+Open data
-Basic information
Entry | Database: PDB / ID: 2eu9 | ||||||
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Title | Crystal Structure of CLK3 | ||||||
Components | Dual specificity protein kinase CLK3 | ||||||
Keywords | TRANSFERASE / kinase domain | ||||||
Function / homology | Function and homology information dual-specificity kinase / intermediate filament cytoskeleton / regulation of RNA splicing / protein serine/threonine/tyrosine kinase activity / acrosomal vesicle / protein tyrosine kinase activity / nuclear speck / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity ...dual-specificity kinase / intermediate filament cytoskeleton / regulation of RNA splicing / protein serine/threonine/tyrosine kinase activity / acrosomal vesicle / protein tyrosine kinase activity / nuclear speck / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / RNA binding / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å | ||||||
Authors | Papagrigoriou, E. / Rellos, P. / Das, S. / Ugochukwu, E. / Turnbull, A. / von Delft, F. / Bunkoczi, G. / Sobott, F. / Bullock, A. / Fedorov, O. ...Papagrigoriou, E. / Rellos, P. / Das, S. / Ugochukwu, E. / Turnbull, A. / von Delft, F. / Bunkoczi, G. / Sobott, F. / Bullock, A. / Fedorov, O. / Gileadi, C. / Savitsky, P. / Edwards, A. / Aerrowsmith, C. / Weigelt, J. / Sundstrom, M. / Knapp, S. | ||||||
Citation | Journal: Structure / Year: 2009 Title: Kinase domain insertions define distinct roles of CLK kinases in SR protein phosphorylation. Authors: Bullock, A.N. / Das, S. / Debreczeni, J.E. / Rellos, P. / Fedorov, O. / Niesen, F.H. / Guo, K. / Papagrigoriou, E. / Amos, A.L. / Cho, S. / Turk, B.E. / Ghosh, G. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2eu9.cif.gz | 91.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2eu9.ent.gz | 68.5 KB | Display | PDB format |
PDBx/mmJSON format | 2eu9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/2eu9 ftp://data.pdbj.org/pub/pdb/validation_reports/eu/2eu9 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | the asymmetric unit contains one biological molecule |
-Components
#1: Protein | Mass: 41792.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CLK3 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)R3 / References: UniProt: P49761, dual-specificity kinase |
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#2: Chemical | ChemComp-EDO / |
#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: 2.23 Å3/Da / Density % sol: 44.76 % |
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Crystal grow | Temperature: 282 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 27% PEG 3350, 30 mM Ammonium acetate, 100 mM Bis Tris pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 282K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9718 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 22, 2005 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9718 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→30.71 Å / Num. all: 55834 / Num. obs: 55697 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.0577 / Rsym value: 0.04 |
Reflection shell | Resolution: 1.53→1.65 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.3784 / Mean I/σ(I) obs: 4.2 / Rsym value: 0.2959 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→30.71 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.667 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.076 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.246 Å2
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Refinement step | Cycle: LAST / Resolution: 1.53→30.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.53→1.57 Å / Total num. of bins used: 20
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