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Yorodumi- PDB-3gxp: Crystal structure of acid-alpha-galactosidase A complexed with ga... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gxp | |||||||||
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Title | Crystal structure of acid-alpha-galactosidase A complexed with galactose at pH 4.5 | |||||||||
Components | Alpha-galactosidase A | |||||||||
Keywords | HYDROLASE / Disease mutation / Disulfide bond / Glycoprotein / Glycosidase / Lysosome / RNA editing | |||||||||
Function / homology | Function and homology information glycosylceramide catabolic process / negative regulation of nitric-oxide synthase activity / alpha-galactosidase / alpha-galactosidase activity / galactoside binding / glycosphingolipid catabolic process / glycoside catabolic process / oligosaccharide metabolic process / negative regulation of nitric oxide biosynthetic process / Glycosphingolipid catabolism ...glycosylceramide catabolic process / negative regulation of nitric-oxide synthase activity / alpha-galactosidase / alpha-galactosidase activity / galactoside binding / glycosphingolipid catabolic process / glycoside catabolic process / oligosaccharide metabolic process / negative regulation of nitric oxide biosynthetic process / Glycosphingolipid catabolism / catalytic activity / lysosomal lumen / azurophil granule lumen / lysosome / hydrolase activity / signaling receptor binding / Neutrophil degranulation / Golgi apparatus / protein homodimerization activity / extracellular exosome / extracellular region / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 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 | 3gxp.cif.gz | 170.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gxp.ent.gz | 138.5 KB | Display | PDB format |
PDBx/mmJSON format | 3gxp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/3gxp ftp://data.pdbj.org/pub/pdb/validation_reports/gx/3gxp | HTTPS FTP |
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-Related structure data
Related structure data | 3gxdC 3gxfC 3gxiC 3gxmC 3gxnC 3gxtC C: citing same article (ref.) |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 45394.543 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GLA / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P06280, alpha-galactosidase |
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-Sugars , 5 types, 11 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-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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#3: 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 #5: Sugar | #7: Sugar | #8: Sugar | |
-Non-polymers , 3 types, 162 molecules
#4: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-TAM / | #9: 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: 2.75 Å3/Da / Density % sol: 55.28 % |
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Crystal grow | Method: vapor diffusion / Details: vapor diffusion |
-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: 2.2→76.6 Å / Num. obs: 42395 |
-Processing
Software |
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Refinement | Resolution: 2.2→38.15 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.271 / WRfactor Rwork: 0.211 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.779 / SU B: 16.64 / SU ML: 0.21 / SU R Cruickshank DPI: 0.356 / SU Rfree: 0.262 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.338 / ESU R Free: 0.258 / 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: 153.81 Å2 / Biso mean: 71.47 Å2 / Biso min: 33.89 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→38.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.258 Å / Total num. of bins used: 20
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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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