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- PDB-6pxc: N-Terminal SH2 domain of the p120RasGAP bound to a p190RhoGAP pho... -
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Basic information
Entry | Database: PDB / ID: 6pxc | ||||||
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Title | N-Terminal SH2 domain of the p120RasGAP bound to a p190RhoGAP phosphotyrosine peptide | ||||||
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![]() | SIGNALING PROTEIN / SH2 GTPase Activating Proteins Ras pathway SIGNALING PROTEIN Rho pathway | ||||||
Function / homology | ![]() central nervous system neuron axonogenesis / neuron projection guidance / establishment or maintenance of actin cytoskeleton polarity / regulation of RNA metabolic process / regulation of actin polymerization or depolymerization / : / regulation of actin filament polymerization / positive regulation of cilium assembly / mammary gland development / potassium channel inhibitor activity ...central nervous system neuron axonogenesis / neuron projection guidance / establishment or maintenance of actin cytoskeleton polarity / regulation of RNA metabolic process / regulation of actin polymerization or depolymerization / : / regulation of actin filament polymerization / positive regulation of cilium assembly / mammary gland development / potassium channel inhibitor activity / negative regulation of cell adhesion / camera-type eye development / RHOD GTPase cycle / negative regulation of vascular permeability / axonal fasciculation / regulation of small GTPase mediated signal transduction / blood vessel morphogenesis / RND1 GTPase cycle / Sema4D mediated inhibition of cell attachment and migration / RND2 GTPase cycle / wound healing, spreading of cells / RND3 GTPase cycle / negative regulation of Rho protein signal transduction / regulation of cell size / negative regulation of cell-matrix adhesion / RHOB GTPase cycle / regulation of axonogenesis / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / Rho protein signal transduction / mitotic cytokinesis / RHOG GTPase cycle / RHOA GTPase cycle / ephrin receptor signaling pathway / RAC2 GTPase cycle / RAC3 GTPase cycle / vasculogenesis / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / forebrain development / ruffle / EPHB-mediated forward signaling / RAC1 GTPase cycle / phosphotyrosine residue binding / Downstream signal transduction / GTPase activator activity / ciliary basal body / VEGFR2 mediated cell proliferation / neural tube closure / regulation of actin cytoskeleton organization / axon guidance / phospholipid binding / positive regulation of neuron projection development / Regulation of RAS by GAPs / cell migration / actin cytoskeleton / GTPase binding / regulation of cell shape / negative regulation of neuron apoptotic process / intracellular signal transduction / signaling receptor binding / GTPase activity / GTP binding / negative regulation of apoptotic process / signal transduction / DNA binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jaber Chehayeb, R. / Stiegler, A.L. / Boggon, T.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structures of p120RasGAP N-terminal SH2 domain in its apo form and in complex with a p190RhoGAP phosphotyrosine peptide. Authors: Jaber Chehayeb, R. / Stiegler, A.L. / Boggon, T.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 66.4 KB | Display | ![]() |
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PDB format | ![]() | 46.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.8 KB | Display | ![]() |
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Full document | ![]() | 428.8 KB | Display | |
Data in XML | ![]() | 7.3 KB | Display | |
Data in CIF | ![]() | 9.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6pxbC ![]() 4k44S S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 12266.827 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1626.547 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.8M Sodium Malonate 0.1M Bis Tris 6.5 2% PEG MME 550 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 6, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→50 Å / Num. obs: 16868 / % possible obs: 100 % / Redundancy: 15.8 % / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.039 / Rrim(I) all: 0.163 / Χ2: 1.151 / Net I/σ(I): 11.3 / Num. measured all: 265969 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4k44 Resolution: 1.6→43.62 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.06
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 141.45 Å2 / Biso mean: 44.7464 Å2 / Biso min: 20.9 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→43.62 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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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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