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Yorodumi- PDB-4jy7: Crystal structure of Acinetobacter baumannii Peptidyl-tRNA Hydrolase -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jy7 | ||||||
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Title | Crystal structure of Acinetobacter baumannii Peptidyl-tRNA Hydrolase | ||||||
Components | Peptidyl-tRNA hydrolaseAlternative ribosome-rescue factor B | ||||||
Keywords | HYDROLASE / Peptidyl-tRNA hydrolase / enzyme / Molecular Conformation / Inhibition | ||||||
Function / homology | Function and homology information peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / translation / cytoplasm Similarity search - Function | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Yamini, S. / Kaushik, S. / 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 | 4jy7.cif.gz | 56.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jy7.ent.gz | 40.4 KB | Display | PDB format |
PDBx/mmJSON format | 4jy7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/4jy7 ftp://data.pdbj.org/pub/pdb/validation_reports/jy/4jy7 | HTTPS FTP |
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-Related structure data
Related structure data | 4fopC 4fotC 4hoyC 4ikoC 4jwkC 4jx9C 2pthS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 20967.957 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: ATCC19606 / Gene: HMPREF0010_01329, pth / Production host: Escherichia coli (E. coli) / Strain (production host): bl21 / References: UniProt: D0C9L6, peptidyl-tRNA hydrolase |
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-Non-polymers , 5 types, 208 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ACT / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 HEPES buffer, 25% PEG 10000, 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: May 5, 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: 1.9→58.28 Å / Num. all: 18051 / Num. obs: 18051 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.9→2 Å / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 4.2 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PTH Resolution: 1.9→58.2 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.117 / 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: 22.552 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→58.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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