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Yorodumi- PDB-2g5k: Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decod... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2g5k | ||||||||||||||||||
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Title | Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site complexed with Apramycin | ||||||||||||||||||
Components | 5'-R(*Keywords | RNA / aminoglycoside / antibiotics / apramycin / ribosome / decoding site / Homo sapiens / cytoplasm | Function / homology | APRAMYCIN / COBALT HEXAMMINE(III) / RNA / RNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | Authors | Kondo, J. / Francois, B. / Urzhumtsev, A. / Westhof, E. | Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2006 | Title: Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site Complexed with Apramycin Authors: Kondo, J. / Francois, B. / Urzhumtsev, A. / Westhof, E. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g5k.cif.gz | 39.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g5k.ent.gz | 27 KB | Display | PDB format |
PDBx/mmJSON format | 2g5k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/2g5k ftp://data.pdbj.org/pub/pdb/validation_reports/g5/2g5k | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: RNA chain | Mass: 7355.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.51 Å3/Da / Density % sol: 50.93 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 50mM sodium cacodylate, 10mM hexammine cobalt chloride, 150mM potassium chloride, 1%(v/v) 2-methyl-2,4-pentanediol, 5%(v/v) glycerol, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 300K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 18, 2003 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→27.85 Å / Num. obs: 3533 / % possible obs: 100 % / Redundancy: 5.59 % / Rmerge(I) obs: 0.056 / Χ2: 0.97 / Net I/σ(I): 16.8 / Scaling rejects: 151 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | % possible obs: 100 %
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→10 Å / FOM work R set: 0.722 / σ(F): 0 Stereochemistry target values: G. Parkinson, J. Vojtechovsky, L. Clowney, A.T. Brunger, H.M. Berman, New Parameters for the Refinement of Nucleic Acid Containing Structures, Acta Cryst. D, 52, 57-64 (1996).
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Solvent computation | Bsol: 75.808 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 93.873 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→10 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Xplor file |
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