+Open data
-Basic information
Entry | Database: PDB / ID: 5yz8 | ||||||
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Title | Crystal Structure of N-terminal C1 domain of KaiC | ||||||
Components | Circadian Clock Protein Kinase KaiC | ||||||
Keywords | TRANSFERASE / CLOCK PROTEIN | ||||||
Function / homology | Function and homology information regulation of phosphorelay signal transduction system / negative regulation of circadian rhythm / entrainment of circadian clock / protein serine/threonine/tyrosine kinase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / circadian rhythm / non-specific serine/threonine protein kinase / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity ...regulation of phosphorelay signal transduction system / negative regulation of circadian rhythm / entrainment of circadian clock / protein serine/threonine/tyrosine kinase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / circadian rhythm / non-specific serine/threonine protein kinase / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / regulation of DNA-templated transcription / magnesium ion binding / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | Synechococcus elongatus PCC 7942 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å | ||||||
Authors | Mukaiyama, A. / Furuike, Y. / Abe, J. / Akiyama, S. | ||||||
Citation | Journal: Sci Rep / Year: 2018 Title: Conformational rearrangements of the C1 ring in KaiC measure the timing of assembly with KaiB. Authors: Mukaiyama, A. / Furuike, Y. / Abe, J. / Yamashita, E. / Kondo, T. / Akiyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yz8.cif.gz | 265.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yz8.ent.gz | 207.3 KB | Display | PDB format |
PDBx/mmJSON format | 5yz8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/5yz8 ftp://data.pdbj.org/pub/pdb/validation_reports/yz/5yz8 | HTTPS FTP |
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-Related structure data
Related structure data | 4tl7S 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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Unit cell |
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-Components
#1: Protein | Mass: 28591.494 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 1-254 / Mutation: S229W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus elongatus PCC 7942 (bacteria) Strain: PCC 7942 / Gene: KAIC, SYNPCC7942_1216, SEE0011 / Production host: Escherichia coli (E. coli) References: UniProt: Q79PF4, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-ANP / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-CL / #5: 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: 2.2 Å3/Da / Density % sol: 44.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: PEG 400, PEG 8000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jul 6, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 37912 / % possible obs: 100 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 10.8 % / Mean I/σ(I) obs: 2.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TL7 Resolution: 2.81→50 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.845 / SU B: 18.146 / SU ML: 0.359 / Cross valid method: FREE R-VALUE / ESU R Free: 0.453
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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: 39.12 Å2
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Refinement step | Cycle: LAST / Resolution: 2.81→50 Å
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Refine LS restraints |
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