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Yorodumi- PDB-5i11: Crystal structure of the intertwined form of the Src tyrosine kin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5i11 | |||||||||
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Title | Crystal structure of the intertwined form of the Src tyrosine kinase SH3 domain T114S-Q128R mutant | |||||||||
Components | Proto-oncogene tyrosine-protein kinase Src | |||||||||
Keywords | SIGNALING PROTEIN / PROTEIN BINDING / SH3 domain / INTERTWINED-DIMER / DOMAIN-SWAPPING | |||||||||
Function / homology | Function and homology information Signaling by ERBB2 / Nuclear signaling by ERBB4 / PIP3 activates AKT signaling / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions ...Signaling by ERBB2 / Nuclear signaling by ERBB4 / PIP3 activates AKT signaling / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions / CD28 co-stimulation / CTLA4 inhibitory signaling / EPHA-mediated growth cone collapse / Ephrin signaling / G alpha (i) signalling events / DCC mediated attractive signaling / GP1b-IX-V activation signalling / Thrombin signalling through proteinase activated receptors (PARs) / VEGFR2 mediated cell proliferation / RAF activation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RET signaling / Receptor Mediated Mitophagy / ADP signalling through P2Y purinoceptor 1 / Downregulation of ERBB4 signaling / EPH-ephrin mediated repulsion of cells / Cyclin D associated events in G1 / Regulation of RUNX3 expression and activity / Activated NTRK3 signals through PI3K / Downstream signal transduction / MAP2K and MAPK activation / Integrin signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / MET activates PTK2 signaling / Extra-nuclear estrogen signaling / EPHB-mediated forward signaling / p130Cas linkage to MAPK signaling for integrins / VEGFA-VEGFR2 Pathway / connexin binding / osteoclast development / progesterone receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / bone resorption / extrinsic component of cytoplasmic side of plasma membrane / negative regulation of extrinsic apoptotic signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / cell junction / protein phosphatase binding / protein tyrosine kinase activity / mitochondrial inner membrane / cell differentiation / cytoskeleton / endosome membrane / cell adhesion / regulation of cell cycle / cell cycle / phosphorylation / signaling receptor binding / focal adhesion / innate immune response / heme binding / perinuclear region of cytoplasm / protein-containing complex / ATP binding / membrane / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Gallus gallus (chicken) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å | |||||||||
Authors | Camara-Artigas, A. | |||||||||
Funding support | Spain, 2items
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Citation | Journal: To Be Published Title: Crystal structure of the intertwined form of the Src tyrosine kinase SH3 domain T114S-Q128R mutant Authors: Camara-Artigas, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5i11.cif.gz | 49 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i11.ent.gz | 34.6 KB | Display | PDB format |
PDBx/mmJSON format | 5i11.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i1/5i11 ftp://data.pdbj.org/pub/pdb/validation_reports/i1/5i11 | HTTPS FTP |
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-Related structure data
Related structure data | 4jz3S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 6920.537 Da / Num. of mol.: 1 / Mutation: T114S, Q128R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: SRC / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P00523, non-specific protein-tyrosine kinase |
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-Non-polymers , 5 types, 24 molecules
#2: Chemical | ChemComp-PGE / | ||||
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#3: Chemical | ChemComp-SO4 / | ||||
#4: Chemical | #5: Chemical | ChemComp-ACT / | #6: 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: 3.15 Å3/Da / Density % sol: 61 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.1M SODIUM ACETATE, 1.9M AMMONIUM SULPHATE, 5% PEG 400, 10% GLYCEROL, PH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2015 / Details: Pair of KB mirrors for adjustable focusing |
Radiation | Monochromator: Channel-cut double crystal monochromator (CINEL), cryocooled, 6mm gap Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→19.99 Å / Num. obs: 11377 / % possible obs: 99.9 % / Redundancy: 12.6 % / Biso Wilson estimate: 30.44 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.064 / Net I/σ(I): 27.8 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.754 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4jz3 Resolution: 1.95→19.988 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.37 / Phase error: 22.92
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 108 Å2 / Biso mean: 43.8468 Å2 / Biso min: 16.91 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.95→19.988 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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