+Open data
-Basic information
Entry | Database: PDB / ID: 5kzx | |||||||||
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Title | Crystal structure of human GAA | |||||||||
Components | Lysosomal alpha-glucosidase | |||||||||
Keywords | HYDROLASE / Pompe disease / Glycogen storage disease 2 / human acid alpha glucosidase / glycoprotein / N-linked glycosylation / lysosomal enzyme | |||||||||
Function / homology | Function and homology information vacuolar sequestering / autolysosome lumen / maltose metabolic process / alpha-glucosidase activity / alpha-1,4-glucosidase activity / sucrose metabolic process / glycophagy / Glycogen storage disease type II (GAA) / maltose alpha-glucosidase activity / alpha-glucosidase ...vacuolar sequestering / autolysosome lumen / maltose metabolic process / alpha-glucosidase activity / alpha-1,4-glucosidase activity / sucrose metabolic process / glycophagy / Glycogen storage disease type II (GAA) / maltose alpha-glucosidase activity / alpha-glucosidase / diaphragm contraction / neuromuscular process controlling posture / tissue development / regulation of the force of heart contraction / glycogen catabolic process / aorta development / azurophil granule membrane / muscle cell cellular homeostasis / Glycogen breakdown (glycogenolysis) / lysosome organization / tertiary granule membrane / neuromuscular process controlling balance / ficolin-1-rich granule membrane / heart morphogenesis / cardiac muscle contraction / lysosomal lumen / locomotory behavior / glucose metabolic process / carbohydrate binding / lysosome / lysosomal membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / extracellular exosome / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å | |||||||||
Model details | Complex with DNJ | |||||||||
Authors | Deming, D.T. / Garman, S.C. | |||||||||
Funding support | United States, 1items
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Citation | Journal: To be published Title: The structure of human GAA: structural basis of Pompe disease Authors: Deming, D.T. / Garman, S.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kzx.cif.gz | 365.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kzx.ent.gz | 291.1 KB | Display | PDB format |
PDBx/mmJSON format | 5kzx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kz/5kzx ftp://data.pdbj.org/pub/pdb/validation_reports/kz/5kzx | HTTPS FTP |
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-Related structure data
Related structure data | 5kzwC 5kzr S: Starting model for refinement 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, 1 molecules A
#1: Protein | Mass: 97141.812 Da / Num. of mol.: 1 / Fragment: UNP residues 79-952 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GAA / Cell line (production host): CHO cells / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P10253, alpha-glucosidase |
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-Sugars , 7 types, 10 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-D-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-D-fucopyranose-(1-6)]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 | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...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 #5: Polysaccharide | alpha-D-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / | #7: Sugar | #8: Sugar | |
-Non-polymers , 5 types, 801 molecules
#9: Chemical | #10: Chemical | ChemComp-PGE / | #11: Chemical | #12: Chemical | #13: 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: 3.38 Å3/Da / Density % sol: 63.57 % / Mosaicity: 0.69 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 sodium HEPES, 2% (v/v) PEG 400, 2M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.18076 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 7, 2015 / Details: Toroidal focusing mirror |
Radiation | Monochromator: SI(111) Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.18076 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→80.31 Å / Num. obs: 90718 / % possible obs: 89.2 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.363 / % possible all: 47.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5KZR 5kzr Resolution: 2→80.31 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.697 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.134 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.23 Å2
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Refinement step | Cycle: LAST / Resolution: 2→80.31 Å
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Refine LS restraints |
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