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Yorodumi- PDB-1r1q: Structural Basis for Differential Recognition of Tyrosine Phospho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r1q | ||||||
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Title | Structural Basis for Differential Recognition of Tyrosine Phosphorylated Sites in the Linker for Activation of T cells (LAT) by the Adaptor Protein Gads | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / SH2 / Gads / LAT / phosphopeptide | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Cho, S. / Mariuzza, R.A. | ||||||
Citation | Journal: Embo J. / Year: 2004 Title: Structural basis for differential recognition of tyrosine-phosphorylated sites in the linker for activation of T cells (LAT) by the adaptor Gads. Authors: Cho, S. / Velikovsky, C.A. / Swaminathan, C.P. / Houtman, J.C. / Samelson, L.E. / Mariuzza, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r1q.cif.gz | 56.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r1q.ent.gz | 45.3 KB | Display | PDB format |
PDBx/mmJSON format | 1r1q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/1r1q ftp://data.pdbj.org/pub/pdb/validation_reports/r1/1r1q | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 11823.300 Da / Num. of mol.: 2 / Fragment: Gads-SH2 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: GADS / Production host: Escherichia coli (E. coli) / References: UniProt: O89100 #2: Protein/peptide | Mass: 885.878 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED #3: Chemical | ChemComp-SO4 / #4: 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: 1.88 Å3/Da / Density % sol: 34.43 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8.7 Details: 0.1mM Tris-HCl, 2.5M ammonium sulfate, pH 8.7, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 23, 2003 / Details: mirrors |
Radiation | Monochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→43.1 Å / Num. all: 117803 / Num. obs: 26632 / % possible obs: 96.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→43.03 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.007 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.155 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.308 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→43.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20 /
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