+Open data
-Basic information
Entry | Database: PDB / ID: 3isu | ||||||
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Title | Crystal structure of the RGC domain of IQGAP3 | ||||||
Components | Ras GTPase-activating-like protein IQGAP3 | ||||||
Keywords | SIGNALING PROTEIN / Structural Genomics / Structural Genomics Consortium (SGC) / RGC domain / Calmodulin-binding / Phosphoprotein / Polymorphism | ||||||
Function / homology | Function and homology information myosin VI light chain binding / small GTPase binding => GO:0031267 / small GTPase binding => GO:0031267 / : / positive regulation of mammary gland epithelial cell proliferation / regulation of cell size / : / regulation of GTPase activity / lateral plasma membrane / RHO GTPases activate IQGAPs ...myosin VI light chain binding / small GTPase binding => GO:0031267 / small GTPase binding => GO:0031267 / : / positive regulation of mammary gland epithelial cell proliferation / regulation of cell size / : / regulation of GTPase activity / lateral plasma membrane / RHO GTPases activate IQGAPs / ERK1 and ERK2 cascade / regulation of actin cytoskeleton organization / G1/S transition of mitotic cell cycle / actin filament binding / cell-cell junction / Ras protein signal transduction / calmodulin binding / negative regulation of gene expression / positive regulation of gene expression / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | ||||||
Authors | Nedyalkova, L. / Tempel, W. / Tong, Y. / Crombet, L. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: to be published Title: Crystal structure of the RGC domain of IQGAP3 Authors: Nedyalkova, L. / Tempel, W. / Tong, Y. / Crombet, L. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3isu.cif.gz | 35.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3isu.ent.gz | 22.8 KB | Display | PDB format |
PDBx/mmJSON format | 3isu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/3isu ftp://data.pdbj.org/pub/pdb/validation_reports/is/3isu | HTTPS FTP |
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-Related structure data
Related structure data | 3iezS S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 14050.223 Da / Num. of mol.: 1 / Fragment: residues 1529-1631 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IQGAP3 / Plasmid: pET28-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q86VI3 |
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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: 2.717 Å3/Da / Density % sol: 54.73 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25% PEG3350, 0.2M lithium sulfate, 0.1 Bis-Tris, pH 6.5, vapor diffusion, sitting drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97711 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 5, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97711 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.88→40 Å / Num. obs: 12943 / % possible obs: 100 % / Redundancy: 20.5 % / Rmerge(I) obs: 0.086 / Χ2: 1.745 / Net I/σ(I): 10.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3IEZ Resolution: 1.88→40 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.239 / WRfactor Rwork: 0.206 / SU B: 2.65 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.811 Å2
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Refinement step | Cycle: LAST / Resolution: 1.88→40 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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