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Yorodumi- PDB-4oml: Crystal structure of the intertwined dimer of the c-Src tyrosine ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oml | ||||||
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Title | Crystal structure of the intertwined dimer of the c-Src tyrosine kinase SH3 domain mutant Q128R | ||||||
Components | Proto-oncogene tyrosine-protein kinase Src | ||||||
Keywords | TRANSFERASE / beta-barrel sandwich / kinase / proline rich motifs | ||||||
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 / GP1b-IX-V activation signalling / Recycling pathway of L1 / 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 / regulation of cell cycle / cell adhesion / 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: 1.6 Å | ||||||
Authors | Camara-Artigas, A. / Bacarizo, J. | ||||||
Citation | Journal: Plos One / Year: 2014 Title: Electrostatic Effects in the Folding of the SH3 Domain of the c-Src Tyrosine Kinase: pH-Dependence in 3D-Domain Swapping and Amyloid Formation. Authors: Bacarizo, J. / Martinez-Rodriguez, S. / Martin-Garcia, J.M. / Andujar-Sanchez, M. / Ortiz-Salmeron, E. / Neira, J.L. / 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 | 4oml.cif.gz | 51.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oml.ent.gz | 36.2 KB | Display | PDB format |
PDBx/mmJSON format | 4oml.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/4oml ftp://data.pdbj.org/pub/pdb/validation_reports/om/4oml | HTTPS FTP |
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-Related structure data
Related structure data | 4jz3C 4jz4SC 4omnC 4omoC 4ompC C: citing same article (ref.) 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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Details | Intertwined dimer. The dimer is generated by symmetry |
-Components
#1: Protein | Mass: 8823.652 Da / Num. of mol.: 1 / Fragment: SH3 domain / Mutation: Q128R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: SRC / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P00523, non-specific protein-tyrosine kinase | ||
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#2: Chemical | ChemComp-PGE / | ||
#3: Chemical | #4: 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: 2.27 Å3/Da / Density % sol: 45.79 % |
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Crystal grow | Temperature: 298 K / pH: 5 Details: 0.1M sodium acetate, 1.6 M ammonium sulphate, 10%PEG 300, 10%Glicerol, pH 5.0, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.97752 | ||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 3, 2008 / Details: MIRRORS | ||||||||||||||||||
Radiation | Monochromator: SI(111) CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.97752 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Redundancy: 12.9 % / Number: 143425 / Rmerge(I) obs: 0.073 / D res high: 1.6 Å / D res low: 19.22 Å / Num. obs: 11086 / % possible obs: 97 | ||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.6→19.22 Å / Num. obs: 11086 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 12.9 % / Biso Wilson estimate: 21.57 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 21.4 | ||||||||||||||||||
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 13 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 4.4 / % possible all: 93.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4JZ4 Resolution: 1.6→19.22 Å / SU ML: 0.12 / Isotropic thermal model: anisotropic / σ(F): 1.45 / Phase error: 17.9 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.89 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→19.22 Å
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Refine LS restraints |
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LS refinement shell |
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