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Yorodumi- PDB-3sog: Crystal structure of the BAR domain of human Amphiphysin, isoform 1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sog | ||||||
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Title | Crystal structure of the BAR domain of human Amphiphysin, isoform 1 | ||||||
Components | Amphiphysin | ||||||
Keywords | STRUCTURAL PROTEIN / Invagination Knobs-in-holes Curvature / Alpha Helix / Plasma Membrane / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information leading edge membrane / synaptic vesicle endocytosis / phospholipid binding / synaptic vesicle membrane / endocytosis / synaptic vesicle / actin cytoskeleton / Clathrin-mediated endocytosis / chemical synaptic transmission / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.3 Å | ||||||
Authors | Allerston, C.K. / Krojer, T. / Chaikuad, A. / Cooper, C.D.O. / Berridge, G. / Savitsky, P. / Vollmar, M. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. ...Allerston, C.K. / Krojer, T. / Chaikuad, A. / Cooper, C.D.O. / Berridge, G. / Savitsky, P. / Vollmar, M. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Bountra, C. / Gileadi, O. / Structural Genomics Consortium (SGC) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sog.cif.gz | 51.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sog.ent.gz | 36.3 KB | Display | PDB format |
PDBx/mmJSON format | 3sog.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/so/3sog ftp://data.pdbj.org/pub/pdb/validation_reports/so/3sog | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24219.393 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AMPH, AMPH1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 / References: UniProt: P49418 | ||
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#2: Chemical | ChemComp-EDO / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.06 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 2.66% PEG 6000, 2.66% PEG 8000, 2.66% PEG 10,000, 0.02M Magnesium Acetate, 0.05M Potassium Chloride, 0.1M MES, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 1, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→49.11 Å / Num. obs: 13758 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 66.41 Å2 / Rmerge(I) obs: 0.025 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 2.3→47.07 Å / Cor.coef. Fo:Fc: 0.9513 / Cor.coef. Fo:Fc free: 0.9374 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 83.23 Å2
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Refine analyze | Luzzati coordinate error obs: 0.483 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→47.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.48 Å / Total num. of bins used: 7
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