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Yorodumi- PDB-2qoi: Human EphA3 kinase and juxtamembrane region, Y596F:Y602F double mutant -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qoi | ||||||
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Title | Human EphA3 kinase and juxtamembrane region, Y596F:Y602F double mutant | ||||||
Components | Ephrin receptor | ||||||
Keywords | TRANSFERASE / receptor tyrosine kinase / juxtamembrane segment / structural genomics / mutants / Structural Genomics Consortium / SGC / ATP-binding / Nucleotide-binding / Phosphorylation / Transmembrane / Tyrosine-protein kinase | ||||||
Function / homology | Function and homology information transmembrane-ephrin receptor activity / axon guidance / receptor protein-tyrosine kinase / dendrite / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å | ||||||
Authors | Davis, T. / Walker, J.R. / Newman, E.M. / Mackenzie, F. / Butler-Cole, C. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. ...Davis, T. / Walker, J.R. / Newman, E.M. / Mackenzie, F. / Butler-Cole, C. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Structure / Year: 2008 Title: Autoregulation by the Juxtamembrane Region of the Human Ephrin Receptor Tyrosine Kinase A3 (EphA3). Authors: Davis, T.L. / Walker, J.R. / Loppnau, P. / Butler-Cole, C. / Allali-Hassani, A. / 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 | 2qoi.cif.gz | 82.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qoi.ent.gz | 59 KB | Display | PDB format |
PDBx/mmJSON format | 2qoi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qoi_validation.pdf.gz | 435.8 KB | Display | wwPDB validaton report |
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Full document | 2qoi_full_validation.pdf.gz | 438.3 KB | Display | |
Data in XML | 2qoi_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 2qoi_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qo/2qoi ftp://data.pdbj.org/pub/pdb/validation_reports/qo/2qoi | HTTPS FTP |
-Related structure data
Related structure data | 2qo2C 2qo7C 2qo9C 2qobC 2qocC 2qodC 2qofC 2qokC 2qolC 2qonC 2qooC 2qoqC 2gsfS S: Starting model for refinement C: citing same article (ref.) |
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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: 41931.863 Da / Num. of mol.: 1 Fragment: Juxtamembrane segment and kinase domain: Residues 577-947 Mutation: Y596F, Y602F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: Placenta / Gene: EPHA3 / Plasmid: pET28a-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q6P4R6, UniProt: P29320*PLUS, receptor protein-tyrosine kinase |
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#2: Chemical | ChemComp-BME / |
#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: 1.83 Å3/Da / Density % sol: 32.92 % |
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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, 0.2M Ammonium sulfate, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 22, 2006 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.25→50 Å / Num. obs: 84211 / % possible obs: 99.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.04 / Χ2: 1.173 / Net I/σ(I): 13.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2GSF Resolution: 1.25→25.42 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.688 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.045 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.856 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→25.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.25→1.283 Å / Total num. of bins used: 20
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