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- PDB-5y98: Crystal structure of native unbound peptidyl tRNA hydrolase from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5y98 | |||||||||
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Title | Crystal structure of native unbound peptidyl tRNA hydrolase from Acinetobacter baumannii at 1.36 A resolution | |||||||||
![]() | Peptidyl-tRNA hydrolase | |||||||||
![]() | HYDROLASE | |||||||||
Function / homology | ![]() peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / translation / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Iqbal, N. / Singh, N. / Kaushik, S. / Singh, P.K. / Sharma, S. / Singh, T.P. | |||||||||
![]() | ![]() Title: Search of multiple hot spots on the surface of peptidyl-tRNA hydrolase: structural, binding and antibacterial studies. Authors: Kaushik, S. / Iqbal, N. / Singh, N. / Sikarwar, J.S. / Singh, P.K. / Sharma, P. / Kaur, P. / Sharma, S. / Owais, M. / 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 | ![]() | 99.8 KB | Display | ![]() |
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PDB format | ![]() | 74.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440 KB | Display | ![]() |
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Full document | ![]() | 442.8 KB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 17.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5y9aC ![]() 3wh4 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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Unit cell |
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Components
#1: Protein | Mass: 21250.232 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81 Gene: pth, F911_03144, HMPREF0010_01329 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.53 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 50mM HEPES, PEG 400, PEG 1500, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 23, 2013 / Details: Mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.36→25.32 Å / Num. obs: 37477 / % possible obs: 99.9 % / Redundancy: 4.2 % / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 1.36→1.395 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3WH4 ![]() 3wh4 Resolution: 1.36→25.32 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.354 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.044 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.678 Å2
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Refinement step | Cycle: 1 / Resolution: 1.36→25.32 Å
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Refine LS restraints |
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