[English] 日本語
Yorodumi- PDB-3s1a: Crystal structure of the phosphorylation-site double mutant S431E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3s1a | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the phosphorylation-site double mutant S431E/T432E of the KaiC circadian clock protein | ||||||
Components | (Circadian clock protein kinase kaiC) x 2 | ||||||
Keywords | TRANSFERASE / hexamer / atp binding / auto-kinase / phophatase / Serine Threonine Kinase / Mg Binding / Phosphorylation | ||||||
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: 3 Å | ||||||
Authors | Pattanayek, R. / Williams, D.W. / Rossi, G. / Weigand, S. / Mori, T. / Johnson, C.H. / Stewart, P.L. / Egli, M. | ||||||
Citation | Journal: Plos One / Year: 2011 Title: Combined SAXS/EM Based Models of the S. elongatus Post-Translational Circadian Oscillator and its Interactions with the Output His-Kinase SasA. Authors: Pattanayek, R. / Williams, D.R. / Rossi, G. / Weigand, S. / Mori, T. / Johnson, C.H. / Stewart, P.L. / Egli, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3s1a.cif.gz | 591 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3s1a.ent.gz | 484.9 KB | Display | PDB format |
PDBx/mmJSON format | 3s1a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s1/3s1a ftp://data.pdbj.org/pub/pdb/validation_reports/s1/3s1a | HTTPS FTP |
---|
-Related structure data
Related structure data | 3dvlS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 59051.691 Da / Num. of mol.: 2 / Mutation: S431E, T432E Source method: isolated from a genetically manipulated source Details: SEP at residue 320 / Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: PCC 7942 / Gene: kaiC, see0011, Synpcc7942_1216 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q79PF4, non-specific serine/threonine protein kinase #2: Protein | Mass: 58971.715 Da / Num. of mol.: 4 / Mutation: S431E, T432E Source method: isolated from a genetically manipulated source Details: SER at residue 320 / Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: PCC 7942 / Gene: kaiC, see0011, Synpcc7942_1216 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q79PF4, non-specific serine/threonine protein kinase #3: Chemical | ChemComp-ATP / #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.64 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 Details: SODIUM FORMATE, GLYCEROL, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 113.15 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 20, 2009 / Details: mirrors |
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→17 Å / Num. all: 73982 / Num. obs: 73982 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 2.3 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 3.34 / Num. unique all: 3536 / % possible all: 96 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3DVL Resolution: 3→17 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→17 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
LS refinement shell | Resolution: 3→3.02 Å
|