+Open data
-Basic information
Entry | Database: PDB / ID: 4hnx | ||||||
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Title | The NatA Acetyltransferase Complex Bound To ppGpp | ||||||
Components |
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Keywords | TRANSFERASE / GNAT/TPR / N-terminal acetyltransferase / ppGpp | ||||||
Function / homology | Function and homology information N-terminal protein amino acid propionylation / N-terminal amino-acid Nalpha-acetyltransferase NatA / peptide-glutamate-alpha-N-acetyltransferase activity / NatA complex / peptide-serine-alpha-N-acetyltransferase activity / N-terminal protein amino acid acetylation / ribosome binding / mitochondrion / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.339 Å | ||||||
Authors | Neubauer, J.L. / Immormino, R.M. / Dollins, D.E. / Endo-Streeter, S.T. / Pemble IV, C.W. / York, J.D. | ||||||
Citation | Journal: To be Published Title: The Protein Complex NatA Binds Inositol Hexakisphosphate and Exhibits Conformational Flexibility Authors: Neubauer, J.L. / Pham, T. / Immormino, R.M. / Dollins, D.E. / Endo-Streeter, S.T. / Li, S. / Pemble IV, C.W. / York, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hnx.cif.gz | 381.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hnx.ent.gz | 309.1 KB | Display | PDB format |
PDBx/mmJSON format | 4hnx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hn/4hnx ftp://data.pdbj.org/pub/pdb/validation_reports/hn/4hnx | HTTPS FTP |
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-Related 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: 100134.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: NAT1, AAA1, YDL040C, D2720 / Plasmid: 22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P12945 |
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#2: Protein | Mass: 28821.457 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: ARD1, YHR013C / Plasmid: 30b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P07347, EC: 2.3.1.88 |
#3: Chemical | ChemComp-G4P / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.78 Å3/Da / Density % sol: 67.45 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: 1-6% Jeffamine ED-2001, pH 7.0; 0.1 M K-HEPES pH 6.3, 0.1-2% PEG200, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97937, 1.0 | |||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 9, 2010 / Details: SAGITALLY FOCUSED Si(111) | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.339→50 Å / Num. obs: 82175 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rsym value: 0.063 | |||||||||
Reflection shell | Resolution: 2.34→2.38 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 2 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.339→40.144 Å / SU ML: 0.37 / σ(F): 0 / Phase error: 22.01 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.237 Å2 / ksol: 0.352 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.339→40.144 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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