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Open data
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Basic information
Entry | Database: PDB / ID: 3dj1 | ||||||
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Title | crystal structure of TIP-1 wild type | ||||||
![]() | Tax1-binding protein 3 | ||||||
![]() | SIGNALING PROTEIN / Tax-interacting protein-1 / PDZ domain / TIP-1 / Cytoplasm / Nucleus / Wnt signaling pathway | ||||||
Function / homology | ![]() RHO GTPases Activate Rhotekin and Rhophilins / embryo development / negative regulation of protein localization to cell surface / receptor localization to synapse / establishment or maintenance of epithelial cell apical/basal polarity / negative regulation of Wnt signaling pathway / receptor clustering / Rho protein signal transduction / postsynaptic density membrane / neuromuscular junction ...RHO GTPases Activate Rhotekin and Rhophilins / embryo development / negative regulation of protein localization to cell surface / receptor localization to synapse / establishment or maintenance of epithelial cell apical/basal polarity / negative regulation of Wnt signaling pathway / receptor clustering / Rho protein signal transduction / postsynaptic density membrane / neuromuscular junction / fibrillar center / beta-catenin binding / Wnt signaling pathway / cell-cell adhesion / actin cytoskeleton / chemical synaptic transmission / basolateral plasma membrane / neuron projection / negative regulation of cell population proliferation / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Shen, Y. | ||||||
![]() | ![]() Title: Structural Basis of beta-Catenin Recognition by Tax-interacting Protein-1 Authors: Zhang, J. / Yan, X. / Shi, C. / Yang, X. / Guo, Y. / Tian, C. / Long, J. / Shen, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.2 KB | Display | ![]() |
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PDB format | ![]() | 42.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.9 KB | Display | ![]() |
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Full document | ![]() | 452 KB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 16.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3diwSC ![]() 3dj3C 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
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 13739.631 Da / Num. of mol.: 2 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: 2.12 Å3/Da / Density % sol: 41.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 1.6M Ammonium sulfate, 0.1M bicine buffer, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 6, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 21968 / Num. obs: 21858 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Biso Wilson estimate: 23.2 Å2 / Rsym value: 0.025 / Net I/σ(I): 63.3 |
Reflection shell | Resolution: 1.77→1.83 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.124 / Mean I/σ(I) obs: 13.2 / Num. unique all: 2104 / % possible all: 95.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3DIW Resolution: 1.8→27.44 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1241665.59 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.8231 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→27.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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