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Yorodumi- PDB-4lwq: Crystal structure of native peptidyl t-RNA hydrolase from Acineto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lwq | ||||||
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Title | Crystal structure of native peptidyl t-RNA hydrolase from Acinetobacter baumannii at 1.38A resolution | ||||||
Components | Peptidyl-tRNA hydrolaseAlternative ribosome-rescue factor B | ||||||
Keywords | HYDROLASE / Protein synthesis | ||||||
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: 1.38 Å | ||||||
Authors | Kaushik, S. / Singh, N. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P. | ||||||
Citation | Journal: To be Published Title: Crystal structure of native peptidyl t-RNA hydrolase from Acinetobacter baumannii at 1.38A resolution Authors: Kaushik, S. / Singh, N. / Sinha, M. / 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 | 4lwq.cif.gz | 94.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lwq.ent.gz | 71.4 KB | Display | PDB format |
PDBx/mmJSON format | 4lwq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lw/4lwq ftp://data.pdbj.org/pub/pdb/validation_reports/lw/4lwq | HTTPS FTP |
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-Related structure data
Related structure data | 4jwkS S: Starting model for refinement |
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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: 21250.232 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: ATCC 19606 / Gene: pth / Production host: Escherichia coli (E. coli) / References: UniProt: D0C9L6, peptidyl-tRNA hydrolase | ||
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#2: Chemical | #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 Å3/Da / Density % sol: 38.55 % |
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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: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 23, 2013 / 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: 1.38→25.31 Å / Num. all: 34019 / Num. obs: 34019 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.38→1.4 Å / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JWK Resolution: 1.38→25.31 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.304 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.055 / ESU R Free: 0.048 / 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: 12.079 Å2
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Refinement step | Cycle: LAST / Resolution: 1.38→25.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.381→1.417 Å / Total num. of bins used: 20
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