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Yorodumi- PDB-6pxc: N-Terminal SH2 domain of the p120RasGAP bound to a p190RhoGAP pho... -
+Open data
-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 | ||||||
Components |
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Keywords | SIGNALING PROTEIN / SH2 GTPase Activating Proteins Ras pathway SIGNALING PROTEIN Rho pathway | ||||||
Function / homology | Function and homology information central nervous system neuron axonogenesis / neuron projection guidance / regulation of RNA metabolic process / establishment or maintenance of actin cytoskeleton polarity / 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 / regulation of RNA metabolic process / establishment or maintenance of actin cytoskeleton polarity / 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 / RHOC GTPase cycle / RHOJ 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 / axon guidance / regulation of actin cytoskeleton organization / phospholipid binding / positive regulation of neuron projection development / Regulation of RAS by GAPs / actin cytoskeleton / cell migration / GTPase binding / regulation of cell shape / negative regulation of neuron apoptotic process / intracellular signal transduction / signaling receptor binding / GTPase activity / negative regulation of apoptotic process / GTP binding / signal transduction / DNA binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Jaber Chehayeb, R. / Stiegler, A.L. / Boggon, T.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Plos One / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pxc.cif.gz | 66.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pxc.ent.gz | 46.9 KB | Display | PDB format |
PDBx/mmJSON format | 6pxc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pxc_validation.pdf.gz | 428.8 KB | Display | wwPDB validaton report |
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Full document | 6pxc_full_validation.pdf.gz | 428.8 KB | Display | |
Data in XML | 6pxc_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | 6pxc_validation.cif.gz | 9.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/px/6pxc ftp://data.pdbj.org/pub/pdb/validation_reports/px/6pxc | HTTPS FTP |
-Related structure data
Related structure data | 6pxbC 4k44S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/699 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Gene: RASA1, GAP, RASA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: P20936 |
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#2: Protein/peptide | Mass: 1626.547 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9NRY4*PLUS |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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