+Open data
-Basic information
Entry | Database: PDB / ID: 1r46 | |||||||||
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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 / 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: 3.25 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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Remark 600 | heterogen The NAG A 639 is one sugar of a polysaccharide. The rest of the sugars were not modelled ...heterogen The NAG A 639 is one sugar of a polysaccharide. The rest of the sugars were not modelled due to missing density |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r46.cif.gz | 175.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r46.ent.gz | 139.3 KB | Display | PDB format |
PDBx/mmJSON format | 1r46.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r46_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 1r46_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 1r46_validation.xml.gz | 35.5 KB | Display | |
Data in CIF | 1r46_validation.cif.gz | 47.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/1r46 ftp://data.pdbj.org/pub/pdb/validation_reports/r4/1r46 | HTTPS FTP |
-Related structure data
Related structure data | 1r47C 1ktbS 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
-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: Homo sapiens (human) / References: UniProt: P06280, alpha-galactosidase |
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-Sugars , 5 types, 6 molecules
#2: 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)-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 | 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 #5: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-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 #6: Sugar | ChemComp-NAG / | |
-Non-polymers , 2 types, 22 molecules
#7: Chemical | ChemComp-EDO / #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: 2.48 Å3/Da / Density % sol: 50 % Description: SMALL CRYSTALS PRODUCED WEAK ANISOTROPIC DIFFRACTION, LEADING TO VERY POOR MERGING STATISTICS | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 30% PEG 4000, 0.1M TRIS HCL (PH 8.0), 0.2M AMMONIUM SULFATE, 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: 3.25→40.92 Å / Num. all: 16005 / Num. obs: 16005 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Redundancy: 9.7 % / Biso Wilson estimate: 80.5 Å2 / Rmerge(I) obs: 0.246 / Rsym value: 0.246 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 3.25→3.37 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1542 / Rsym value: 0.74 / % possible all: 98.7 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 16080 / % possible obs: 99.8 % / Num. measured all: 156309 |
Reflection shell | *PLUS % possible obs: 98.7 % / Num. unique obs: 1542 / Num. measured obs: 9921 / Rmerge(I) obs: 0.74 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Homology model derived from 1KTB Resolution: 3.25→40.92 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1225510.47 / Data cutoff high rms absF: 1225510.47 / Data cutoff low absF: 0 / 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: 10.2863 Å2 / ksol: 0.256366 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.25→40.92 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: 3.25→3.45 Å / Rfactor Rfree error: 0.036 / 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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