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Open data
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Basic information
Entry | Database: PDB / ID: 5nn3 | |||||||||
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Title | Crystal structure of human lysosomal acid-alpha-glucosidase, GAA | |||||||||
![]() | Lysosomal alpha-glucosidase | |||||||||
![]() | ![]() ![]() ![]() ![]() | |||||||||
Function / homology | ![]() vacuolar sequestering / autolysosome lumen / maltose metabolic process / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Roig-Zamboni, V. / Cobucci-Ponzano, B. / Iacono, R. / Ferrara, M.C. / Germany, S. / Parenti, G. / Bourne, Y. / Moracci, M. | |||||||||
![]() | ![]() Title: Structure of human lysosomal acid alpha-glucosidase-a guide for the treatment of Pompe disease. Authors: Roig-Zamboni, V. / Cobucci-Ponzano, B. / Iacono, R. / Ferrara, M.C. / Germany, S. / Bourne, Y. / Parenti, G. / Moracci, M. / Sulzenbacher, G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 367.9 KB | Display | ![]() |
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PDB format | ![]() | 294.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5nn4C ![]() 5nn5C ![]() 5nn6C ![]() 5nn8C ![]() 2qlyS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 96978.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Full length rhGAA has been treated with alpha-chymotrypsin, leading to a sample starting at residue Gln81. Missing surface loops have equally been removed by proteolytic cleavage Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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-Sugars , 4 types, 5 molecules
#2: Polysaccharide | ![]() Source method: isolated from a genetically manipulated source #3: 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 #4: 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: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-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, 691 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ![]() #7: Chemical | ChemComp-CL / ![]() #8: Chemical | ChemComp-PGE / | ![]() #9: Chemical | ChemComp-PEG / | ![]() #10: Chemical | ChemComp-EDO / ![]() #11: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.94 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.9 M ammonium sulfate, 0.1 M HEPES pH 7.0, 2% v/v PEG400 PH range: 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.9→49 Å / Num. obs: 102224 / % possible obs: 100 % / Redundancy: 9 % / Biso Wilson estimate: 28.51 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.05 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 9.2 % / Rmerge(I) obs: 1.711 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5033 / CC1/2: 0.661 / Rpim(I) all: 0.823 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2QLY Resolution: 1.9→48.88 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 4.728 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.103 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.138 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→48.88 Å
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Refine LS restraints |
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