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- PDB-4jy7: Crystal structure of Acinetobacter baumannii Peptidyl-tRNA Hydrolase -
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Open data
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Basic information
Entry | Database: PDB / ID: 4jy7 | ||||||
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Title | Crystal structure of Acinetobacter baumannii Peptidyl-tRNA Hydrolase | ||||||
![]() | Peptidyl-tRNA hydrolase | ||||||
![]() | HYDROLASE / Peptidyl-tRNA hydrolase / enzyme / Molecular Conformation / Inhibition | ||||||
Function / homology | ![]() peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / translation / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yamini, S. / Kaushik, S. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.8 KB | Display | ![]() |
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PDB format | ![]() | 40.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.1 KB | Display | ![]() |
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Full document | ![]() | 466.6 KB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 17.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4fopC ![]() 4fotC ![]() 4hoyC ![]() 4ikoC ![]() 4jwkC ![]() 4jx9C ![]() 2pthS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 208 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ACT / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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