[English] 日本語
![](img/lk-miru.gif)
- PDB-4y49: Crystal structure of yeast N-terminal acetyltransferase (ppGpp) N... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4y49 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of yeast N-terminal acetyltransferase (ppGpp) NatE in complex with a bisubstrate | ||||||
![]() |
| ||||||
![]() | TRANSFERASE / N-terminal acetyltransferase / NatE / ppGpp / bisubstrate | ||||||
Function / homology | ![]() 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 / Opioid Signalling / N-terminal methionine Nalpha-acetyltransferase NatE / N-terminal amino-acid Nalpha-acetyltransferase NatA / peptide-glutamate-alpha-N-acetyltransferase activity / NatA complex / Androgen biosynthesis / peptide-serine-alpha-N-acetyltransferase activity / 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 / cell-cell signaling / ribosome binding / glucose homeostasis / G alpha (i) signalling events / G alpha (s) signalling events / Interleukin-4 and Interleukin-13 signaling / secretory granule lumen / 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 | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Dong, J. / Wang, S. / York, J.D. | ||||||
![]() | ![]() Title: Crystal structure of yeast N-terminal acetyltransferase (ppGpp) NatE in complex with a bisubstrate Authors: Dong, J. / Wang, S. / York, J.D. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 989.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 760.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 114 KB | Display | |
Data in CIF | ![]() | 154.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
|
-
Components
-N-terminal acetyltransferase A complex subunit ... , 2 types, 6 molecules AGMCIO
#1: Protein | Mass: 99084.195 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() #3: Protein | Mass: 19753.727 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: Q08689, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
---|
-Protein / Protein/peptide , 2 types, 6 molecules BHNEKQ
#2: Protein | Mass: 27635.168 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() #4: Protein/peptide | Mass: 1058.169 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) ![]() |
---|
-Non-polymers , 3 types, 9 molecules ![](data/chem/img/G4P.gif)
![](data/chem/img/CMC.gif)
![](data/chem/img/ACO.gif)
![](data/chem/img/CMC.gif)
![](data/chem/img/ACO.gif)
#5: Chemical | #6: Chemical | #7: Chemical | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.64 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 17% Jeffamine ED-2001 pH 7.0, 0.1 M imidazole, pH 6.2 PH range: 6.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 30, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 3.95→49.63 Å / Num. obs: 36307 / % possible obs: 97 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 3.95→4.09 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 4.5 / % possible all: 83.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 3.95→49.63 Å / Cor.coef. Fo:Fc: 0.864 / Cor.coef. Fo:Fc free: 0.839 / SU B: 222.871 / SU ML: 1.31 / Cross valid method: THROUGHOUT / ESU R Free: 1.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 84.988 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.95→49.63 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|