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Yorodumi- PDB-4qaj: Crystal structure of Peptidyl-tRNA hydrolase from Pseudomonas aer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qaj | ||||||
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Title | Crystal structure of Peptidyl-tRNA hydrolase from Pseudomonas aeruginosa at 1.5 Angstrom resolution | ||||||
Components | Peptidyl-tRNA hydrolaseAlternative ribosome-rescue factor B | ||||||
Keywords | HYDROLASE / Pth | ||||||
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: 1.5 Å | ||||||
Authors | Singh, A. / Kumar, A. / Gautam, L. / 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 | 4qaj.cif.gz | 56 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qaj.ent.gz | 39.7 KB | Display | PDB format |
PDBx/mmJSON format | 4qaj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/4qaj ftp://data.pdbj.org/pub/pdb/validation_reports/qa/4qaj | HTTPS FTP |
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-Related structure data
Related structure data | 4fnoC 4jc4SC 4qbkC 4qd3C 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: PAO1 / Gene: PA4672, pth / Plasmid: pEt28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(De3) / References: UniProt: Q9HVC3, peptidyl-tRNA hydrolase |
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#2: 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: 2.21 Å3/Da / Density % sol: 44.39 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, 5% isoproponal, 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: Nov 2, 2013 / 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: 1.5→29.64 Å / Num. all: 31169 / Num. obs: 31169 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Net I/σ(I): 50.3 |
Reflection shell | Resolution: 1.5→1.53 Å / Mean I/σ(I) obs: 2 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JC4 Resolution: 1.5→29.64 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.077 / ESU R Free: 0.082 / 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: 24.75 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→29.64 Å
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