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Yorodumi- PDB-2cy4: Crystal structure of phosphotyrosine binding (PTB) domain of epid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cy4 | ||||||
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Title | Crystal structure of phosphotyrosine binding (PTB) domain of epidermal growth factor receptor pathway substrate-8 (EPS8) related protein 1 from Mus musculus (form-1 crystal) | ||||||
Components | epidermal growth factor receptor pathway substrate 8-like protein 1 | ||||||
Keywords | SIGNALING PROTEIN / structural genomics / signal transduction / phosphorylation / PTB domain / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information regulation of Rho protein signal transduction / positive regulation of ruffle assembly / Rac protein signal transduction / Rho protein signal transduction / ruffle / T cell receptor binding / ruffle membrane / actin filament binding / actin binding / protein-containing complex ...regulation of Rho protein signal transduction / positive regulation of ruffle assembly / Rac protein signal transduction / Rho protein signal transduction / ruffle / T cell receptor binding / ruffle membrane / actin filament binding / actin binding / protein-containing complex / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.94 Å | ||||||
Authors | Mizohata, E. / Hamana, H. / Morita, S. / Kinoshita, Y. / Nagano, K. / Uda, H. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of phosphotyrosine binding (PTB) domain of epidermal growth factor receptor pathway substrate-8 (EPS8) related protein 1 from Mus musculus (form-1 crystal) Authors: Mizohata, E. / Hamana, H. / Morita, S. / Kinoshita, Y. / Nagano, K. / Uda, H. / Terada, T. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cy4.cif.gz | 36.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cy4.ent.gz | 28.3 KB | Display | PDB format |
PDBx/mmJSON format | 2cy4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/2cy4 ftp://data.pdbj.org/pub/pdb/validation_reports/cy/2cy4 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15881.384 Da / Num. of mol.: 1 / Fragment: phosphotyrosine binding (PTB) domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) Description: cell free synthesis using S30 extract from E. coli Plasmid: PK030114-32 / References: GenBank: 18874094, UniProt: Q8R5F8*PLUS |
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#2: Chemical | ChemComp-CA / |
#3: 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: 60.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG400, HEPES, Tris, calcium chloride, sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 26, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→50 Å / Num. obs: 14643 / Biso Wilson estimate: 23.4 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→24.29 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 722475 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.7066 Å2 / ksol: 0.364266 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.94→24.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.94→2.06 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
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