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Yorodumi- PDB-2oox: Crystal structure of the adenylate sensor from AMP-activated prot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2oox | ||||||
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Title | Crystal structure of the adenylate sensor from AMP-activated protein kinase complexed with AMP | ||||||
Components |
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Keywords | TRANSFERASE / AMPK / kinase / AMP | ||||||
Function / homology | Function and homology information positive regulation of flocculation / positive regulation of ascus development / positive regulation of cell cycle switching, mitotic to meiotic cell cycle / AMPK inhibits chREBP transcriptional activation activity / Carnitine metabolism / induction of conjugation with cellular fusion / Energy dependent regulation of mTOR by LKB1-AMPK / TP53 Regulates Metabolic Genes / Macroautophagy / SREBP signaling pathway ...positive regulation of flocculation / positive regulation of ascus development / positive regulation of cell cycle switching, mitotic to meiotic cell cycle / AMPK inhibits chREBP transcriptional activation activity / Carnitine metabolism / induction of conjugation with cellular fusion / Energy dependent regulation of mTOR by LKB1-AMPK / TP53 Regulates Metabolic Genes / Macroautophagy / SREBP signaling pathway / mitotic spindle pole body / CAMKK-AMPK signaling cascade / nucleotide-activated protein kinase complex / protein kinase regulator activity / protein kinase activator activity / AMP binding / negative regulation of cytoplasmic translation / negative regulation of TORC1 signaling / ADP binding / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / regulation of transcription by RNA polymerase II / protein kinase binding / signal transduction / positive regulation of transcription by RNA polymerase II / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å | ||||||
Authors | Townley, R. / Shapiro, L. | ||||||
Citation | Journal: Science / Year: 2007 Title: Crystal structures of the adenylate sensor from fission yeast AMP-activated protein kinase. Authors: Townley, R. / Shapiro, L. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). AUTHORS STATE THAT THE DEFINITIVE BIOLOGICAL UNIT IS A HETEROTRIMER (THERE ARE TWO SUCH TRIMERS: A+B+G AND C+D+E IN THE ASYMMETRIC UNIT), AND THAT THE DIMER OF THESE HETEROTRIMERS (SEE REMARK 350) IS ALSO PHYSIOLOGICALLY RELEVANT. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oox.cif.gz | 244.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oox.ent.gz | 192.9 KB | Display | PDB format |
PDBx/mmJSON format | 2oox.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2oox_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 2oox_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 2oox_validation.xml.gz | 55.9 KB | Display | |
Data in CIF | 2oox_validation.cif.gz | 78.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/2oox ftp://data.pdbj.org/pub/pdb/validation_reports/oo/2oox | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Details | The biological assembly is a dimer in the asymmetric unit |
-Components
#1: Protein | Mass: 15903.413 Da / Num. of mol.: 2 / Fragment: C-terminal domain: Residues 440-576 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Strain: 972 / Gene: ssp2, SPCC74.03c / Plasmid: pSMT3, pET-Duet-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: O74536, non-specific serine/threonine protein kinase #2: Protein | Mass: 10865.345 Da / Num. of mol.: 2 / Fragment: C-terminal domain: Residues 203-298 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Strain: 972 / Gene: SPCC1919.03c / Plasmid: pSMT3, pET-Duet-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P78789 #3: Protein | Mass: 37364.992 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Strain: 972 / Gene: SPAC1556.08c, SPAC1F12.01c / Plasmid: pSMT3, pET-Duet-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q10343 #4: Chemical | #5: 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: 47.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 6.2-7.2% PEG6000, 10% Ethylene glycol, 0.1M HEPES, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97898, 0.97919 | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 1, 2006 | |||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.6→50 Å / Num. all: 38169 / Num. obs: 38081 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 11.8 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 20.1 | |||||||||
Reflection shell | Resolution: 2.6→2.7 Å / Rmerge(I) obs: 0.469 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.878 / SU B: 11.317 / SU ML: 0.25 / Cross valid method: THROUGHOUT / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.309 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.665 Å / Total num. of bins used: 20
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