+Open data
-Basic information
Entry | Database: PDB / ID: 6ko6 | ||||||
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Title | Crystal structure of AMPPNP bound Cka1 from C. neoformans | ||||||
Components | CMGC/CK2 protein kinase | ||||||
Keywords | TRANSFERASE / kinase | ||||||
Function / homology | Function and homology information protein phosphorylation / protein serine/threonine kinase activity / ATP binding Similarity search - Function | ||||||
Biological species | Cryptococcus neoformans var. grubii serotype A (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Cho, H.S. / Yoo, Y. | ||||||
Citation | Journal: Sci Rep / Year: 2019 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. #1: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ko6.cif.gz | 86.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ko6.ent.gz | 62.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ko6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ko/6ko6 ftp://data.pdbj.org/pub/pdb/validation_reports/ko/6ko6 | HTTPS FTP |
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-Related structure data
Related structure data | 6k3lC 1lp4S 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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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 serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487) (fungus) Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: CNAG_05694 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: J9VNH4, UniProt: A0A226BA59*PLUS | ||||
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#2: Chemical | ChemComp-ANP / | ||||
#3: Chemical | ChemComp-MG / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.07 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M lithium sulfate, 0.1M Tris pH 8.5, 30%(w/v) PEG 4000, 30%(w/v) dextran sulfate sodium salt, 5mM AMPPNP, 5mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 0.97 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 27, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→46.67 Å / Num. obs: 15949 / % possible obs: 99.5 % / Redundancy: 2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.0417 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.4→2.486 Å / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 2.35 / Num. unique obs: 1554 / CC1/2: 0.929 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LP4 Resolution: 2.4→46.67 Å / Cross valid method: THROUGHOUT
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Refinement step | Cycle: LAST / Resolution: 2.4→46.67 Å
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LS refinement shell | Resolution: 2.4→2.486 Å /
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