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Yorodumi- PDB-4jc4: Crystal structure of Peptidyl-tRNA hydrolase from Pseudomonas aer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jc4 | ||||||
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Title | Crystal structure of Peptidyl-tRNA hydrolase from Pseudomonas aeruginosa at 2.25 angstrom resolution | ||||||
Components | Peptidyl-tRNA hydrolaseAlternative ribosome-rescue factor B | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / translation / cytoplasm Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Singh, A. / Kumar, A. / Sinha, M. / Bhushan, A. / Kaur, P. / Sharma, S. / Arora, A. / Singh, T.P. | ||||||
Citation | Journal: Biochem.J. / Year: 2014 Title: Structural and binding studies of peptidyl-tRNA hydrolase from Pseudomonas aeruginosa provide a platform for the structure-based inhibitor design against peptidyl-tRNA hydrolase Authors: Singh, A. / Kumar, A. / Gautam, L. / Sharma, P. / Sinha, M. / Bhushan, A. / Kaur, P. / Sharma, S. / Arora, A. / Singh, T.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jc4.cif.gz | 52.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jc4.ent.gz | 37.3 KB | Display | PDB format |
PDBx/mmJSON format | 4jc4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/4jc4 ftp://data.pdbj.org/pub/pdb/validation_reports/jc/4jc4 | HTTPS FTP |
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-Related structure data
Related structure data | 4fnoC 4qajC 4qbkC 4qd3C 4dhwS 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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Unit cell |
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-Components
#1: Protein | Mass: 20832.793 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA4672, pth / Plasmid: pETNH6 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q9HVC3, peptidyl-tRNA hydrolase |
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#2: Chemical | ChemComp-GOL / |
#3: 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: 2.11 Å3/Da / Density % sol: 41.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25% w/v PEG 4000, 5% isopropanol, 100mM HEPES buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 20, 2012 / Details: MIRROR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→54.22 Å / Num. all: 16115 / Num. obs: 16115 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.07 |
Reflection shell | Resolution: 2.25→2.33 Å / Mean I/σ(I) obs: 3.8 / % possible all: 88.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DHW Resolution: 2.25→54.22 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.359 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. THE FRIEDEL PAIRS WERE USED IN PHASING.
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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: 30.55 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→54.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.308 Å / Total num. of bins used: 20
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