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Yorodumi- PDB-6ag4: Crystal structure of Ard1 N-terminal acetyltransferase H88A/E127A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ag4 | ||||||
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Title | Crystal structure of Ard1 N-terminal acetyltransferase H88A/E127A mutant from Sulfolobus solfataricus | ||||||
Components | N-alpha-acetyltransferase | ||||||
Keywords | TRANSFERASE / Acetyltransferase | ||||||
Function / homology | Function and homology information N-terminal amino-acid Nalpha-acetyltransferase NatA / N-terminal methionine Nalpha-acetyltransferase NatE / NatA complex / peptide alpha-N-acetyltransferase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Sulfolobus solfataricus P2 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.256 Å | ||||||
Authors | Chang, Y.Y. / Hsu, C.H. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Chem.Commun.(Camb.) / Year: 2020 Title: Adaptation of thermophilic acetyltransferase to a water-mediated catalytic mechanism. Authors: Chang, Y.Y. / Hagawa, S. / Hsu, C.H. #1: Journal: SCI REP / Year: 2015 Title: Structural Basis for Substrate-specific Acetylation of Nalpha-acetyltransferase Ard1 from Sulfolobus solfataricus Authors: Chang, Y.Y. / Hsu, C.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ag4.cif.gz | 84.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ag4.ent.gz | 60.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ag4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/6ag4 ftp://data.pdbj.org/pub/pdb/validation_reports/ag/6ag4 | HTTPS FTP |
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-Related structure data
Related structure data | 6ag5C 4r3kS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 20177.338 Da / Num. of mol.: 1 / Mutation: H88A, E127A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus P2 (archaea) / Strain: P2 / Gene: SsArd1 / Production host: Escherichia coli (E. coli) References: UniProt: Q980R9, N-terminal amino-acid Nalpha-acetyltransferase NatA, N-terminal methionine Nalpha-acetyltransferase NatE |
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#2: Chemical | ChemComp-ACO / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-CA / |
#5: 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: 2.08 Å3/Da / Density % sol: 40.78 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 0.75M ammonium sulfate, 0.1M sodium acetate trihydrate, pH 4.2, 0.1M lithium sulfate |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 8, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→30 Å / Num. obs: 8167 / % possible obs: 98.1 % / Redundancy: 4.9 % / Net I/σ(I): 24.6 |
Reflection shell | Resolution: 2.25→2.36 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4R3K Resolution: 2.256→27.967 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.64 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.256→27.967 Å
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Refine LS restraints |
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LS refinement shell |
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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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