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- PDB-2ag4: Crystal Structure Analysis of GM2-activator protein complexed wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ag4 | ||||||
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Title | Crystal Structure Analysis of GM2-activator protein complexed with phosphatidylcholine | ||||||
![]() | Ganglioside GM2 activator | ||||||
![]() | LIPID BINDING PROTEIN / complex of single chain lipid and fatty acids | ||||||
Function / homology | ![]() sphingolipid activator protein activity / beta-N-acetylgalactosaminidase activity / glycosphingolipid catabolic process / maintenance of location in cell / lipid transporter activity / lipid storage / 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 transporter activity / lipid storage / 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. / Mi, L.Z. / Lee, S. / Rastinejad, F. | ||||||
![]() | ![]() Title: Crystal Structure Analysis of Phosphatidylcholine-GM2-Activator Product Complexes: Evidence for Hydrolase Activity. Authors: Wright, C.S. / Mi, L.Z. / Lee, S. / Rastinejad, F. #1: ![]() Title: Crystal Structure of Human GM2- Activator Protein with a Novel beta-cup Topology Authors: Wright, C.S. / Li, S.C. / Rastinejad, F. #2: ![]() Title: Structure Analysis of Lipid Complexes of GM2-Activator Protein Authors: Wright, C.S. / Zhao, Q. / Rastinejad, F. #3: ![]() Title: Evidence for Lipid Packaging in the Crystal Structure of the GM2-Activator Complex with Platelet Activating Factor Authors: Wright, C.S. / Mi, L.Z. / Rastinejad, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97.2 KB | Display | ![]() |
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PDB format | ![]() | 72.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 946.6 KB | Display | ![]() |
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Full document | ![]() | 962.3 KB | Display | |
Data in XML | ![]() | 24.6 KB | Display | |
Data in CIF | ![]() | 36.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2af9C ![]() 2ag2C ![]() 2ag9C ![]() 2agcC ![]() 1pu5S 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17827.557 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-IPA / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 47.9 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: Peg 4000, Hepes buffer, isopropanol, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Aug 23, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97943 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→28 Å / Num. all: 56004 / Num. obs: 52552 / % possible obs: 93.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 3.9 / Num. unique all: 5632 / % possible all: 89.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1PU5 monomer B Resolution: 1.8→19.85 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 973814.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 85.9495 Å2 / ksol: 0.348594 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→19.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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