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Yorodumi- PDB-3k0e: Crystal structure of the phosphorylation-site mutant T426N of the... -
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-Basic information
Entry | Database: PDB / ID: 3k0e | ||||||
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Title | Crystal structure of the phosphorylation-site mutant T426N of the KaiC circadian clock protein | ||||||
Components | Circadian clock protein kinase KaiC | ||||||
Keywords | CIRCADIAN CLOCK PROTEIN / TRANSFERASE / kaic / kinase / hexamer / ATP-binding / Biological rhythms / DNA-binding / Magnesium / Metal-binding / Nucleotide-binding / Phosphoprotein / Repressor / Serine/threonine-protein kinase / Transcription / Transcription regulation | ||||||
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 / protein serine kinase activity / protein serine/threonine kinase activity / regulation of DNA-templated transcription ...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 / 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: 3.2 Å | ||||||
Authors | Pattanayek, R. / Egli, M. / Pattanayek, S. | ||||||
Citation | Journal: Plos One / Year: 2009 Title: Structures of KaiC Circadian Clock Mutant Proteins: A New Phosphorylation Site at T426 and Mechanisms of Kinase, ATPase and Phosphatase. Authors: Pattanayek, R. / Mori, T. / Xu, Y. / Pattanayek, S. / Johnson, C.H. / Egli, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3k0e.cif.gz | 593.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k0e.ent.gz | 486.8 KB | Display | PDB format |
PDBx/mmJSON format | 3k0e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3k0e_validation.pdf.gz | 3.4 MB | Display | wwPDB validaton report |
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Full document | 3k0e_full_validation.pdf.gz | 3.6 MB | Display | |
Data in XML | 3k0e_validation.xml.gz | 142.4 KB | Display | |
Data in CIF | 3k0e_validation.cif.gz | 184.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/3k0e ftp://data.pdbj.org/pub/pdb/validation_reports/k0/3k0e | HTTPS FTP |
-Related structure data
Related structure data | 3jzmC 3k09C 3k0aC 3k0cC 3k0fC 2gblS 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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Unit cell |
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-Components
#1: Protein | Mass: 58245.727 Da / Num. of mol.: 6 / Mutation: T426N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus elongatus PCC 7942 (bacteria) Strain: PCC7942 / Gene: kaic, see0011, Synpcc7942_1216 / Plasmid: PET3 / Production host: Escherichia coli (E. coli) / Strain (production host): B121(DE3) References: UniProt: Q79PF4, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-ATP / #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: 2.65 Å3/Da / Density % sol: 53.59 % |
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Crystal grow | Temperature: 291 K / pH: 4 Details: SODIUM FORMATE, GLYCEROL, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 113.15 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1 |
Detector | Type: MAR 300MM CCD / Detector: CCD / Date: Apr 9, 2008 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→30 Å / Num. obs: 57564 / % possible obs: 92.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 3.2→3.3 Å / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.8 / % possible all: 81.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GBL Resolution: 3.2→30 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 4762
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Solvent computation | Bsol: 17.54 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 82.88 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.35 Å
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