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Yorodumi- PDB-3juh: Crystal structure of a mutant of human protein kinase CK2alpha wi... -
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-Basic information
Entry | Database: PDB / ID: 3juh | |||||||||
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Title | Crystal structure of a mutant of human protein kinase CK2alpha with altered cosubstrate specificity | |||||||||
Components | Casein kinase II subunit alpha | |||||||||
Keywords | TRANSFERASE / eukaryotic protein kinase / ATP-binding / Kinase / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase / Wnt signaling pathway | |||||||||
Function / homology | Function and homology information regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Sin3-type complex / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ...regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Sin3-type complex / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Maturation of hRSV A proteins / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / chaperone-mediated protein folding / negative regulation of ubiquitin-dependent protein catabolic process / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / KEAP1-NFE2L2 pathway / double-strand break repair / rhythmic process / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / protein stabilization / negative regulation of translation / non-specific serine/threonine protein kinase / regulation of cell cycle / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / positive regulation of cell population proliferation / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.66 Å | |||||||||
Authors | Niefind, K. / Issinger, O.-G. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Inclining the purine base binding plane in protein kinase CK2 by exchanging the flanking side-chains generates a preference for ATP as a cosubstrate Authors: Yde, C.W. / Ermakova, I. / Issinger, O.-G. / Niefind, K. #1: Journal: Chem.Biol. / Year: 2008 Title: The CK2 alpha/CK2 beta interface of human protein kinase CK2 harbors a binding pocket for small molecules Authors: Raaf, J. / Brunstein, E. / Issinger, O.-G. / Niefind, K. #2: Journal: Biochim.Biophys.Acta / Year: 2010 Title: Conformational plasticity of the catalytic subunit of protein kinase CK2 and its consequences for regulation and drug design Authors: Niefind, K. / Issinger, O.-G. #3: Journal: Cell.Mol.Life Sci. / Year: 2009 Title: Protein kinase CK2 in health and disease: Protein kinase CK2: from structures to insights Authors: Niefind, K. / Raaf, J. / Issinger, O.-G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3juh.cif.gz | 265.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3juh.ent.gz | 209 KB | Display | PDB format |
PDBx/mmJSON format | 3juh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3juh_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3juh_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3juh_validation.xml.gz | 36.2 KB | Display | |
Data in CIF | 3juh_validation.cif.gz | 52.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ju/3juh ftp://data.pdbj.org/pub/pdb/validation_reports/ju/3juh | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 40020.652 Da / Num. of mol.: 2 / Fragment: residues 1-335 / Mutation: V66A, M163L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: csnk2a1 / Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): bl21(de3) References: UniProt: P68400, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-CL / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 2.2M sodium citrate, 2mM AMPPNP, 4mM magnesium chloride, 0.62mM peptide RRRADDSDDDDD, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.811 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 19, 2004 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.811 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.66→39.5 Å / Num. all: 74683 / Num. obs: 72782 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 30.398 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 17.51 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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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 / Resolution: 1.66→39.45 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.825 / SU B: 4.569 / SU ML: 0.065 / SU R Cruickshank DPI: 0.021 / SU Rfree: 0.023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.021 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: RESIDUAL ONLY
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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 max: 57.09 Å2 / Biso mean: 25.858 Å2 / Biso min: 6.35 Å2
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Refinement step | Cycle: LAST / Resolution: 1.66→39.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.658→1.701 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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