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Open data
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Basic information
Entry | Database: PDB / ID: 2agc | ||||||
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Title | Crystal Structure of mouse GM2- activator Protein | ||||||
![]() | Ganglioside GM2 activator | ||||||
![]() | LIPID BINDING PROTEIN / constricted lipid binding pocket | ||||||
Function / homology | ![]() Glycosphingolipid metabolism / beta-N-acetylgalactosaminidase activity / positive regulation of hydrolase activity / beta-N-acetylhexosaminidase activity / lipid storage / lipid transporter activity / ganglioside catabolic process / oligosaccharide catabolic process / nervous system process / lipid transport ...Glycosphingolipid metabolism / beta-N-acetylgalactosaminidase activity / positive regulation of hydrolase activity / beta-N-acetylhexosaminidase activity / lipid storage / lipid transporter activity / ganglioside catabolic process / oligosaccharide catabolic process / nervous system process / lipid transport / phospholipase activator activity / neuromuscular process controlling balance / enzyme activator activity / Neutrophil degranulation / cytoplasmic side of plasma membrane / basolateral plasma membrane / learning or memory / lysosome / apical plasma membrane / mitochondrion 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 | ![]() | 47.9 KB | Display | ![]() |
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PDB format | ![]() | 32.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445 KB | Display | ![]() |
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Full document | ![]() | 451.5 KB | Display | |
Data in XML | ![]() | 10.7 KB | Display | |
Data in CIF | ![]() | 13.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2af9C ![]() 2ag2C ![]() 2ag4C ![]() 2ag9C ![]() 1g13S 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
#1: Protein | Mass: 17496.936 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-MYR / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 47.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: Peg 4000, acetate buffer , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 2, 1996 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 7535 / Num. obs: 7121 / % possible obs: 94.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.8 % / Biso Wilson estimate: 55.1 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 3.1 / Num. unique all: 738 / % possible all: 94.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1G13 monomer A Resolution: 2.5→8 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 794095.52 / 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: 80.096 Å2 / ksol: 0.281038 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 52.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
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Xplor file |
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