+Open data
-Basic information
Entry | Database: PDB / ID: 5x18 | ||||||
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Title | Crystal structure of Casein kinase I homolog 1 | ||||||
Components | Casein kinase I homolog 1 | ||||||
Keywords | TRANSFERASE / Casein kinase I homolog 1 / KINASE | ||||||
Function / homology | Function and homology information glucose mediated signaling pathway / response to glucose / cell periphery / mitochondrial membrane / cell morphogenesis / endocytosis / peptidyl-serine phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation ...glucose mediated signaling pathway / response to glucose / cell periphery / mitochondrial membrane / cell morphogenesis / endocytosis / peptidyl-serine phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / protein serine/threonine kinase activity / endoplasmic reticulum / mitochondrion / ATP binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Kikuchi, M. / Shinohara, Y. / Ueda, H.R. / Umehara, T. | ||||||
Citation | Journal: Mol. Cell / Year: 2017 Title: Temperature-Sensitive Substrate and Product Binding Underlie Temperature-Compensated Phosphorylation in the Clock Authors: Shinohara, Y. / Koyama, Y.M. / Ukai-Tadenuma, M. / Hirokawa, T. / Kikuchi, M. / Yamada, R.G. / Ukai, H. / Fujishima, H. / Umehara, T. / Tainaka, K. / Ueda, H.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5x18.cif.gz | 255 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x18.ent.gz | 205.8 KB | Display | PDB format |
PDBx/mmJSON format | 5x18.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x1/5x18 ftp://data.pdbj.org/pub/pdb/validation_reports/x1/5x18 | HTTPS FTP |
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-Related structure data
Related structure data | 5x17C 3uysS C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33898.754 Da / Num. of mol.: 2 / Fragment: UNP residues 62-355 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: YCK1, CKI2, YHR135C / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) References: UniProt: P23291, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-GOL / #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.78 Å3/Da / Density % sol: 55.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2 M sodium malonate, 20 % polyethylene glycol 3350, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Oct 21, 2016 |
Radiation | Monochromator: Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 67599 / % possible obs: 98.4 % / Redundancy: 3.7 % / Net I/σ(I): 27 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 2 / Num. unique obs: 2974 / % possible all: 86.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3UYS Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.959 / SU B: 7.002 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.106 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.195 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→50 Å
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Refine LS restraints |
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