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Yorodumi- PDB-8pvo: Crystal structure of human Casein Kinase II subunit alpha (CK2a1)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pvo | ||||||
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Title | Crystal structure of human Casein Kinase II subunit alpha (CK2a1) in complex with allosteric compound FG5 | ||||||
Components | CSNK2A1 proteinCasein kinase 2, alpha 1 | ||||||
Keywords | TRANSFERASE / Kinase / CK2 / Allosteric Inhibitor | ||||||
Function / homology | Function and homology information protein kinase CK2 complex / non-specific serine/threonine protein kinase / regulation of cell cycle / protein serine/threonine kinase activity / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Kraemer, A. / Greco, F. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Crystal structure of human Casein Kinase II subunit alpha (CK2a1) in complex with allosteric compound FG5 Authors: Kraemer, A. / Greco, F. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pvo.cif.gz | 157.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pvo.ent.gz | 122.7 KB | Display | PDB format |
PDBx/mmJSON format | 8pvo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/8pvo ftp://data.pdbj.org/pub/pdb/validation_reports/pv/8pvo | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 40327.977 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5U5J2 |
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-Non-polymers , 5 types, 177 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 3.13 Å3/Da / Density % sol: 60.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.5 Details: 0.2 M ammonia sulphate 0.1 M bis-tris pH 5.5 23-26% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 24, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→45.17 Å / Num. obs: 49160 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.999 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 2.25→2.32 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4463 / CC1/2: 0.778 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→45.17 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.521 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.204 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.18 Å2
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Refinement step | Cycle: 1 / Resolution: 2.25→45.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.308 Å / Total num. of bins used: 20
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