+Open data
-Basic information
Entry | Database: PDB / ID: 3dae | ||||||
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Title | Crystal structure of phosphorylated SNF1 kinase domain | ||||||
Components | Carbon catabolite-derepressing protein kinase | ||||||
Keywords | TRANSFERASE / kinase / AMPK / snf1 / ATP-binding / Carbohydrate metabolism / Membrane / Nucleotide-binding / Nucleus / Phosphoprotein / Serine/threonine-protein kinase | ||||||
Function / homology | Function and homology information fungal-type cell wall assembly / positive regulation of pseudohyphal growth / positive regulation of filamentous growth of a population of unicellular organisms in response to starvation / AMPK inhibits chREBP transcriptional activation activity / Energy dependent regulation of mTOR by LKB1-AMPK / single-species surface biofilm formation / regulation of cellular response to glucose starvation / regulation of invasive growth in response to glucose limitation / cellular bud neck septin ring / Carnitine metabolism ...fungal-type cell wall assembly / positive regulation of pseudohyphal growth / positive regulation of filamentous growth of a population of unicellular organisms in response to starvation / AMPK inhibits chREBP transcriptional activation activity / Energy dependent regulation of mTOR by LKB1-AMPK / single-species surface biofilm formation / regulation of cellular response to glucose starvation / regulation of invasive growth in response to glucose limitation / cellular bud neck septin ring / Carnitine metabolism / invasive growth in response to glucose limitation / Macroautophagy / filamentous growth / nucleotide-activated protein kinase complex / vacuolar membrane / AMP-activated protein kinase activity / nuclear envelope lumen / establishment of mitotic spindle orientation / positive regulation of macroautophagy / response to unfolded protein / cellular response to glucose starvation / positive regulation of gluconeogenesis / response to endoplasmic reticulum stress / guanyl-nucleotide exchange factor activity / molecular function activator activity / nuclear membrane / non-specific serine/threonine protein kinase / negative regulation of translation / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / mitochondrion / ATP binding / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.899 Å | ||||||
Authors | Zheng, L.-S. / Chen, L. / Jiao, Z.-H. / Wu, J.-W. | ||||||
Citation | Journal: Nature / Year: 2009 Title: Structural insight into the autoinhibition mechanism of AMP-activated protein kinase Authors: Chen, L. / Jiao, Z.-H. / Zheng, L.-S. / Zhang, Y.-Y. / Xie, S.-T. / Wang, Z.-X. / Wu, J.-W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dae.cif.gz | 116 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dae.ent.gz | 89.1 KB | Display | PDB format |
PDBx/mmJSON format | 3dae.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/3dae ftp://data.pdbj.org/pub/pdb/validation_reports/da/3dae | HTTPS FTP |
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-Related structure data
Related structure data | 3h4jC 2eue S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Details | THE DEPOSITORS THINK THE SOFTWARE PREDICTED QUATERNARY STRUCTURE IS NOT CONSISTENT WITH BIOCHEMICAL DATA AND MONOMER IS THE BIOLOGICAL UNIT. THE DIMER FORMATION MAY BE DUE TO CRYSTAL PACKING. |
-Components
#1: Protein | Mass: 32436.666 Da / Num. of mol.: 2 / Fragment: Kinase Domain, UNP residue 41-315 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SNF1 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P06782, non-specific serine/threonine protein kinase #2: 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: 2.35 Å3/Da / Density % sol: 47.65 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Tris pH 8.5, 3.2-3.6M NH4Ac, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1.00001 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 24, 2007 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00001 Å / Relative weight: 1 |
Reflection | Resolution: 2.899→47.2 Å / Num. all: 14122 / Num. obs: 14122 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 50.35 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 20.7 / Num. measured all: 102012 |
Reflection shell | Resolution: 2.899→3 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 4.29 / Num. unique all: 1369 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2EUE 2eue Resolution: 2.899→47.192 Å / FOM work R set: 0.792 / σ(F): 1.36 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.136 Å2 / ksol: 0.317 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 8.63 Å2 / Biso mean: 53.73 Å2 / Biso min: 205.13 Å2
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Refinement step | Cycle: LAST / Resolution: 2.899→47.192 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %
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