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- PDB-6xx6: Arabidopsis thaliana Casein Kinase 2 (CK2) alpha-1 crystal form I -
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Open data
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Basic information
Entry | Database: PDB / ID: 6xx6 | |||||||||
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Title | Arabidopsis thaliana Casein Kinase 2 (CK2) alpha-1 crystal form I | |||||||||
![]() | Casein kinase II subunit alpha-1 | |||||||||
![]() | CELL CYCLE / Kinase / CK2 / Casein Kinase / PLANT PROTEIN | |||||||||
Function / homology | ![]() protein kinase CK2 complex / regulation of circadian rhythm / kinase activity / non-specific serine/threonine protein kinase / regulation of cell cycle / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / ATP binding ...protein kinase CK2 complex / regulation of circadian rhythm / kinase activity / non-specific serine/threonine protein kinase / regulation of cell cycle / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / ATP binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Demulder, M. / De Veylder, L. / Loris, R. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of Arabidopsis thaliana casein kinase 2 alpha 1. Authors: Demulder, M. / De Veylder, L. / Loris, R. #1: ![]() Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Demulder, M. / De Veylder, L. / Loris, R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.1 KB | Display | ![]() |
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PDB format | ![]() | 69.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.4 KB | Display | ![]() |
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Full document | ![]() | 459 KB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 27 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6xx7C ![]() 6xx8C ![]() 6xx9C ![]() 3pzhS 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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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 40521.512 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q08467, non-specific serine/threonine protein kinase |
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-Non-polymers , 5 types, 358 molecules ![](data/chem/img/PIV.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PIV / | ||||
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#3: Chemical | ChemComp-SO4 / | ||||
#4: Chemical | #5: Chemical | ChemComp-PGE / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M sodium sulfate 0.1M Bis-Tris propane pH 6.5 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Apr 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.849→50 Å / Num. obs: 38648 / % possible obs: 98.7 % / Redundancy: 8.4 % / Biso Wilson estimate: 29.0568885607 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.85→1.96 Å / Num. unique obs: 5815 / CC1/2: 0.704 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3PZH Resolution: 1.84919690899→48.0095807101 Å / SU ML: 0.245576210565 / Cross valid method: FREE R-VALUE / σ(F): 1.362077121 / Phase error: 20.1312265863
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.560177005 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.84919690899→48.0095807101 Å
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Refine LS restraints |
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LS refinement shell |
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