+Open data
-Basic information
Entry | Database: PDB / ID: 6qy8 | ||||||
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Title | Human CSNK2A2 bound to ERB-041 | ||||||
Components | Casein kinase II subunit alpha'Casein kinase 2 | ||||||
Keywords | TRANSFERASE / Kinase / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information regulation of mitophagy / regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / positive regulation of protein targeting to mitochondrion / Receptor Mediated Mitophagy / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of apoptotic signaling pathway ...regulation of mitophagy / regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / positive regulation of protein targeting to mitochondrion / Receptor Mediated Mitophagy / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of apoptotic signaling pathway / negative regulation of ubiquitin-dependent protein catabolic process / acrosomal vesicle / Signal transduction by L1 / liver regeneration / cerebral cortex development / Wnt signaling pathway / Regulation of PTEN stability and activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / KEAP1-NFE2L2 pathway / double-strand break repair / spermatogenesis / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / cell cycle / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / chromatin / nucleoplasm / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Abdul Azeez, K.R. / Sorrell, F.J. / Krojer, T. / Bountra, C. / Edwards, A.M. / Arrowsmith, C. / Knapp, S. / Elkins, J.M. | ||||||
Citation | Journal: To Be Published Title: CSNK2A1 bound to ERB-041 Authors: Abdul Azeez, K.R. / Elkins, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qy8.cif.gz | 284.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qy8.ent.gz | 229.1 KB | Display | PDB format |
PDBx/mmJSON format | 6qy8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qy/6qy8 ftp://data.pdbj.org/pub/pdb/validation_reports/qy/6qy8 | HTTPS FTP |
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-Related structure data
Related structure data | 6qy7C 3ofmS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: 0
NCS ensembles :
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-Components
#1: Protein | Mass: 39932.723 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A2, CK2A2 / Details (production host): pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P19784, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-041 / #3: 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: 2.23 Å3/Da / Density % sol: 44.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% (w/v) PEG10000, 0.1M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→86.82 Å / Num. obs: 153463 / % possible obs: 99.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.21 / Net I/σ(I): 3.8 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 7634 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3OFM Resolution: 1.7→86.8 Å / Cor.coef. Fo:Fc: 0.868 / Cor.coef. Fo:Fc free: 0.849 / SU B: 3.877 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.141 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.532 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→86.8 Å
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Refine LS restraints |
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