+Open data
-Basic information
Entry | Database: PDB / ID: 7dye | ||||||
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Title | Crystal Structure of Cyanobacterial Circadian Clock Protein 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 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Furuike, Y. / Akiyama, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2022 Title: Regulation mechanisms of the dual ATPase in KaiC. Authors: Furuike, Y. / Mukaiyama, A. / Koda, S.I. / Simon, D. / Ouyang, D. / Ito-Miwa, K. / Saito, S. / Yamashita, E. / Nishiwaki-Ohkawa, T. / Terauchi, K. / 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 | 7dye.cif.gz | 183 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dye.ent.gz | 138.8 KB | Display | PDB format |
PDBx/mmJSON format | 7dye.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/7dye ftp://data.pdbj.org/pub/pdb/validation_reports/dy/7dye | HTTPS FTP |
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-Related structure data
Related structure data | 7dy1C 2gblS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 58026.750 Da / Num. of mol.: 2 / Mutation: S431A, T432A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus elongatus (strain PCC 7942 / FACHB-805) (bacteria) Strain: PCC 7942 / FACHB-805 / Gene: kaiC, Synpcc7942_1216, see0011 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q79PF4, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-ATP / #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.07 Å3/Da / Density % sol: 40.44 % |
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Crystal grow | Temperature: 313 K / Method: evaporation / pH: 7 / Details: sodium/potassium tartrate, sodium acetate, KCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 9, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→47.5 Å / Num. obs: 28555 / % possible obs: 99.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.6→2.72 Å / Rmerge(I) obs: 0.612 / Num. unique obs: 3485 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GBL Resolution: 2.6→47.5 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.878 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.033 / ESU R Free: 0.438 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 102.57 Å2 / Biso mean: 47.208 Å2 / Biso min: 28.77 Å2
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Refinement step | Cycle: final / Resolution: 2.6→47.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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