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Yorodumi- PDB-5icv: Crystal structure of human NatF (hNaa60) bound to a bisubstrate a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5icv | ||||||||||||||||||
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Title | Crystal structure of human NatF (hNaa60) bound to a bisubstrate analogue | ||||||||||||||||||
Components |
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Keywords | TRANSFERASE / Acetylation / GNAT / NAT | ||||||||||||||||||
Function / homology | Function and homology information N-terminal methionine Nalpha-acetyltransferase NatF / N-terminal peptidyl-methionine acetylation / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / histone H4 acetyltransferase activity / histone acetyltransferase activity / histone acetyltransferase / chromosome segregation / nucleosome assembly / cell population proliferation ...N-terminal methionine Nalpha-acetyltransferase NatF / N-terminal peptidyl-methionine acetylation / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / histone H4 acetyltransferase activity / histone acetyltransferase activity / histone acetyltransferase / chromosome segregation / nucleosome assembly / cell population proliferation / Golgi membrane / protein homodimerization activity Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å | ||||||||||||||||||
Authors | Stove, S.I. / Magin, R.S. / Marmorstein, R. / Arnesen, T. | ||||||||||||||||||
Funding support | Norway, United States, 5items
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Citation | Journal: Structure / Year: 2016 Title: Crystal Structure of the Golgi-Associated Human N alpha-Acetyltransferase 60 Reveals the Molecular Determinants for Substrate-Specific Acetylation. Authors: Stve, S.I. / Magin, R.S. / Foyn, H. / Haug, B.E. / Marmorstein, R. / Arnesen, T. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5icv.cif.gz | 98.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5icv.ent.gz | 74.5 KB | Display | PDB format |
PDBx/mmJSON format | 5icv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ic/5icv ftp://data.pdbj.org/pub/pdb/validation_reports/ic/5icv | HTTPS FTP |
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-Related structure data
Related structure data | 5icwC 4lx9S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20539.344 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NAA60, HAT4, NAT15, UNQ2771/PRO7155 / Production host: Escherichia coli (E. coli) References: UniProt: Q9H7X0, histone acetyltransferase, EC: 2.3.1.88 #2: Protein/peptide | Mass: 448.599 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.09 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 4% Tascimate pH 4.0 and 12% PEG 3500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→40.564 Å / Num. obs: 51410 / % possible obs: 99.8 % / Redundancy: 13 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 18.62 |
Reflection shell | Resolution: 1.53→1.568 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.635 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LX9 Resolution: 1.53→40.564 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.7
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.53→40.564 Å
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Refine LS restraints |
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LS refinement shell |
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