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Yorodumi- PDB-1fot: STRUCTURE OF THE UNLIGANDED CAMP-DEPENDENT PROTEIN KINASE CATALYT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fot | ||||||
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Title | STRUCTURE OF THE UNLIGANDED CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT FROM SACCHAROMYCES CEREVISIAE | ||||||
Components | CAMP-DEPENDENT PROTEIN KINASE TYPE 1CAMP-dependent pathway | ||||||
Keywords | TRANSFERASE / cAMP-dependent Protein Kinase / open conformation / protein kinase | ||||||
Function / homology | Function and homology information : / : / PKA activation / PKA activation in glucagon signalling / DARPP-32 events / Vasopressin regulates renal water homeostasis via Aquaporins / CREB1 phosphorylation through the activation of Adenylate Cyclase / Hedgehog 'off' state / Factors involved in megakaryocyte development and platelet production / negative regulation of cytoplasmic mRNA processing body assembly ...: / : / PKA activation / PKA activation in glucagon signalling / DARPP-32 events / Vasopressin regulates renal water homeostasis via Aquaporins / CREB1 phosphorylation through the activation of Adenylate Cyclase / Hedgehog 'off' state / Factors involved in megakaryocyte development and platelet production / negative regulation of cytoplasmic mRNA processing body assembly / MAPK6/MAPK4 signaling / chromatin => GO:0000785 / cAMP-dependent protein kinase / cAMP-dependent protein kinase activity / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / regulation of macroautophagy / protein kinase A signaling / peptidyl-serine phosphorylation / Ras protein signal transduction / protein kinase activity / cell cycle / cell division / protein phosphorylation / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å | ||||||
Authors | Mashhoon, N. / Carmel, G. / Pflugrath, J.W. / Kuret, J. | ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2001 Title: Structure of the unliganded cAMP-dependent protein kinase catalytic subunit from Saccharomyces cerevisiae. Authors: Mashhoon, N. / Carmel, G. / Pflugrath, J.W. / Kuret, J. #1: Journal: Biochemistry / Year: 1991 Title: Crystallization and Preliminary X-ray Analysis of the cAMP-Depende Protein Kinase Catalytic Subunit from Saccharomyces cerevisiae Authors: Kuret, J. / Pflugrath, J.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fot.cif.gz | 71.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fot.ent.gz | 56.9 KB | Display | PDB format |
PDBx/mmJSON format | 1fot.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fo/1fot ftp://data.pdbj.org/pub/pdb/validation_reports/fo/1fot | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37414.500 Da / Num. of mol.: 1 / Fragment: N-TERMINUS TRUNCATED TPK1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Description: SACCHAROMYCES CEREVISIAE / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P06244, EC: 2.7.1.37 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 9 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.75 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Tris-HCl, Propanol, MgCl2, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Details: Kuret, J., (1991) Biochemistry, 30, 10595. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 289 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER |
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→98 Å / Num. all: 9224 / Num. obs: 7854 / % possible obs: 82.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 9.3 % / Biso Wilson estimate: 76.4 Å2 / Rmerge(I) obs: 0.083 |
Reflection shell | Resolution: 2.8→2.97 Å / Num. unique all: 801 / % possible all: 52.7 |
Reflection | *PLUS Num. measured all: 86072 |
Reflection shell | *PLUS % possible obs: 52.7 % |
-Processing
Software |
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Refinement | Resolution: 2.8→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 3942096.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1 / Stereochemistry target values: CNS 0.5 standard tables
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 63.54 Å2 / ksol: 0.309 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.97 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: 'X-PLOR AND CNS 0.5' / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 50.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.384 / % reflection Rfree: 10 % / Rfactor Rwork: 0.31 |