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Yorodumi- PDB-4yly: Crystal structure of peptidyl-tRNA hydrolase from a Gram-positive... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yly | |||||||||
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Title | Crystal structure of peptidyl-tRNA hydrolase from a Gram-positive bacterium, staphylococcus aureus at 2.25 angstrom resolution | |||||||||
Components | Peptidyl-tRNA hydrolaseAlternative ribosome-rescue factor B | |||||||||
Keywords | HYDROLASE / Gram-positive | |||||||||
Function / homology | Function and homology information peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / translation / cytoplasm Similarity search - Function | |||||||||
Biological species | Staphylococcus aureus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | |||||||||
Authors | Zhang, F. / Song, Y. / Li, X. / Teng, M.K. | |||||||||
Funding support | China, 2items
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Citation | Journal: Acta Biochim.Biophys.Sin. / Year: 2015 Title: Crystal structure of Staphylococcus aureus peptidyl-tRNA hydrolase at a 2.25 angstrom resolution. Authors: Zhang, F. / Song, Y. / Niu, L. / Teng, M. / Li, X. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yly.cif.gz | 91.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yly.ent.gz | 68.8 KB | Display | PDB format |
PDBx/mmJSON format | 4yly.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yl/4yly ftp://data.pdbj.org/pub/pdb/validation_reports/yl/4yly | HTTPS FTP |
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-Related structure data
Related structure data | 1rynS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22803.211 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: pth / Production host: Escherichia coli (E. coli) / References: UniProt: Q6YP15, peptidyl-tRNA hydrolase #2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.84 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 7.5 Details: 25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 21922 / % possible obs: 99.6 % / Redundancy: 4.3 % / Net I/σ(I): 15.27 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RYN Resolution: 2.25→34.07 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.163 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.312 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.562 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→34.07 Å
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Refine LS restraints |
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