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Yorodumi- PDB-1k9a: Crystal structure analysis of full-length carboxyl-terminal Src k... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k9a | ||||||
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Title | Crystal structure analysis of full-length carboxyl-terminal Src kinase at 2.5 A resolution | ||||||
Components | Carboxyl-terminal Src kinase | ||||||
Keywords | TRANSFERASE / carboxyl-terminal Src kinase / COOH-terminal Src kinase / Csk / Src / SFK / signal transduction / SH2 / SH3 / Src Homology / tyrosine kinase / cytoplasmic tyrosine kinase / Cbp / oncogene / cancer | ||||||
Function / homology | Function and homology information GAB1 signalosome / PD-1 signaling / Phosphorylation of CD3 and TCR zeta chains / Integrin signaling / negative regulation of Golgi to plasma membrane protein transport / RHOH GTPase cycle / regulation of Fc receptor mediated stimulatory signaling pathway / MAP2K and MAPK activation / negative regulation of low-density lipoprotein particle clearance / proline-rich region binding ...GAB1 signalosome / PD-1 signaling / Phosphorylation of CD3 and TCR zeta chains / Integrin signaling / negative regulation of Golgi to plasma membrane protein transport / RHOH GTPase cycle / regulation of Fc receptor mediated stimulatory signaling pathway / MAP2K and MAPK activation / negative regulation of low-density lipoprotein particle clearance / proline-rich region binding / adherens junction organization / negative regulation of bone resorption / negative regulation of phagocytosis / cellular response to peptide hormone stimulus / oligodendrocyte differentiation / protein kinase A catalytic subunit binding / negative regulation of interleukin-6 production / protein tyrosine kinase binding / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / negative regulation of ERK1 and ERK2 cascade / cell-cell junction / protein phosphatase binding / protein tyrosine kinase activity / adaptive immune response / negative regulation of cell population proliferation / ATP binding / identical protein binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.5 Å | ||||||
Authors | Ogawa, A. / Takayama, Y. / Nagata, A. / Chong, K.T. / Takeuchi, S. / Sakai, H. / Nakagawa, A. / Nada, S. / Okada, M. / Tsukihara, T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Structure of the carboxyl-terminal Src kinase, Csk. Authors: Ogawa, A. / Takayama, Y. / Sakai, H. / Chong, K.T. / Takeuchi, S. / Nakagawa, A. / Nada, S. / Okada, M. / Tsukihara, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k9a.cif.gz | 508.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k9a.ent.gz | 436.2 KB | Display | PDB format |
PDBx/mmJSON format | 1k9a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/1k9a ftp://data.pdbj.org/pub/pdb/validation_reports/k9/1k9a | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 50813.219 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P32577, EC: 2.7.1.112 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.56 Å3/Da / Density % sol: 65.47 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: ammonium sulphate, HEPES buffer, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 288K | ||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: OXFORD PX210 / Detector: CCD / Date: Jun 9, 2001 |
Radiation | Monochromator: ROTATED-INCLINED SI(111) DOUBLE CRYSTAL MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→73.5 Å / Num. all: 150489 / Num. obs: 150489 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 62.8 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 1.7 / Num. unique all: 17029 / % possible all: 98.2 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 73 Å |
Reflection shell | *PLUS % possible obs: 98.2 % / Num. unique obs: 17029 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 2.5→73.5 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→73.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.52 Å / Rfactor Rfree error: 0.053
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Refinement | *PLUS Lowest resolution: 73.5 Å / σ(F): 0 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.41 / Rfactor Rwork: 0.36 |