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Yorodumi- PDB-2j0j: Crystal structure of a fragment of focal adhesion kinase containi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2j0j | ||||||
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Title | Crystal structure of a fragment of focal adhesion kinase containing the FERM and kinase domains. | ||||||
Components | FOCAL ADHESION KINASE 1PTK2 | ||||||
Keywords | TRANSFERASE / CELL MIGRATION / FERM / INTEGRIN SIGNALING | ||||||
Function / homology | Function and homology information Apoptotic cleavage of cellular proteins / NCAM signaling for neurite out-growth / RHO GTPases Activate WASPs and WAVEs / RAF/MAP kinase cascade / Regulation of actin dynamics for phagocytic cup formation / radial glia-guided pyramidal neuron migration / negative regulation of protein autophosphorylation / calcium-dependent cysteine-type endopeptidase activity / positive regulation of substrate-dependent cell migration, cell attachment to substrate / Integrin signaling ...Apoptotic cleavage of cellular proteins / NCAM signaling for neurite out-growth / RHO GTPases Activate WASPs and WAVEs / RAF/MAP kinase cascade / Regulation of actin dynamics for phagocytic cup formation / radial glia-guided pyramidal neuron migration / negative regulation of protein autophosphorylation / calcium-dependent cysteine-type endopeptidase activity / positive regulation of substrate-dependent cell migration, cell attachment to substrate / 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 / angiogenesis involved in wound healing / signal complex assembly / response to pH / negative regulation of cell-substrate adhesion / wound healing, spreading of cells / positive regulation of focal adhesion assembly / negative regulation of anoikis / positive regulation of protein tyrosine kinase activity / regulation of cell adhesion / response to muscle stretch / ciliary basal body / actin filament organization / molecular function activator activity / sarcolemma / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / integrin binding / cell cortex / positive regulation of protein binding / angiogenesis / protein tyrosine kinase activity / protease binding / dendritic spine / protein autophosphorylation / positive regulation of cell migration / focal adhesion / centrosome / positive regulation of cell population proliferation / perinuclear region of cytoplasm / ATP binding / nucleus / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | GALLUS GALLUS (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Lietha, D. / Cai, X. / Li, Y. / Schaller, M.D. / Eck, M.J. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2007 Title: Structural Basis for the Autoinhibition of Focal Adhesion Kinase Authors: Lietha, D. / Cai, X. / Ceccarelli, D.F.J. / Li, Y. / Schaller, M.D. / Eck, M.J. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2j0j.cif.gz | 138.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j0j.ent.gz | 106.9 KB | Display | PDB format |
PDBx/mmJSON format | 2j0j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j0/2j0j ftp://data.pdbj.org/pub/pdb/validation_reports/j0/2j0j | HTTPS FTP |
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-Related structure data
Related structure data | 2j0kC 2j0lC 2j0mC 1mp8S 2aehS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 75351.281 Da / Num. of mol.: 1 / Fragment: FERM AND KINASE DOMAINS, RESIDUES 31-686 Source method: isolated from a genetically manipulated source Details: UNPHOSPHORYLATED / Source: (gene. exp.) GALLUS GALLUS (chicken) / Plasmid: PACG2T / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) References: UniProt: Q00944, non-specific protein-tyrosine kinase |
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#2: Chemical | ChemComp-4ST / |
#3: Water | ChemComp-HOH / |
Sequence details | RESIDUES 31-686 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.1 % |
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Crystal grow | pH: 8.5 Details: 13% PEG 10K, 250MM NACL, 100MM TRIS PH 8.5, 10MM TCEP. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 20, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 17892 / % possible obs: 91.2 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.84 / % possible all: 64.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1MP8 AND 2AEH Resolution: 2.8→45.55 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.893 / SU B: 26.03 / SU ML: 0.348 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.437 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.63 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→45.55 Å
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Refine LS restraints |
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