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Yorodumi- PDB-8wni: Crystal structure of H. pylori isoleucyl-tRNA synthetase (HpIleRS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8wni | ||||||
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Title | Crystal structure of H. pylori isoleucyl-tRNA synthetase (HpIleRS) in complex with Val | ||||||
Components | Isoleucine--tRNA ligase | ||||||
Keywords | LIGASE / isoleucyl-tRNA synthetase / Helicobacter pylori / HpIleRS / IleRS / aminoacylation | ||||||
Function / homology | Function and homology information isoleucine-tRNA ligase / isoleucine-tRNA ligase activity / isoleucyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / tRNA binding / zinc ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Guo, Y. / Li, S. / Zhang, T. | ||||||
Funding support | China, 1items
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Citation | Journal: Febs Lett. / Year: 2024 Title: Structural basis for substrate and antibiotic recognition by Helicobacter pylori isoleucyl-tRNA synthetase. Authors: Chen, X. / Guo, Y. / Shi, J. / Wang, Y. / Guo, X. / Wu, G. / Li, S. / Zhang, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wni.cif.gz | 399.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wni.ent.gz | 319.9 KB | Display | PDB format |
PDBx/mmJSON format | 8wni.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/8wni ftp://data.pdbj.org/pub/pdb/validation_reports/wn/8wni | HTTPS FTP |
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-Related structure data
Related structure data | 8wnfC 8wngC 8wnjC 8wo2C 8wo3C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 106320.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: ileS, C2840_07400 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2J9KLI1, isoleucine-tRNA ligase |
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-Non-polymers , 6 types, 883 molecules
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | ChemComp-VAL / | ||||||
#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-ACT / | #6: Chemical | ChemComp-TRS / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.59 Å3/Da / Density % sol: 52.57 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.1 M Hepes, pH 7.5, 2% (v/v) Tacsimate, and 20% (w/v) polyethylene glycol (PEG) 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9785 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 19, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→51.19 Å / Num. obs: 74517 / % possible obs: 95.8 % / Redundancy: 3.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.075 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.95→2.02 Å / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 2.37 / Num. unique obs: 6902 / CC1/2: 0.828 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→51.19 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 20.73 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→51.19 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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