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Yorodumi- PDB-6jj1: Crystal structure of peptidyl-tRNA hydrolase from Acinetobacter b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jj1 | ||||||
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Title | Crystal structure of peptidyl-tRNA hydrolase from Acinetobacter baumannii at 0.97 A resolution with disordered five N-terminal residues | ||||||
Components | Peptidyl-tRNA hydrolaseAlternative ribosome-rescue factor B | ||||||
Keywords | HYDROLASE | ||||||
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: 0.97 Å | ||||||
Authors | Iqbal, N. / Sharma, P. / Chaudhary, A. / Sharma, S. / Singh, T.P. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of peptidyl-tRNA hydrolase from Acinetobacter baumannii at 0.97 A resolution with disordered five N-terminal residues Authors: Iqbal, N. / Sharma, P. / Chaudhary, A. / 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 | 6jj1.cif.gz | 133.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jj1.ent.gz | 103.7 KB | Display | PDB format |
PDBx/mmJSON format | 6jj1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jj/6jj1 ftp://data.pdbj.org/pub/pdb/validation_reports/jj/6jj1 | HTTPS FTP |
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-Related structure data
Related structure data | 5y9aS 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 (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) (bacteria) Strain: ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81 Gene: pth, HMPREF0010_01329 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: D0C9L6, peptidyl-tRNA hydrolase | ||||
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#2: Chemical | #3: Chemical | ChemComp-EDO / | #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: 2.01 Å3/Da / Density % sol: 38.87 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 12% PEG 1500, 0.1M HEPES, pH 7.5, 20% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97199 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97199 Å / Relative weight: 1 |
Reflection | Resolution: 0.97→38.08 Å / Num. obs: 94081 / % possible obs: 92 % / Redundancy: 8.3 % / Rpim(I) all: 0.028 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 0.97→1 Å / Num. unique obs: 3426 / Rpim(I) all: 0.629 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5Y9A Resolution: 0.97→38.08 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.578 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.02 / ESU R Free: 0.023 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 14.612 Å2
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Refinement step | Cycle: 1 / Resolution: 0.97→38.08 Å
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Refine LS restraints |
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