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Yorodumi- PDB-1pjk: Crystal Structure of a C-terminal deletion mutant of human protei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pjk | ||||||
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Title | Crystal Structure of a C-terminal deletion mutant of human protein kinase CK2 catalytic subunit | ||||||
Components | Casein kinase II, alpha chain | ||||||
Keywords | TRANSFERASE / eukaryotic protein kinase fold | ||||||
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: 2.5 Å | ||||||
Authors | Ermakova, I. / Boldyreff, B. / Issinger, O.-G. / Niefind, K. | ||||||
Citation | 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. #1: 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. | ||||||
History |
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Remark 999 | sequence The enzyme CK2 was co crystallized with an artificial peptide substrate (RRRADDSDDDDD). ...sequence The enzyme CK2 was co crystallized with an artificial peptide substrate (RRRADDSDDDDD). However, the peptide could not be located in the electron density. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pjk.cif.gz | 86.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pjk.ent.gz | 63.8 KB | Display | PDB format |
PDBx/mmJSON format | 1pjk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pjk_validation.pdf.gz | 735.6 KB | Display | wwPDB validaton report |
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Full document | 1pjk_full_validation.pdf.gz | 741.8 KB | Display | |
Data in XML | 1pjk_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 1pjk_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pj/1pjk ftp://data.pdbj.org/pub/pdb/validation_reports/pj/1pjk | HTTPS FTP |
-Related structure data
Related structure data | 1jwhS 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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-Components
#1: Protein | Mass: 39935.547 Da / Num. of mol.: 1 / Fragment: residue 2-335 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1 OR CK2A1 / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P68400, EC: 2.7.1.37 |
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#2: Chemical | ChemComp-CL / |
#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: 2.05 Å3/Da / Density % sol: 39.92 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 6, 2002 / Details: Osmic mirrors |
Radiation | Monochromator: Osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→17.3 Å / Num. all: 11207 / Num. obs: 11207 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 41.3 Å2 / Rsym value: 0.118 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.5→2.59 Å / % possible all: 99.9 |
Reflection | *PLUS Rmerge(I) obs: 0.118 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / % possible obs: 99.9 % / Redundancy: 2.3 % / Num. unique obs: 1136 / Rmerge(I) obs: 0.602 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: CHAIN A of PDB ENTRY 1JWH Resolution: 2.5→17.3 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.903 / SU B: 12.297 / SU ML: 0.269 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC/TLS-REFINEMENT / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.36 / 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: 12.728 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→17.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.564 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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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 17.3 Å / Rfactor Rfree: 0.257 / Rfactor Rwork: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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