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Yorodumi- PDB-3fxx: Human EphA3 Kinase and Juxtamembrane Region Bound to Substrate KQ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fxx | ||||||
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Title | Human EphA3 Kinase and Juxtamembrane Region Bound to Substrate KQWDNYE[pTyr]IW | ||||||
Components |
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Keywords | TRANSFERASE / receptor tyrosine kinase / juxtamembrane segment / structural genomics / peptide co-crystal structure / substrate complex / Structural Genomics Consortium / SGC / ATP-binding / Cell membrane / Glycoprotein / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Receptor / Secreted / Transmembrane / Tyrosine-protein kinase | ||||||
Function / homology | Function and homology information fasciculation of sensory neuron axon / fasciculation of motor neuron axon / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / regulation of epithelial to mesenchymal transition / ephrin receptor activity / negative regulation of endocytosis / EPH-Ephrin signaling / regulation of focal adhesion assembly / regulation of GTPase activity ...fasciculation of sensory neuron axon / fasciculation of motor neuron axon / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / regulation of epithelial to mesenchymal transition / ephrin receptor activity / negative regulation of endocytosis / EPH-Ephrin signaling / regulation of focal adhesion assembly / regulation of GTPase activity / EPHA-mediated growth cone collapse / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / regulation of microtubule cytoskeleton organization / cellular response to retinoic acid / axon guidance / regulation of actin cytoskeleton organization / positive regulation of protein localization to plasma membrane / receptor protein-tyrosine kinase / positive regulation of neuron projection development / peptidyl-tyrosine phosphorylation / cell migration / actin cytoskeleton / nuclear membrane / early endosome / cell adhesion / dendrite / extracellular region / nucleoplasm / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å | ||||||
Authors | Davis, T. / Walker, J.R. / Mackenzie, F. / Weigelt, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Febs J. / Year: 2009 Title: Structural recognition of an optimized substrate for the ephrin family of receptor tyrosine kinases. Authors: Davis, T.L. / Walker, J.R. / Allali-Hassani, A. / Parker, S.A. / Turk, B.E. / Dhe-Paganon, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fxx.cif.gz | 88.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fxx.ent.gz | 62.1 KB | Display | PDB format |
PDBx/mmJSON format | 3fxx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fx/3fxx ftp://data.pdbj.org/pub/pdb/validation_reports/fx/3fxx | HTTPS FTP |
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-Related structure data
Related structure data | 3fy2C 2gsfS C: citing same article (ref.) 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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Details | BIOLOGICAL UNIT IS THE SAME AS ASYMMETRIC UNIT |
-Components
#1: Protein | Mass: 41819.730 Da / Num. of mol.: 1 Fragment: Juxtamembrane segment and kinase domain: residues 577-947 Mutation: Y608A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA3, ETK, ETK1, HEK, TYRO4 / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P29320, receptor protein-tyrosine kinase |
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#2: Protein/peptide | Mass: 1525.532 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Peptide synthesized with phosphorylation at the +2 tyrosine position |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-ANP / |
#5: 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: 1.77 Å3/Da / Density % sol: 30.4 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20 mg/mL Protein, 25% PEG 3350, 0.04M Ammonium sulfate, 0.1M Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 6, 2007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 3.4 % / Av σ(I) over netI: 28.36 / Number: 113957 / Rmerge(I) obs: 0.044 / Χ2: 1.43 / D res high: 1.7 Å / D res low: 30 Å / Num. obs: 33335 / % possible obs: 98.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.7→30 Å / Num. obs: 33335 / % possible obs: 98.3 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.044 / Χ2: 1.427 / Net I/σ(I): 28.359 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 34.22 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2GSF Resolution: 1.7→26.47 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.198 / WRfactor Rwork: 0.169 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.885 / SU B: 1.942 / SU ML: 0.065 / SU R Cruickshank DPI: 0.106 / SU Rfree: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.1 / 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 max: 76.97 Å2 / Biso mean: 26.127 Å2 / Biso min: 12.3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.176 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→26.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.74 Å / Total num. of bins used: 20
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