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Yorodumi- PDB-2d0n: Crystal structure of the C-terminal SH3 domain of the adaptor pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d0n | ||||||
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Title | Crystal structure of the C-terminal SH3 domain of the adaptor protein GADS in complex with SLP-76 motif peptide reveals a unique SH3-SH3 interaction | ||||||
Components |
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Keywords | SIGNALING PROTEIN / SH3 DOMAIN-COMPLEX / MONA/GADS SH3C DOMAIN | ||||||
Function / homology | Function and homology information FLT3 Signaling / CD28 co-stimulation / FCERI mediated MAPK activation / Signaling by SCF-KIT / Generation of second messenger molecules / FCERI mediated Ca+2 mobilization / DAP12 signaling / regulation of MAPK cascade / phosphotyrosine residue binding / endosome ...FLT3 Signaling / CD28 co-stimulation / FCERI mediated MAPK activation / Signaling by SCF-KIT / Generation of second messenger molecules / FCERI mediated Ca+2 mobilization / DAP12 signaling / regulation of MAPK cascade / phosphotyrosine residue binding / endosome / signal transduction / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | ||||||
Authors | Dimasi, N. | ||||||
Citation | Journal: Int.J.Biochem.Cell Biol. / Year: 2007 Title: Crystal structure of the C-terminal SH3 domain of the adaptor protein GADS in complex with SLP-76 motif peptide reveals a unique SH3-SH3 interaction Authors: Dimasi, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d0n.cif.gz | 43.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d0n.ent.gz | 30.5 KB | Display | PDB format |
PDBx/mmJSON format | 2d0n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/2d0n ftp://data.pdbj.org/pub/pdb/validation_reports/d0/2d0n | HTTPS FTP |
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-Related structure data
Related structure data | 1oebS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 6719.488 Da / Num. of mol.: 2 / Fragment: C-terminal SH3 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pT7-GADS-cSH3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O89100 #2: Protein/peptide | Mass: 1002.123 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: The SLP-76 peptide was synthesized synthetically with the F-moc chemistry #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: 2.08 Å3/Da / Density % sol: 42.04 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.26M ammonium sulfate, 0.1M cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 13, 2005 |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→36.18 Å / Num. obs: 16893 / % possible obs: 85.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.043 / Rsym value: 0.178 |
Reflection shell | Resolution: 1.54→1.59 Å / Rmerge(I) obs: 0.043 / % possible all: 85.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OEB Chain A Resolution: 1.57→7.9 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.57→7.9 Å
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LS refinement shell | Highest resolution: 1.57 Å |