entry | Database: PDB / ID: 2nt0 | ||||||
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Title | Acid-beta-glucosidase low pH, glycerol bound | ||||||
Components | Glucosylceramidase | ||||||
Keywords | HYDROLASE / cerezyme / glucocerebrosidase / glucosylceramide / hydrolysis / gaucher disease | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.79 Å | ||||||
Authors | Lieberman, R.L. / Petsko, G.A. / Ringe, D. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2007 Title: Structure of acid beta-glucosidase with pharmacological chaperone provides insight into Gaucher disease. Authors: Lieberman, R.L. / Wustman, B.A. / Huertas, P. / Powe, A.C. / Pine, C.W. / Khanna, R. / Schlossmacher, M.G. / Ringe, D. / Petsko, G.A. #1: Journal: Nat.Chem.Biol. / Year: 2006 Title: Structure of acid-beta-glucosidase with pharmacological chaperone provides insight into Gaucher disease | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nt0.cif.gz | 432.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nt0.ent.gz | 353.5 KB | Display | PDB format |
PDBx/mmJSON format | 2nt0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2nt0_validation.pdf.gz | 509.8 KB | Display | wwPDB validaton report |
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Full document | 2nt0_full_validation.pdf.gz | 540.1 KB | Display | |
Data in XML | 2nt0_validation.xml.gz | 89.6 KB | Display | |
Data in CIF | 2nt0_validation.cif.gz | 132.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/2nt0 ftp://data.pdbj.org/pub/pdb/validation_reports/nt/2nt0 | HTTPS FTP |
-Related structure data
Related structure data | 2nsxC 2nt1C 1ogsS 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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-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 / Organ (production host): Ovary / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P04062, glucosylceramidase #2: Sugar | ChemComp-NAG / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / #5: 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: 3.17 Å3/Da / Density % sol: 61.24 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 1 M Ammonium Sulfate 0.17 M Guanidinium HCl 0.02 M KCl 0.1 M Acetate buffer pH 4.5 Cryoprotectant includes 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 30, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 220956 / % possible obs: 84.8 % / Redundancy: 2.1 % / Biso Wilson estimate: 24.35 Å2 / Rsym value: 0.062 / Χ2: 1.025 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 18569 / Rsym value: 0.417 / Χ2: 0.622 / % possible all: 71.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OGS monomer Resolution: 1.79→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.437 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 mean: 24.352 Å2
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Refinement step | Cycle: LAST / Resolution: 1.79→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.788→1.835 Å / Total num. of bins used: 20
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