+Open data
-Basic information
Entry | Database: PDB / ID: 1r47 | |||||||||
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Title | Structure of human alpha-galactosidase | |||||||||
Components | Alpha-galactosidase A | |||||||||
Keywords | HYDROLASE / glycoprotein / carbohydrate-binding protein / glycosidase / lysosomal enzyme / (beta/alpha)8 barrel | |||||||||
Function / homology | Function and homology information glycosylceramide catabolic process / negative regulation of nitric-oxide synthase activity / alpha-galactosidase / alpha-galactosidase activity / glycosphingolipid catabolic process / galactoside binding / oligosaccharide metabolic process / glycoside catabolic 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 / glycosphingolipid catabolic process / galactoside binding / oligosaccharide metabolic process / glycoside catabolic 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 / FOURIER SYNTHESIS / Resolution: 3.45 Å | |||||||||
Authors | Garman, S.C. / Garboczi, D.N. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: The molecular defect leading to Fabry disease: structure of human alpha-galactosidase Authors: Garman, S.C. / Garboczi, D.N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r47.cif.gz | 177.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r47.ent.gz | 141.2 KB | Display | PDB format |
PDBx/mmJSON format | 1r47.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/1r47 ftp://data.pdbj.org/pub/pdb/validation_reports/r4/1r47 | HTTPS FTP |
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-Related 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 Details: complex with alpha-galactose / Source: (gene. exp.) Homo sapiens (human) / Gene: GLA / Production host: Homo sapiens (human) / References: UniProt: P06280, alpha-galactosidase |
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-Sugars , 5 types, 8 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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#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Sugar | |
-Non-polymers , 2 types, 20 molecules
#7: Chemical | #8: 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: 2.58 Å3/Da / Density % sol: 52 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 30% PEG 4000, 0.1M TRIS HCl, 0.2M AMMONIUM SULFATE, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.033 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 23, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 3.45→41.55 Å / Num. all: 13878 / Num. obs: 13878 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.2 / Rsym value: 0.2 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 3.45→3.57 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.745 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1323 / Rsym value: 0.745 / % possible all: 98.9 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 13922 / % possible obs: 99.7 % / Num. measured all: 91651 / Rmerge(I) obs: 0.2 |
Reflection shell | *PLUS % possible obs: 98.9 % / Num. unique obs: 1323 / Num. measured obs: 8610 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: Structure without ligand Resolution: 3.45→41.55 Å / Rfactor Rfree error: 0.012 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: 300 KCAL/MOL/A^2 NCS RESTRAINTS APPLIED TO ALL ATOMS IN EARLY ROUNDS OF REFINEMENT AND RELAXED IN LATER ROUNDS.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.411 Å2 / ksol: 0.233224 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.45→41.55 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR / Weight Biso : 2 / Weight position: 300 | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.45→3.67 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
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Refinement | *PLUS Lowest resolution: 50 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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