+Open data
-Basic information
Entry | Database: PDB / ID: 1pu5 | ||||||
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Title | GM2-activator Protein crystal structure | ||||||
Components | Ganglioside GM2 activator | ||||||
Keywords | LIPID BINDING PROTEIN / Beta cup / large lipid binding pocket / protein dynamics | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Wright, C.S. / Zhao, Q. / Rastinejad, F. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Structural analysis of lipid complexes of GM2-activator protein. Authors: Wright, C.S. / Zhao, Q. / Rastinejad, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pu5.cif.gz | 113.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pu5.ent.gz | 88.4 KB | Display | PDB format |
PDBx/mmJSON format | 1pu5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pu5_validation.pdf.gz | 455 KB | Display | wwPDB validaton report |
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Full document | 1pu5_full_validation.pdf.gz | 463.5 KB | Display | |
Data in XML | 1pu5_validation.xml.gz | 25 KB | Display | |
Data in CIF | 1pu5_validation.cif.gz | 36.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pu/1pu5 ftp://data.pdbj.org/pub/pdb/validation_reports/pu/1pu5 | HTTPS FTP |
-Related structure data
Related structure data | 1pubC 1g13S 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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Unit cell |
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-Components
#1: Protein | Mass: 17827.557 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GM2A / Plasmid: pET16b (Novagen) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P17900 #2: Chemical | #3: 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: 3.06 Å3/Da / Density % sol: 59.83 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.7 Details: Peg 4000, iso-propanol, Hepes buffer, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 278.0K |
-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.979 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 51764 / Num. obs: 50312 / % possible obs: 97.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 5 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.515 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1G13 Resolution: 1.9→7.99 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2018589.88 / Data cutoff high rms absF: 2018589.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 92.897 Å2 / ksol: 0.512718 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→7.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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