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- PDB-7brd: Crystal structure of Peptidyl-tRNA hydrolase from Klebsiella pneu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7brd | ||||||
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Title | Crystal structure of Peptidyl-tRNA hydrolase from Klebsiella pneumoniae | ||||||
![]() | Peptidyl-tRNA hydrolase | ||||||
![]() | HYDROLASE / tRNA-binding / Antibiotic target | ||||||
Function / homology | ![]() peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / translation / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Mundra, S. / Zohib, M. / Pal, R.K. / Biswal, B.K. / Arora, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and functional characterization of peptidyl-tRNA hydrolase from Klebsiella pneumoniae. Authors: Mundra, S. / Pal, R.K. / Tripathi, S. / Jain, A. / Arora, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 155.4 KB | Display | ![]() |
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PDB format | ![]() | 116.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 503.1 KB | Display | ![]() |
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Full document | ![]() | 508.8 KB | Display | |
Data in XML | ![]() | 20.5 KB | Display | |
Data in CIF | ![]() | 29.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2pthS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 21060.191 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: pth, BL124_00016980, EAO17_03025, F3P37_02700, SAMEA3538476_04832, SK89_03098 Production host: ![]() ![]() |
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-Non-polymers , 8 types, 327 molecules ![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PGE / | ||||||||||||
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#3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-ACT / #6: Chemical | ChemComp-CL / #7: Chemical | ChemComp-SO4 / #8: Chemical | ChemComp-BME / | #9: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.42 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M Ammonium Sulfate 0.1M Sodium cacodylate 30% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 2, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→31.97 Å / Num. obs: 31852 / % possible obs: 100 % / Redundancy: 10.6 % / Biso Wilson estimate: 22.06 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.049 / Rrim(I) all: 0.163 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.127 / Num. unique obs: 31899 / CC1/2: 0.827 / Rpim(I) all: 0.271 / Rrim(I) all: 0.89 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2PTH Resolution: 1.892→25.208 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.924 / SU B: 6.264 / SU ML: 0.095 / Cross valid method: FREE R-VALUE / ESU R: 0.147 / ESU R Free: 0.141 Details: Hydrogens have been added in their 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.807 Å2
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Refinement step | Cycle: LAST / Resolution: 1.892→25.208 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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