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Open data
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Basic information
Entry | Database: PDB / ID: 1g13 | ||||||
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Title | HUMAN GM2 ACTIVATOR STRUCTURE | ||||||
![]() | GANGLIOSIDE M2 ACTIVATOR PROTEIN | ||||||
![]() | Ligand Binding Protein / beta cup | ||||||
Function / homology | ![]() sphingolipid activator protein activity / beta-N-acetylgalactosaminidase activity / glycosphingolipid catabolic process / maintenance of location in cell / lipid storage / lipid transporter activity / Glycosphingolipid catabolism / ganglioside catabolic process / oligosaccharide catabolic process / lipid transport ...sphingolipid activator protein activity / beta-N-acetylgalactosaminidase activity / glycosphingolipid catabolic process / maintenance of location in cell / lipid storage / lipid transporter activity / Glycosphingolipid catabolism / ganglioside catabolic process / oligosaccharide catabolic process / lipid transport / phospholipase activator activity / neuromuscular process controlling balance / lysosomal lumen / cytoplasmic side of plasma membrane / azurophil granule lumen / basolateral plasma membrane / learning or memory / apical plasma membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / extracellular exosome / extracellular region / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wright, C.S. / Li, S.C. / Rastinejad, F. | ||||||
![]() | ![]() Title: Crystal structure of human GM2-activator protein with a novel beta-cup topology. Authors: Wright, C.S. / Li, S.C. / Rastinejad, F. #1: ![]() Title: Crystallization and preliminary X-ray characterization of GM2-activator protein Authors: Wright, C.S. / Li, S.-C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.7 KB | Display | ![]() |
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PDB format | ![]() | 88.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453 KB | Display | ![]() |
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Full document | ![]() | 459.4 KB | Display | |
Data in XML | ![]() | 24 KB | Display | |
Data in CIF | ![]() | 34.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17698.096 Da / Num. of mol.: 3 / Fragment: RESIDUES 39-200 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-EPE / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 4000, propanol, sodium Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ccd / Detector: CCD / Date: May 28, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 44590 / Num. obs: 44581 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6 % / Biso Wilson estimate: 33.3 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 45.7 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 10 % / Rmerge(I) obs: 0.33 / Num. unique all: 4326 / % possible all: 99 |
Reflection | *PLUS Num. measured all: 84502 |
Reflection shell | *PLUS % possible obs: 99 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: Least Squares / Bsol: 136.55 Å2 / ksol: 0.7133 e/Å3 | |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34 Å2 | |||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.24 Å / Luzzati sigma a obs: 0.09 Å | |||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→6 Å / Total num. of bins used: 10
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | |||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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