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Yorodumi- PDB-2pvr: Crystal structure of the catalytic subunit of protein kinase CK2 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pvr | ||||||
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Title | Crystal structure of the catalytic subunit of protein kinase CK2 (C-terminal deletion mutant 1-335) in complex with two sulfate ions | ||||||
Components | Casein kinase II subunit alpha, catalytic subunit | ||||||
Keywords | SIGNALING PROTEIN / TRANSFERASE / EUKARYOTIC PROTEIN KINASE FOLD / CMGC kinases | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.605 Å | ||||||
Authors | Niefind, K. / Yde, C.W. / Ermakova, I. / Issinger, O.-G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Evolved to Be Active: Sulfate Ions Define Substrate Recognition Sites of CK2alpha and Emphasise its Exceptional Role within the CMGC Family of Eukaryotic Protein Kinases Authors: Niefind, K. / Yde, C.W. / Ermakova, I. / Issinger, O.G. #1: 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. #2: 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. / Ermakova, I. / Issinger, O.-G. #3: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pvr.cif.gz | 93 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pvr.ent.gz | 69.2 KB | Display | PDB format |
PDBx/mmJSON format | 2pvr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2pvr_validation.pdf.gz | 680.1 KB | Display | wwPDB validaton report |
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Full document | 2pvr_full_validation.pdf.gz | 682.6 KB | Display | |
Data in XML | 2pvr_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 2pvr_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/2pvr ftp://data.pdbj.org/pub/pdb/validation_reports/pv/2pvr | HTTPS FTP |
-Related structure data
Related structure data | 1pjkS 1ymi 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 molecule occurs as a monomer |
-Components
#1: Protein | Mass: 39935.547 Da / Num. of mol.: 1 / Fragment: catalytic domain, residues 1-335 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(de3) References: UniProt: P68400, non-specific serine/threonine protein kinase | ||||
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#2: Chemical | #3: Chemical | ChemComp-ANP / | #4: 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: 1.97 Å3/Da / Density % sol: 37.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEGmme 5000, ammonium sulfate, MES, adenylyl imidodiphosphate, magnesium chloride, peptide RRRADDSDDDDD, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 30, 2003 / Details: Osmic multilayer mirror |
Radiation | Monochromator: Osmic multilayer mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.605→19.71 Å / Num. all: 40626 / Num. obs: 40464 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 21.6 Å2 / Rsym value: 0.142 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.605→1.7 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 5999 / Rsym value: 46.6 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1PJK Resolution: 1.605→19.71 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.917 / SU B: 3.882 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.105 / ESU R Free: 0.113 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.401 Å2
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Refinement step | Cycle: LAST / Resolution: 1.605→19.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.605→1.647 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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