+Open data
-Basic information
Entry | Database: PDB / ID: 2nyc | ||||||
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Title | Crystal structure of the Bateman2 domain of yeast Snf4 | ||||||
Components | Nuclear protein SNF4 | ||||||
Keywords | PROTEIN BINDING / bateman2 domain / snf4 / amp kinase | ||||||
Function / homology | Function and homology information AMPK inhibits chREBP transcriptional activation activity / Energy dependent regulation of mTOR by LKB1-AMPK / regulation of cellular response to glucose starvation / regulation of invasive growth in response to glucose limitation / Carnitine metabolism / peroxisome organization / Macroautophagy / filamentous growth / protein kinase regulator activity / nucleotide-activated protein kinase complex ...AMPK inhibits chREBP transcriptional activation activity / Energy dependent regulation of mTOR by LKB1-AMPK / regulation of cellular response to glucose starvation / regulation of invasive growth in response to glucose limitation / Carnitine metabolism / peroxisome organization / Macroautophagy / filamentous growth / protein kinase regulator activity / nucleotide-activated protein kinase complex / nuclear envelope lumen / AMP binding / positive regulation of gluconeogenesis / protein serine/threonine kinase activator activity / autophagy / carbohydrate metabolic process / regulation of transcription by RNA polymerase II / protein kinase binding / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Rudolph, M.J. / Amodeo, G.A. / Iram, S. / Hong, S. / Pirino, G. / Carlson, M. / Tong, L. | ||||||
Citation | Journal: Structure / Year: 2007 Title: Structure of the Bateman2 domain of yeast Snf4: dimeric association and relevance for AMP binding. Authors: Rudolph, M.J. / Amodeo, G.A. / Iram, S. / Hong, S.P. / Pirino, G. / Carlson, M. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nyc.cif.gz | 38.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nyc.ent.gz | 26.8 KB | Display | PDB format |
PDBx/mmJSON format | 2nyc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ny/2nyc ftp://data.pdbj.org/pub/pdb/validation_reports/ny/2nyc | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16174.684 Da / Num. of mol.: 1 / Fragment: bateman2 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SNF4, CAT3 / Plasmid: pet26b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): bl21 de3 / References: UniProt: P12904 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.27 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 4.5 Details: 30% (w/v) PEG4000 and 200 mM (NH4)Acetate, pH 4.5, VAPOR DIFFUSION, temperature 294K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A |
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 22, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 11833 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→28.4 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.873 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.142 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.626 Å2
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Refine analyze | Luzzati coordinate error free: 0.14 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→28.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 46.049 Å / Origin y: 9.126 Å / Origin z: 4.001 Å
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