+Open data
-Basic information
Entry | Database: PDB / ID: 1ywp | ||||||
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Title | Phospholipase Cgamma1 SH3 | ||||||
Components | 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma 1 | ||||||
Keywords | HYDROLASE / SH3 / Phospholipase C-gamma1 / SLP-76 / SH2 domain-containing leukocyte phosphoprotein of 76 kD | ||||||
Function / homology | Function and homology information PECAM1 interactions / EGFR interacts with phospholipase C-gamma / Activated NTRK2 signals through PLCG1 / Activated NTRK3 signals through PLCG1 / phosphatidylinositol catabolic process / Phospholipase C-mediated cascade: FGFR1 / Phospholipase C-mediated cascade; FGFR3 / Phospholipase C-mediated cascade; FGFR4 / ISG15 antiviral mechanism / Generation of second messenger molecules ...PECAM1 interactions / EGFR interacts with phospholipase C-gamma / Activated NTRK2 signals through PLCG1 / Activated NTRK3 signals through PLCG1 / phosphatidylinositol catabolic process / Phospholipase C-mediated cascade: FGFR1 / Phospholipase C-mediated cascade; FGFR3 / Phospholipase C-mediated cascade; FGFR4 / ISG15 antiviral mechanism / Generation of second messenger molecules / Phospholipase C-mediated cascade; FGFR2 / Downstream signal transduction / Signaling by ALK / Role of phospholipids in phagocytosis / inositol trisphosphate biosynthetic process / DAP12 signaling / FCERI mediated Ca+2 mobilization / VEGFR2 mediated cell proliferation / calcium-dependent phospholipase C activity / Synthesis of IP3 and IP4 in the cytosol / RET signaling / inositol trisphosphate metabolic process / response to curcumin / phosphoinositide phospholipase C / FCERI mediated MAPK activation / response to gravity / phosphatidylinositol metabolic process / phosphatidylinositol phospholipase C activity / COP9 signalosome / phospholipase C activity / neurotrophin TRKA receptor binding / positive regulation of endothelial cell apoptotic process / clathrin-coated vesicle / positive regulation of vascular endothelial cell proliferation / positive regulation of epithelial cell migration / phosphatidylinositol-mediated signaling / cellular response to epidermal growth factor stimulus / positive regulation of blood vessel endothelial cell migration / glutamate receptor binding / release of sequestered calcium ion into cytosol / ruffle / : / positive regulation of release of sequestered calcium ion into cytosol / guanyl-nucleotide exchange factor activity / epidermal growth factor receptor signaling pathway / cell projection / phosphoprotein binding / ruffle membrane / calcium-mediated signaling / insulin receptor binding / modulation of chemical synaptic transmission / response to hydrogen peroxide / Schaffer collateral - CA1 synapse / receptor tyrosine kinase binding / positive regulation of angiogenesis / calcium ion transport / cell-cell junction / cell migration / lamellipodium / T cell receptor signaling pathway / in utero embryonic development / glutamatergic synapse / calcium ion binding / protein kinase binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Deng, L. / Velikovsky, C.A. / Swaminathan, C.P. / Cho, S. / Mariuzza, R.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Structural Basis for Recognition of the T Cell Adaptor Protein SLP-76 by the SH3 Domain of Phospholipase Cgamma1 Authors: Deng, L. / Velikovsky, C.A. / Swaminathan, C.P. / Cho, S. / Mariuzza, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ywp.cif.gz | 27.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ywp.ent.gz | 17.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ywp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ywp_validation.pdf.gz | 405.1 KB | Display | wwPDB validaton report |
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Full document | 1ywp_full_validation.pdf.gz | 405.1 KB | Display | |
Data in XML | 1ywp_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | 1ywp_validation.cif.gz | 7.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/1ywp ftp://data.pdbj.org/pub/pdb/validation_reports/yw/1ywp | HTTPS FTP |
-Related structure data
Related structure data | 1ywoC 1oebS 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: 7414.259 Da / Num. of mol.: 1 / Fragment: Phospholipase C-gamma1 / Mutation: C5S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Plcg1 / Plasmid: pGEX-4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P10686, phosphoinositide phospholipase C |
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#2: 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: 1.8 Å3/Da / Density % sol: 31.4 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 Details: PEG 4000, sodium acetate, Tris-HCl, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.009 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 9, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.009 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 6979 / % possible obs: 97.5 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 42.2 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.168 / Mean I/σ(I) obs: 10.5 / % possible all: 94.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OEB Resolution: 1.6→29.49 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.516 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.417 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→29.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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