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Yorodumi- PDB-4jx9: Crystal structure of the complex of peptidyl t-RNA hydrolase from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jx9 | ||||||
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Title | Crystal structure of the complex of peptidyl t-RNA hydrolase from Acinetobacter baumannii with uridine at 1.4A resolution | ||||||
Components | Peptidyl-tRNA hydrolaseAlternative ribosome-rescue factor B | ||||||
Keywords | HYDROLASE / Protein synthesis / complex | ||||||
Function / homology | Function and homology information peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / translation / cytoplasm Similarity search - Function | ||||||
Biological species | Acinetobacter baumannii ATCC 19606 = CIP 70.34 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Kaushik, S. / Singh, N. / Yamini, S. / Singh, A. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: The Mode of Inhibitor Binding to Peptidyl-tRNA Hydrolase: Binding Studies and Structure Determination of Unbound and Bound Peptidyl-tRNA Hydrolase from Acinetobacter baumannii Authors: Kaushik, S. / Singh, N. / Yamini, S. / Singh, A. / Sinha, M. / Arora, A. / Kaur, P. / Sharma, S. / 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 | 4jx9.cif.gz | 55.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jx9.ent.gz | 38.4 KB | Display | PDB format |
PDBx/mmJSON format | 4jx9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jx/4jx9 ftp://data.pdbj.org/pub/pdb/validation_reports/jx/4jx9 | HTTPS FTP |
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-Related structure data
Related structure data | 4fopC 4fotC 4hoyC 4ikoSC 4jwkC 4jy7C 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: 20967.957 Da / Num. of mol.: 1 / Fragment: Peptidyl-tRNA hydrolase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii ATCC 19606 = CIP 70.34 (bacteria) Gene: pth, HMPREF0010_01329 / Production host: Escherichia coli (E. coli) / References: UniProt: D0C9L6, peptidyl-tRNA hydrolase |
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#2: Chemical | ChemComp-URI / |
#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: 2.02 Å3/Da / Density % sol: 39.01 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M HEPES, 25% PEG400, 30% PEG1500, pH 6.5, 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 20, 2012 |
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: 1.4→28.04 Å / Num. all: 32452 / Num. obs: 32452 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.4→1.43 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IKO Resolution: 1.4→28.04 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.945 / SU B: 0.944 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.071 / ESU R Free: 0.068 / 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: 12.554 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→28.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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