+Open data
-Basic information
Entry | Database: PDB / ID: 2exe | ||||||
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Title | Crystal structure of the phosphorylated CLK3 | ||||||
Components | Dual specificity protein kinase CLK3 | ||||||
Keywords | TRANSFERASE / dual-specificity kinase / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
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: 2.35 Å | ||||||
Authors | Papagrigoriou, E. / Rellos, P. / Das, S. / Bullock, A. / Ball, L.J. / Turnbull, A. / Savitsky, P. / Fedorov, O. / Johansson, C. / Ugochukwu, E. ...Papagrigoriou, E. / Rellos, P. / Das, S. / Bullock, A. / Ball, L.J. / Turnbull, A. / Savitsky, P. / Fedorov, O. / Johansson, C. / Ugochukwu, E. / Sobott, F. / von Delft, F. / Edwards, A. / Sundstrom, M. / Weigelt, J. / Arrowsmith, C. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of the phosphorylated CLK3 Authors: Papagrigoriou, E. / Rellos, P. / Das, S. / Bullock, A. / Ball, L.J. / Turnbull, A. / Fedorov, O. / Johansson, C. / Ugochukwu, E. / Sobott, F. / von Delft, F. / Edwards, A. / Sundstrom, M. / ...Authors: Papagrigoriou, E. / Rellos, P. / Das, S. / Bullock, A. / Ball, L.J. / Turnbull, A. / Fedorov, O. / Johansson, C. / Ugochukwu, E. / Sobott, F. / von Delft, F. / Edwards, A. / Sundstrom, M. / Weigelt, J. / Arrowsmith, C. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2exe.cif.gz | 70.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2exe.ent.gz | 50.1 KB | Display | PDB format |
PDBx/mmJSON format | 2exe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/2exe ftp://data.pdbj.org/pub/pdb/validation_reports/ex/2exe | HTTPS FTP |
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-Related structure data
Related structure data | 1z57S 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 | The biological unit is a monomer one monomer is found in the asu |
-Components
#1: Protein | Mass: 41999.039 Da / Num. of mol.: 1 / Fragment: PROTEIN KINASE domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CLK3 / Plasmid: pNIC28-Bsa4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: P49761, receptor protein-tyrosine kinase |
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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: 2.5 Å3/Da / Density % sol: 51.1 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.8M (NH4)3(cit), pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9764 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 3, 2005 / Details: Si(111) |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9764 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→32.82 Å / Num. all: 23758 / Num. obs: 23665 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.0495 / Rsym value: 0.0495 / Net I/σ(I): 13.59 |
Reflection shell | Highest resolution: 2.35 Å / Rmerge(I) obs: 0.3432 / Num. unique all: 2769 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1z57 Resolution: 2.35→32.82 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.91 / SU B: 11.667 / SU ML: 0.148 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The N-terminal domain of CLK3 is highly mobile and, hence, was not built. This is probably due to phosphorylation. The effect of ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The N-terminal domain of CLK3 is highly mobile and, hence, was not built. This is probably due to phosphorylation. The effect of phosphorylation on the CLK3 structure can be more clearly demonstrated if the structure of the phosphotylated molecule is compared with the structure of the dephosphorylated CLK3 (PDB ID:2EU9)
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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: 50.851 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→32.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.411 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -8.7673 Å / Origin y: 18.2037 Å / Origin z: 30.2449 Å
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