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Yorodumi- PDB-4lx9: Archaeal amino-terminal acetyltransferase (NAT) bound to acetyl c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lx9 | ||||||
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Title | Archaeal amino-terminal acetyltransferase (NAT) bound to acetyl coenzyme A | ||||||
Components | ARCHAEAL AMINO-TERMINAL ACETYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / amino-terminal acetyltransferase / GNAT fold / amino-terminal acetyltransferase (NAT) | ||||||
Function / homology | Function and homology information N-terminal methionine Nalpha-acetyltransferase NatE / N-terminal amino-acid Nalpha-acetyltransferase NatA / peptide-glutamate-alpha-N-acetyltransferase activity / NatA complex / peptide-serine-alpha-N-acetyltransferase activity / peptide alpha-N-acetyltransferase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Liszczak, G.P. / Marmorstein, R. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Implications for the evolution of eukaryotic amino-terminal acetyltransferase (NAT) enzymes from the structure of an archaeal ortholog. Authors: Liszczak, G. / Marmorstein, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lx9.cif.gz | 82.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lx9.ent.gz | 61.5 KB | Display | PDB format |
PDBx/mmJSON format | 4lx9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lx9_validation.pdf.gz | 737 KB | Display | wwPDB validaton report |
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Full document | 4lx9_full_validation.pdf.gz | 739.6 KB | Display | |
Data in XML | 4lx9_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 4lx9_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lx/4lx9 ftp://data.pdbj.org/pub/pdb/validation_reports/lx/4lx9 | HTTPS FTP |
-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
#1: Protein | Mass: 19473.561 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: SSO0209 / Production host: Escherichia coli (E. coli) References: UniProt: Q980R9, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups | ||
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#2: Chemical | ChemComp-ACO / | ||
#3: Chemical | #4: 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: 2.29 Å3/Da / Density % sol: 46.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 14% PEG 3350, 0.1 M zinc acetate, Protein: 7.5 mg/mL, 20 mM tris, 150 mM NaCl, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 1, 2013 |
Radiation | Monochromator: Rigaku Osmic VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→50 Å / Num. all: 37578 / Num. obs: 12433 / % possible obs: 98 % / Observed criterion σ(F): 1.9 / Observed criterion σ(I): 1.9 / Redundancy: 3 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 7.66 |
Reflection shell | Resolution: 1.98→2.05 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.9 / Num. unique all: 1223 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→21.049 Å / SU ML: 0.21 / σ(F): 1.33 / Phase error: 26.58 / 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: 1.98→21.049 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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