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Yorodumi- PDB-6t13: CRYSTAL STRUCTURE OF GLUCOCEREBROSIDASE IN COMPLEX WITH A PYRROLO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6t13 | ||||||
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Title | CRYSTAL STRUCTURE OF GLUCOCEREBROSIDASE IN COMPLEX WITH A PYRROLOPYRAZINE | ||||||
Components | Glucosylceramidase | ||||||
Keywords | HYDROLASE / GCASE / GLYCOSIDASE / CEREZYME / HYDROLYSIS / GLYCOSYLCERAMIDASE | ||||||
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 / glucosylceramide catabolic process / scavenger receptor binding / regulation of lysosomal protein catabolic process / autophagosome organization / sphingosine biosynthetic process / glucosylceramidase activity / microglial cell proliferation / glucosyltransferase activity / regulation of TOR signaling / ceramide biosynthetic process / lipid storage / response to thyroid hormone / microglia differentiation / sphingolipid metabolic process / 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 / glycosyltransferase activity / Association of TriC/CCT with target proteins during biosynthesis / negative regulation of interleukin-6 production / antigen processing and presentation / 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 / respiratory electron transport chain / cellular response to starvation / 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 / molecular replacement / Resolution: 1.85 Å | ||||||
Authors | Benz, J. / Ehler, A. / Hug, M. / Huber, S. / Rufer, A.C. / Guba, W. / Jagasia, R. / Hofmann, E.C. / Rodriguez Sarmiento, R.M. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2021 Title: Novel beta-Glucocerebrosidase Activators That Bind to a New Pocket at a Dimer Interface and Induce Dimerization. Authors: Benz, J. / Rufer, A.C. / Huber, S. / Ehler, A. / Hug, M. / Topp, A. / Guba, W. / Hofmann, E.C. / Jagasia, R. / Rodriguez Sarmiento, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6t13.cif.gz | 832.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t13.ent.gz | 688.1 KB | Display | PDB format |
PDBx/mmJSON format | 6t13.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t1/6t13 ftp://data.pdbj.org/pub/pdb/validation_reports/t1/6t13 | HTTPS FTP |
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-Related structure data
Related structure data | 1ogsS 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 59761.969 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) References: UniProt: B2R6A7, UniProt: P04062*PLUS, glucosylceramidase |
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-Sugars , 2 types, 4 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#6: Sugar |
-Non-polymers , 7 types, 1506 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-GOL / | #8: Chemical | #9: Chemical | #10: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.46 Å3/Da / Density % sol: 50.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2M ammonium sulfate 0.1M Tris 17.5% PEG MME 5000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 22, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→191 Å / Num. obs: 201063 / % possible obs: 100 % / Redundancy: 6.79 % / Biso Wilson estimate: 34.28 Å2 / Rsym value: 0.08 / Net I/σ(I): 11.08 |
Reflection shell | Resolution: 1.85→1.94 Å / Num. unique obs: 26445 / Rsym value: 0.88 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OGS Resolution: 1.85→48.71 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / SU R Cruickshank DPI: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.121 / SU Rfree Blow DPI: 0.113 / SU Rfree Cruickshank DPI: 0.111
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Displacement parameters | Biso max: 202.47 Å2 / Biso mean: 53.68 Å2 / Biso min: 21.23 Å2
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Refine analyze | Luzzati coordinate error obs: 0.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→48.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.86 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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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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