+Open data
-Basic information
Entry | Database: PDB / ID: 4x5k | ||||||
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Title | Human NAA50 complex with coenzyme A and an acetylated peptide | ||||||
Components |
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Keywords | Transferase/Peptide / N-acetyl transferase / GCN-5. cotranslation modification / Transferase-Peptide complex | ||||||
Function / homology | Function and homology information : / 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 / mitotic sister chromatid cohesion / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups ...: / 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 / mitotic sister chromatid cohesion / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / nucleolus / extracellular exosome / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.494 Å | ||||||
Authors | Reddi, R. / Addlagatta, A. | ||||||
Citation | Journal: To Be Published Title: Human NAA50 with coenzymeA and a peptide Authors: Reddi, R. / Addlagatta, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x5k.cif.gz | 47.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x5k.ent.gz | 31.5 KB | Display | PDB format |
PDBx/mmJSON format | 4x5k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4x5k_validation.pdf.gz | 784 KB | Display | wwPDB validaton report |
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Full document | 4x5k_full_validation.pdf.gz | 785.8 KB | Display | |
Data in XML | 4x5k_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 4x5k_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x5/4x5k ftp://data.pdbj.org/pub/pdb/validation_reports/x5/4x5k | HTTPS FTP |
-Related structure data
Related structure data | 2ob0S S: Starting model for refinement |
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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: 19427.373 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: A549 / Gene: NAA50, MAK3, NAT13, NAT5 / Plasmid: pET15b / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: Q9GZZ1, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
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#2: Protein/peptide | Mass: 464.600 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-COA / |
#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: 2.02 Å3/Da / Density % sol: 39 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium formate, 20% PEG 3350 |
-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 RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 20, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→30.49 Å / Num. obs: 5836 / % possible obs: 91.2 % / Redundancy: 2.3 % / Net I/σ(I): 11.27 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OB0 Resolution: 2.494→28.524 Å / SU ML: 0.38 / σ(F): 1.35 / Phase error: 33.54 / 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: final / Resolution: 2.494→28.524 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2
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