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Yorodumi- PDB-6ibm: Crystal structure of human alpha-galactosidase A in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ibm | |||||||||
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Title | Crystal structure of human alpha-galactosidase A in complex with alpha-galactose configured cyclosulfate ME776 | |||||||||
Components | Alpha-galactosidase A | |||||||||
Keywords | HYDROLASE / glycosidase / galactose / carbohydrate | |||||||||
Function / homology | Function and homology information glycosylceramide catabolic process / negative regulation of nitric-oxide synthase activity / alpha-galactosidase / alpha-galactosidase activity / glycosphingolipid catabolic process / oligosaccharide metabolic process / glycoside catabolic process / galactoside binding / negative regulation of nitric oxide biosynthetic process / Glycosphingolipid catabolism ...glycosylceramide catabolic process / negative regulation of nitric-oxide synthase activity / alpha-galactosidase / alpha-galactosidase activity / glycosphingolipid catabolic process / oligosaccharide metabolic process / glycoside catabolic process / galactoside binding / 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 / MOLECULAR REPLACEMENT / Resolution: 2.07 Å | |||||||||
Authors | Rowland, R.J. / Wu, L. / Davies, G.J. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Chem Sci / Year: 2019 Title: Alpha-d-Gal-cyclophellitol cyclosulfamidate is a Michaelis complex analog that stabilizes therapeutic lysosomal alpha-galactosidase A in Fabry disease Authors: Artola, M. / Hedberg, C. / Rowland, R.J. / Wu, L. / Raich, L. / Ferraz, M.J. / Kytidou, K. / Marel, G.A. / Codee, J.D.C. / Rovira, C. / Aerts, J.M.F.G. / Davies, G.J. / Overkleeft, H.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ibm.cif.gz | 185.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ibm.ent.gz | 146.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ibm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ibm_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
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Full document | 6ibm_full_validation.pdf.gz | 3.1 MB | Display | |
Data in XML | 6ibm_validation.xml.gz | 34.4 KB | Display | |
Data in CIF | 6ibm_validation.cif.gz | 48.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/6ibm ftp://data.pdbj.org/pub/pdb/validation_reports/ib/6ibm | HTTPS FTP |
-Related structure data
Related structure data | 6ibkC 6ibrC 6ibtC 1r46S 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 on special symmetry positions |
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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 , 3 types, 6 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-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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-Non-polymers , 6 types, 304 molecules
#5: Chemical | #6: Chemical | ChemComp-ACT / #7: Chemical | ChemComp-SO4 / #8: Chemical | #9: Chemical | ChemComp-EDO / #10: 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: 2.8 Å3/Da / Density % sol: 56.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: PEG 4000 (50%), sodium acetate (pH 4.6) and lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 25, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97951 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→78.36 Å / Num. obs: 63220 / % possible obs: 100 % / Redundancy: 12.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.052 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.07→2.12 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 54492 / CC1/2: 0.745 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1r46 Resolution: 2.07→78.36 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.953 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.173 / 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 mean: 55.243 Å2
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Refinement step | Cycle: 1 / Resolution: 2.07→78.36 Å
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