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Yorodumi- PDB-5zx8: Crystal structure of peptidyl-tRNA hydrolase from Thermus thermophilus -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zx8 | ||||||
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Title | Crystal structure of peptidyl-tRNA hydrolase from Thermus thermophilus | ||||||
Components | Peptidyl-tRNA hydrolaseAlternative ribosome-rescue factor B | ||||||
Keywords | HYDROLASE / peptidyl-tRNA hydrolase / Thermus thermophilus | ||||||
Function / homology | Function and homology information peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / translation / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus HB8 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å | ||||||
Authors | Matsumoto, A. / Uehara, U. / Shimizu, Y. / Ueda, T. / Uchiumi, T. / Ito, K. | ||||||
Citation | Journal: Proteins / Year: 2019 Title: High-resolution crystal structure of peptidyl-tRNA hydrolase from Thermus thermophilus. Authors: Matsumoto, A. / Uehara, Y. / Shimizu, Y. / Ueda, T. / Uchiumi, T. / Ito, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zx8.cif.gz | 94.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zx8.ent.gz | 70.5 KB | Display | PDB format |
PDBx/mmJSON format | 5zx8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/5zx8 ftp://data.pdbj.org/pub/pdb/validation_reports/zx/5zx8 | HTTPS FTP |
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-Related structure data
Related structure data | 1rybS 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: 20620.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: pth, TTHA1588 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SHZ2, peptidyl-tRNA hydrolase | ||||
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#2: Chemical | #3: Chemical | #4: 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: 1.82 Å3/Da / Density % sol: 32.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 100 mM phosphate-citrate buffer pH 4.2, 50%(v/v) 2-methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 16, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1→50 Å / Num. obs: 75984 / % possible obs: 92.6 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 57.2 |
Reflection shell | Resolution: 1→1.04 Å / Rmerge(I) obs: 0.46 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RYB Resolution: 1→23.45 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.543 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.022 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.198 Å2
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Refinement step | Cycle: 1 / Resolution: 1→23.45 Å
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Refine LS restraints |
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