+Open data
-Basic information
Entry | Database: PDB / ID: 7wdc | ||||||
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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: 2.84 Å | ||||||
Authors | Furuike, Y. / Akiyama, S. | ||||||
Funding support | 1items
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Citation | Journal: Biochem.J. / Year: 2022 Title: Highly sensitive tryptophan fluorescence probe for detecting rhythmic conformational changes of KaiC in the cyanobacterial circadian clock system. Authors: Mukaiyama, A. / Furuike, Y. / Yamashita, E. / Akiyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wdc.cif.gz | 186.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wdc.ent.gz | 141.5 KB | Display | PDB format |
PDBx/mmJSON format | 7wdc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/7wdc ftp://data.pdbj.org/pub/pdb/validation_reports/wd/7wdc | HTTPS FTP |
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-Related structure data
Related structure data | 7dyjS S: Starting model for refinement |
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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: 58111.812 Da / Num. of mol.: 2 / Mutation: F419W 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 / Details (production host): 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: 2.06 Å3/Da / Density % sol: 40.26 % |
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Crystal grow | Temperature: 313 K / Method: evaporation / Details: sodium/pottasium tartrae, 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: 2.84→47.6 Å / Num. obs: 43729 / % possible obs: 99.4 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.84→3.01 Å / Rmerge(I) obs: 0.915 / Num. unique obs: 6952 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7DYJ Resolution: 2.84→46.13 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.872 / SU B: 27.696 / SU ML: 0.521 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.527 / 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: 144.89 Å2 / Biso mean: 69.253 Å2 / Biso min: 42.55 Å2
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Refinement step | Cycle: final / Resolution: 2.84→46.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.84→2.909 Å / Rfactor Rfree error: 0
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