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Yorodumi- PDB-3td0: Crystal structure of the bacterial A1408G-mutant and the protozoa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3td0 | ||||||||||||||||||
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Title | Crystal structure of the bacterial A1408G-mutant and the protozoa cytoplasmic ribosomal decoding site | ||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / Decoding / ribosome | Function / homology | RNA / RNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å | Authors | Kondo, J. | Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2012 | Title: A structural basis for the antibiotic resistance conferred by an A1408G mutation in 16S rRNA and for the antiprotozoal activity of aminoglycosides Authors: Kondo, J. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3td0.cif.gz | 40.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3td0.ent.gz | 28.1 KB | Display | PDB format |
PDBx/mmJSON format | 3td0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/td/3td0 ftp://data.pdbj.org/pub/pdb/validation_reports/td/3td0 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 7450.304 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic RNA #2: Chemical | ChemComp-MG / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Sodium Cacodylate, Spermine tetrahydrochloride, Magnesium chloride, 2-methyl-2,4-pentanediol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.6→35.7 Å / Num. obs: 16037 / % possible obs: 99.4 % / Redundancy: 7 % / Rmerge(I) obs: 0.049 | ||||||||||||||||||
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.235 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.6→35.7 Å
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Refinement step | Cycle: LAST / Resolution: 1.6→35.7 Å
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Refine LS restraints |
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