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Yorodumi- PDB-2qrd: Crystal Structure of the Adenylate Sensor from AMP-activated Prot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qrd | ||||||
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Title | Crystal Structure of the Adenylate Sensor from AMP-activated Protein Kinase in complex with ADP and ATP | ||||||
Components |
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Keywords | TRANSFERASE / AMPK / ADP / ATP-binding / Kinase / Nucleotide-binding / Serine/threonine-protein kinase / CBS domain | ||||||
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 / mitotic spindle pole body ...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 / mitotic spindle pole body / SREBP signaling pathway / 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 / carbohydrate metabolic process / non-specific serine/threonine protein kinase / phosphorylation / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.41 Å | ||||||
Authors | Jin, X. / Townley, R. / Shapiro, L. | ||||||
Citation | Journal: Structure / Year: 2007 Title: Structural Insight into AMPK Regulation: ADP Comes into Play. Authors: Jin, X. / Townley, R. / Shapiro, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qrd.cif.gz | 232.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qrd.ent.gz | 184.5 KB | Display | PDB format |
PDBx/mmJSON format | 2qrd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qr/2qrd ftp://data.pdbj.org/pub/pdb/validation_reports/qr/2qrd | HTTPS FTP |
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-Related structure data
Related structure data | 2qr1C 2qrcC 2qreC 2ooyS 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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2 |
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3 |
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Unit cell |
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Details | The biological unit is a heterotrimer (There are two such trimers: A+B+G and C+D+E in the asymmetric unit). The dimer of these heterotrimers is also physiologically relevant. |
-Components
-Protein , 3 types, 6 molecules ACBDGE
#1: Protein | Mass: 15903.413 Da / Num. of mol.: 2 / Fragment: C-terminal residues:440-576 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: ssp2 / Plasmid: PSMT3 / 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 residues:203-298 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Plasmid: 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: 37436.070 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Plasmid: PET-DUET-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q10343 |
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-Non-polymers , 3 types, 418 molecules
#4: Chemical | #5: Chemical | ChemComp-ATP / #6: 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: 2.32 Å3/Da / Density % sol: 46.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 6-10% PEG 3350, 0.1M Sodium Citrate, pH 5.5, 5mM ADP, 5mM ATP, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97926 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2007 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 47233 / Num. obs: 45186 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 3.5 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2ooy Resolution: 2.41→35.94 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.924 / SU B: 17.487 / SU ML: 0.215 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.52 / ESU R Free: 0.294 / 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: 52.553 Å2
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Refinement step | Cycle: LAST / Resolution: 2.41→35.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.41→2.47 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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