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Yorodumi- PDB-4qt4: Crystal structure of Peptidyl-tRNA hydrolase from a Gram-positive... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qt4 | |||||||||
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Title | Crystal structure of Peptidyl-tRNA hydrolase from a Gram-positive bacterium, Streptococcus pyogenes at 2.19 Angstrom resolution shows the Closed Structure of the Substrate Binding Cleft | |||||||||
Components | Peptidyl-tRNA hydrolaseAlternative ribosome-rescue factor B | |||||||||
Keywords | HYDROLASE / Pth / peptidyl-tRNA | |||||||||
Function / homology | Function and homology information peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / translation / cytoplasm Similarity search - Function | |||||||||
Biological species | Streptococcus pyogenes NZ131 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å | |||||||||
Authors | Singh, A. / Gautam, L. / Sinha, M. / Bhushan, A. / Kaur, P. / Sharma, S. / Singh, T.P. | |||||||||
Citation | Journal: FEBS Open Bio / Year: 2014 Title: Crystal structure of peptidyl-tRNA hydrolase from a Gram-positive bacterium, Streptococcus pyogenes at 2.19 angstrom resolution shows the closed structure of the substrate-binding cleft. Authors: Singh, A. / Gautam, L. / Sinha, M. / Bhushan, A. / 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 | 4qt4.cif.gz | 88.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qt4.ent.gz | 68 KB | Display | PDB format |
PDBx/mmJSON format | 4qt4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qt/4qt4 ftp://data.pdbj.org/pub/pdb/validation_reports/qt/4qt4 | HTTPS FTP |
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-Related structure data
Related structure data | 4jc4S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21224.510 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes NZ131 (bacteria) Strain: NZ131 / Gene: pth, Spy49_0005 / Plasmid: pET28a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: B5XIP6, peptidyl-tRNA hydrolase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.35 % |
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Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP |
-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: Nov 26, 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: 2.19→35.37 Å / Num. obs: 17325 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.062 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 2.19→2.23 Å / Mean I/σ(I) obs: 7.6 / Rsym value: 0.157 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JC4 Resolution: 2.19→35.37 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.371 / ESU R Free: 0.199 / 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: 17.196 Å2
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Refinement step | Cycle: LAST / Resolution: 2.19→35.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.193→2.25 Å / Total num. of bins used: 20
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