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Yorodumi- PDB-5ike: Crystal structure of mutant-D97N of peptidyl-tRNA hydrolase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ike | ||||||
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Title | Crystal structure of mutant-D97N of peptidyl-tRNA hydrolase from Vibrio cholerae | ||||||
Components | Peptidyl-tRNA hydrolaseAlternative ribosome-rescue factor B | ||||||
Keywords | HYDROLASE / Peptidyl-tRNA hydrolase / D97N mutant / Vibrio cholerae | ||||||
Function / homology | Function and homology information peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / translation / cytoplasm Similarity search - Function | ||||||
Biological species | Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||
Authors | Shahid, S. / Kabra, A. / Pal, R.K. / Arora, A. | ||||||
Citation | Journal: RNA / Year: 2017 Title: Unraveling the stereochemical and dynamic aspects of the catalytic site of bacterial peptidyl-tRNA hydrolase. Authors: Kabra, A. / Shahid, S. / Pal, R.K. / Yadav, R. / Pulavarti, S.V. / Jain, A. / Tripathi, S. / Arora, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ike.cif.gz | 89.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ike.ent.gz | 67.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ike.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/5ike ftp://data.pdbj.org/pub/pdb/validation_reports/ik/5ike | HTTPS FTP |
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-Related structure data
Related structure data | 4z86C 4zxpSC 5b6jC 5imbC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 21775.182 Da / Num. of mol.: 2 / Mutation: D97N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria) Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: pth, VC_2184 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KQ21, peptidyl-tRNA hydrolase #2: Water | ChemComp-HOH / | Sequence details | TEV protease site was present cleaved in the purification process | |
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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: 2.29 Å3/Da / Density % sol: 46.35 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop Details: 100 mM Sodium citrate, 200 mM Ammonium acetate, 20% Polyethylene glycol 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 21, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→50 Å / Num. obs: 23401 / % possible obs: 97.3 % / Redundancy: 6.6 % / Net I/σ(I): 19.68 |
Reflection shell | Resolution: 2.1→2.14 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZXP Resolution: 2.09→35.79 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.882 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.206 / 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: 36.957 Å2
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Refinement step | Cycle: LAST / Resolution: 2.09→35.79 Å
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Refine LS restraints |
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