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- PDB-3tfy: Naa50p amino-terminal acetyltransferase bound to substrate peptid... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3tfy | ||||||
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Title | Naa50p amino-terminal acetyltransferase bound to substrate peptide fragment and CoA | ||||||
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![]() | TRANSFERASE / GNAT Family / N(alpha)-acetyltransferase | ||||||
Function / homology | ![]() : / mitotic sister chromatid cohesion, centromeric / N-terminal methionine Nalpha-acetyltransferase NatE / NatA complex / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / histone H4 acetyltransferase activity / establishment of mitotic sister chromatid cohesion / FGFR2 alternative splicing / mitotic sister chromatid cohesion ...: / mitotic sister chromatid cohesion, centromeric / N-terminal methionine Nalpha-acetyltransferase NatE / NatA complex / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / histone H4 acetyltransferase activity / establishment of mitotic sister chromatid cohesion / FGFR2 alternative splicing / mitotic sister chromatid cohesion / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / RNA processing / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / mRNA splicing, via spliceosome / single-stranded RNA binding / ribonucleoprotein complex / synapse / nucleolus / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liszczak, G.P. / Marmorstein, R. | ||||||
![]() | ![]() Title: Structure of a Ternary Naa50p (NAT5/SAN) N-terminal Acetyltransferase Complex Reveals the Molecular Basis for Substrate-specific Acetylation. Authors: Liszczak, G. / Arnesen, T. / Marmorstein, R. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113.4 KB | Display | ![]() |
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PDB format | ![]() | 87.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2pswS S: Starting model for refinement |
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Similar structure data |
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Links
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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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Components
#1: Protein | Mass: 19427.373 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9GZZ1, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups #2: Protein/peptide | Mass: 1060.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / References: UniProt: P52597*PLUS #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.09 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 5 Details: well solution: 16% PEG 8000, 20% glycerol, 40mM potassium phosphate (monobasic), pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 10, 2010 / Details: Toroidal focusing mirror |
Radiation | Monochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1271 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→50 Å / Num. all: 17043 / Num. obs: 16856 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 12.9 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.75→2.8 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 682 / Rsym value: 40.9 / % possible all: 93.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2PSW (cofactor and solvent removed) Resolution: 2.75→33.659 Å / SU ML: 0.39 / σ(F): 0.19 / Phase error: 27.65 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.837 Å2 / ksol: 0.315 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.75→33.659 Å
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Refine LS restraints |
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LS refinement shell |
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