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Open data
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Basic information
Entry | Database: PDB / ID: 6k3l | ||||||
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Title | Crystal structure of CX-4945 bound Cka1 from C. neoformans | ||||||
![]() | CMGC/CK2 protein kinase | ||||||
![]() | TRANSFERASE / kinase | ||||||
Function / homology | ![]() protein phosphorylation / protein serine/threonine kinase activity / ATP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cho, H.S. / Yoo, Y. | ||||||
![]() | ![]() Title: Structural analysis of fungal pathogenicity-related casein kinase alpha subunit, Cka1, in the human fungal pathogen Cryptococcus neoformans. Authors: Ong, B.X. / Yoo, Y. / Han, M.G. / Park, J.B. / Choi, M.K. / Choi, Y. / Shin, J.S. / Bahn, Y.S. / Cho, H.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 86.2 KB | Display | ![]() |
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PDB format | ![]() | 63.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 760.9 KB | Display | ![]() |
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Full document | ![]() | 764 KB | Display | |
Data in XML | ![]() | 14.8 KB | Display | |
Data in CIF | ![]() | 20.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ko6C ![]() 1lp4S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: CNAG_05694 Production host: ![]() ![]() References: UniProt: J9VNH4, UniProt: A0A226BA59*PLUS |
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#2: Chemical | ChemComp-3NG / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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, 5mM CX-4945 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 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: 2.09→65.79 Å / Num. obs: 23770 / % possible obs: 97 % / Redundancy: 2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.02506 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.094→2.169 Å / Rmerge(I) obs: 0.2672 / Num. unique obs: 1908 / CC1/2: 0.884 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1LP4 Resolution: 2.09→47.74 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.085 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.173 / 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: 36.927 Å2
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Refinement step | Cycle: 1 / Resolution: 2.09→47.74 Å
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Refine LS restraints |
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