+Open data
-Basic information
Entry | Database: PDB / ID: 4eih | ||||||
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Title | Crystal structure of Arg SH2 domain | ||||||
Components | Abelson tyrosine-protein kinase 2 | ||||||
Keywords | TRANSFERASE / SH2 domain / Protein/protein interaction / phosphotyrosine / Phosphopeptide | ||||||
Function / homology | Function and homology information positive regulation of oxidoreductase activity / Role of ABL in ROBO-SLIT signaling / regulation of cell motility / exploration behavior / negative regulation of Rho protein signal transduction / regulation of endocytosis / actin monomer binding / RAC3 GTPase cycle / positive regulation of T cell migration / regulation of cell adhesion ...positive regulation of oxidoreductase activity / Role of ABL in ROBO-SLIT signaling / regulation of cell motility / exploration behavior / negative regulation of Rho protein signal transduction / regulation of endocytosis / actin monomer binding / RAC3 GTPase cycle / positive regulation of T cell migration / regulation of cell adhesion / : / cellular response to retinoic acid / Negative regulation of FLT3 / RAC1 GTPase cycle / positive regulation of establishment of T cell polarity / phosphotyrosine residue binding / regulation of autophagy / regulation of actin cytoskeleton organization / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / protein modification process / epidermal growth factor receptor signaling pathway / positive regulation of neuron projection development / peptidyl-tyrosine phosphorylation / actin filament binding / actin cytoskeleton / manganese ion binding / positive regulation of cytosolic calcium ion concentration / regulation of apoptotic process / protein tyrosine kinase activity / cell adhesion / protein kinase activity / magnesium ion binding / signal transduction / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Liu, W. / MacGrath, S.M. / Koleske, A.J. / Boggon, T.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Two Amino Acid Residues Confer Different Binding Affinities of Abelson Family Kinase Src Homology 2 Domains for Phosphorylated Cortactin. Authors: Gifford, S.M. / Liu, W. / Mader, C.C. / Halo, T.L. / Machida, K. / Boggon, T.J. / Koleske, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4eih.cif.gz | 58.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4eih.ent.gz | 41.7 KB | Display | PDB format |
PDBx/mmJSON format | 4eih.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/4eih ftp://data.pdbj.org/pub/pdb/validation_reports/ei/4eih | HTTPS FTP |
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-Related structure data
Related structure data | 3k2mS 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
#1: Protein | Mass: 12763.295 Da / Num. of mol.: 1 / Fragment: SH2 domain, UNP residues 165-273 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ABL2, ABLL, ARG / Plasmid: pGEX6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: P42684, non-specific protein-tyrosine kinase |
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#2: Chemical | ChemComp-CL / |
#3: 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: 1.7 Å3/Da / Density % sol: 27.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: pH8.5 100mM Tris, 15-17% PEG4000 0.2M Na Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.0781 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 5, 2010 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0781 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→20 Å / Num. all: 25920 / Num. obs: 25189 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 17.6 Å2 / Rsym value: 0.046 / Net I/σ(I): 29 |
Reflection shell | Resolution: 1.2→1.24 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 5.27 / Num. unique all: 1844 / Rsym value: 0.237 / % possible all: 69.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3K2M Resolution: 1.2→19.75 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.779 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.278 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→19.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.235 Å / Total num. of bins used: 20
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