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Yorodumi- PDB-4uba: Low-salt structure of protein kinase CK2 catalytic subunit with 4... -
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-Basic information
Entry | Database: PDB / ID: 4uba | ||||||
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Title | Low-salt structure of protein kinase CK2 catalytic subunit with 4'-carboxy-6,8-bromo-flavonol (FLC26) | ||||||
Components | Casein kinase II subunit alphaCasein kinase 2 | ||||||
Keywords | TRANSFERASE / protein kinase CK2 / ATP-competitive inhibitors / halogen bond / 4'-carboxy-6 / 8-bromo-flavonol | ||||||
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 / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / chaperone-mediated protein folding / negative regulation of ubiquitin-dependent protein catabolic process / Signal transduction by L1 / Hsp90 protein binding / peptidyl-threonine phosphorylation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / positive regulation of protein catabolic process / rhythmic process / KEAP1-NFE2L2 pathway / double-strand break repair / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / protein stabilization / regulation of cell cycle / non-specific serine/threonine protein kinase / 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 / Resolution: 2.995 Å | ||||||
Authors | Niefind, K. / Bischoff, N. / Guerra, B. / Golub, A. / Issinger, O.-G. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2015 Title: A Note of Caution on the Role of Halogen Bonds for Protein Kinase/Inhibitor Recognition Suggested by High- And Low-Salt CK2 alpha Complex Structures. Authors: Guerra, B. / Bischoff, N. / Bdzhola, V.G. / Yarmoluk, S.M. / Issinger, O.G. / Golub, A.G. / Niefind, K. #1: Journal: Mol. Cell. Biochem. / Year: 2011 Title: Structure-based discovery of novel flavonol inhibitors of human protein kinase CK2. Authors: Golub, A.G. / Bdzhola, V.G. / Kyshenia, Y.V. / Sapelkin, V.M. / Prykhod'ko, A.O. / Kukharenko, O.P. / Ostrynska, O.V. / Yarmoluk, S.M. #2: Journal: J. Mol. Biol. / Year: 2003 Title: Crystal structure of a C-terminal deletion mutant of human protein kinase CK2 catalytic subunit. Authors: Ermakova, I. / Boldyreff, B. / Issinger, O.G. / Niefind, K. #3: Journal: EMBO J. / Year: 2001 Title: Crystal structure of human protein kinase CK2: insights into basic properties of the CK2 holoenzyme. Authors: Niefind, K. / Guerra, B. / Ermakowa, I. / 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 | 4uba.cif.gz | 289.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uba.ent.gz | 247.3 KB | Display | PDB format |
PDBx/mmJSON format | 4uba.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ub/4uba ftp://data.pdbj.org/pub/pdb/validation_reports/ub/4uba | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 40066.742 Da / Num. of mol.: 2 / Fragment: UNP residues 1-335 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Plasmid: pT7-7 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P68400, non-specific serine/threonine protein kinase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: Reservoir: 30 %(w/v) PEG4000, 0.2 M ammonium acetate, 0.1 M trisodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.995→44.55 Å / Num. obs: 20425 / % possible obs: 98.5 % / Redundancy: 6.5 % / Rsym value: 0.172 / Net I/σ(I): 10.6 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.995→44.548 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.995→44.548 Å
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Refine LS restraints |
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LS refinement shell |
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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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