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Yorodumi- PDB-4xpd: Crystal structure of yeast N-terminal acetyltransferase NatE (ppG... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xpd | ||||||
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Title | Crystal structure of yeast N-terminal acetyltransferase NatE (ppGpp) in complex with a bisubstrate | ||||||
Components |
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Keywords | TRANSFERASE / N-terminal acetyltransferase / NatE / ppGpp / bisubstrate | ||||||
Function / homology | Function and homology information cellular pigmentation / positive regulation of oxytocin production / Peptide hormone biosynthesis / Defective ACTH causes obesity and POMCD / type 1 melanocortin receptor binding / N-terminal protein amino acid propionylation / type 3 melanocortin receptor binding / type 4 melanocortin receptor binding / regulation of corticosterone secretion / response to melanocyte-stimulating hormone ...cellular pigmentation / positive regulation of oxytocin production / Peptide hormone biosynthesis / Defective ACTH causes obesity and POMCD / type 1 melanocortin receptor binding / N-terminal protein amino acid propionylation / type 3 melanocortin receptor binding / type 4 melanocortin receptor binding / regulation of corticosterone secretion / response to melanocyte-stimulating hormone / N-terminal amino-acid Nalpha-acetyltransferase NatA / peptide-glutamate-alpha-N-acetyltransferase activity / Opioid Signalling / N-terminal methionine Nalpha-acetyltransferase NatE / NatA complex / peptide-serine-alpha-N-acetyltransferase activity / Androgen biosynthesis / regulation of appetite / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / Glucocorticoid biosynthesis / regulation of glycogen metabolic process / neuropeptide hormone activity / mitotic sister chromatid cohesion / positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / negative regulation of tumor necrosis factor production / neuropeptide signaling pathway / Endogenous sterols / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Peptide ligand-binding receptors / secretory granule / generation of precursor metabolites and energy / G protein-coupled receptor binding / calcium-mediated signaling / G-protein activation / hormone activity / regulation of blood pressure / ribosome binding / cell-cell signaling / glucose homeostasis / G alpha (i) signalling events / G alpha (s) signalling events / secretory granule lumen / Interleukin-4 and Interleukin-13 signaling / signaling receptor binding / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular space / extracellular region / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.81 Å | ||||||
Authors | Dong, J. / Wang, S. / York, J.D. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of yeast N-terminal acetyltransferase NatE (ppGpp) in complex with a bisubstrate Authors: Dong, J. / Wang, S. / York, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xpd.cif.gz | 237.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xpd.ent.gz | 193.6 KB | Display | PDB format |
PDBx/mmJSON format | 4xpd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xp/4xpd ftp://data.pdbj.org/pub/pdb/validation_reports/xp/4xpd | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-N-terminal acetyltransferase A complex subunit ... , 2 types, 2 molecules AC
#1: Protein | Mass: 99050.133 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli) / References: UniProt: P12945 |
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#3: Protein | Mass: 19753.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli) References: UniProt: Q08689, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
-Protein / Protein/peptide , 2 types, 2 molecules BF
#2: Protein | Mass: 27635.168 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli) / References: UniProt: P07347, EC: 2.3.1.88 |
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#4: Protein/peptide | Mass: 1058.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01189*PLUS |
-Non-polymers , 4 types, 16 molecules
#5: Chemical | ChemComp-G4P / |
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#6: Chemical | ChemComp-ACO / |
#7: Chemical | ChemComp-CMC / |
#8: 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: 2.42 Å3/Da / Density % sol: 49.14 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 17% PEG 550 MME, 0.1 M MES pH 6.5 / PH range: 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 9, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 35928 / % possible obs: 99.5 % / Redundancy: 7.4 % / Net I/σ(I): 15 |
-Processing
Software |
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Refinement | Resolution: 2.81→50 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.833 / SU B: 15.852 / SU ML: 0.322 / Cross valid method: THROUGHOUT / ESU R Free: 0.502 / 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: 48.318 Å2
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Refinement step | Cycle: LAST / Resolution: 2.81→50 Å
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