+Open data
-Basic information
Entry | Database: PDB / ID: 6isj | ||||||
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Title | Crystal structure of CX-4945 bound CK2 alpha from C. neoformans | ||||||
Components | Casein kinase II subunit alpha | ||||||
Keywords | TRANSFERASE / kinase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cryptococcus neoformans var. grubii Bt85 (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Cho, H.S. | ||||||
Citation | Journal: To be published Title: Crystal structure of CX-4945 bound CK2 alpha from C. neoformans Authors: Cho, H.S. #1: Journal: Biochemistry / Year: 2011 Title: Unprecedented selectivity and structural determinants of a new class of protein kinase CK2 inhibitors in clinical trials for the treatment of cancer. Authors: Battistutta, R. / Cozza, G. / Pierre, F. / Papinutto, E. / Lolli, G. / Sarno, S. / O'Brien, S.E. / Siddiqui-Jain, A. / Haddach, M. / Anderes, K. / Ryckman, D.M. / Meggio, F. / Pinna, L.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6isj.cif.gz | 83.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6isj.ent.gz | 60.8 KB | Display | PDB format |
PDBx/mmJSON format | 6isj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6isj_validation.pdf.gz | 755.3 KB | Display | wwPDB validaton report |
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Full document | 6isj_full_validation.pdf.gz | 759.8 KB | Display | |
Data in XML | 6isj_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 6isj_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/6isj ftp://data.pdbj.org/pub/pdb/validation_reports/is/6isj | HTTPS FTP |
-Related structure data
Related structure data | 1lp4S 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: 39580.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptococcus neoformans var. grubii Bt85 (fungus) Gene: C365_06417 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A226BA59 | ||
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#2: Chemical | ChemComp-3NG / | ||
#3: Chemical | #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: 2.61 Å3/Da / Density % sol: 52.79 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M lithium sulfate, 0.1 M Tris pH 8.5, 30 %(w/v) PEG 4000, 30%(w/v) dextran sulfate sodium salt, 5 mM CX-4945 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→94.6 Å / Num. obs: 17652 / % possible obs: 99.07 % / Redundancy: 8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.329 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LP4 Resolution: 2.3→65.99 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.924 / SU B: 6.445 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.314 / ESU R Free: 0.214 / 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: 30.94 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→65.99 Å
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Refine LS restraints |
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