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Open data
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Basic information
Entry | Database: PDB / ID: 1u5d | ||||||
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Title | Crystal Structure of the PH domain of SKAP55 | ||||||
![]() | Src Kinase-associated Phosphoprotein of 55 kDa | ||||||
![]() | SIGNALING PROTEIN / PH Domain | ||||||
Function / homology | ![]() positive regulation of leukocyte cell-cell adhesion / positive regulation of cell-cell adhesion mediated by integrin / positive regulation of adaptive immune response / positive regulation of integrin activation / positive regulation of heterotypic cell-cell adhesion / positive regulation of cell-matrix adhesion / T cell receptor complex / plasma membrane raft / immunological synapse / SH2 domain binding ...positive regulation of leukocyte cell-cell adhesion / positive regulation of cell-cell adhesion mediated by integrin / positive regulation of adaptive immune response / positive regulation of integrin activation / positive regulation of heterotypic cell-cell adhesion / positive regulation of cell-matrix adhesion / T cell receptor complex / plasma membrane raft / immunological synapse / SH2 domain binding / protein localization to plasma membrane / SH3 domain binding / cell-cell junction / T cell receptor signaling pathway / protein phosphatase binding / adaptive immune response / protein-containing complex binding / protein kinase binding / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tang, Y. / Swanson, K.D. / Neel, B.G. / Eck, M.J. | ||||||
![]() | ![]() Title: Structural Basis for the Dimerization and Phosphoinositide Specificity of the Src Kinase-associated Phosphoproteins SKAP55 and SKAP-Hom Authors: Tang, Y. / Swanson, K.D. / Neel, B.G. / Eck, M.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.7 KB | Display | ![]() |
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PDB format | ![]() | 86.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.3 KB | Display | ![]() |
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Full document | ![]() | 474.4 KB | Display | |
Data in XML | ![]() | 23.8 KB | Display | |
Data in CIF | ![]() | 34.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1u5eC ![]() 1u5fC ![]() 1u5gS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
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Components
#1: Protein | Mass: 12723.417 Da / Num. of mol.: 4 / Fragment: PH Domain (residues 106-213) / Mutation: D106G, N107S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: Ammonium Sulfate, Sodium Acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD / Date: Dec 1, 2003 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→35 Å / Num. all: 45815 / Num. obs: 45007 / % possible obs: 83.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 30 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 4 / Num. unique all: 2179 / % possible all: 40.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Structure of the PH Domain of SKAP-Hom, PDb entry 1u5g Resolution: 1.7→35 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Displacement parameters | Biso mean: 24.8 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.74 Å
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