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- PDB-4p20: Crystal structures of the bacterial ribosomal decoding site compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4p20 | |||||||||||||||||||||||
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Title | Crystal structures of the bacterial ribosomal decoding site complexed with amikacin | |||||||||||||||||||||||
![]() | 5'-R(*![]() RNA/ANTIBIOTIC / AMINOGLYCOSIDE / HABA GROUP / RIBOSOMAL DECODING SITE / X-RAY ANALYSIS / RNA / AMIKACIN / RNA-ANTIBIOTIC complex | Function / homology | Chem-AKN / RNA / RNA (> 10) | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() ![]() Kondo, J. / Francois, B. / Russell, R.J.M. / Murray, J.B. / Westhof, E. | ![]() ![]() Title: Crystal structure of the bacterial ribosomal decoding site complexed with amikacin containing the gamma-amino-alpha-hydroxybutyryl (haba) group. Authors: Kondo, J. / Francois, B. / Russell, R.J. / Murray, J.B. / Westhof, E. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 38.8 KB | Display | ![]() |
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PDB format | ![]() | 26 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1006.7 KB | Display | ![]() |
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Full document | ![]() | 1011.4 KB | Display | |
Data in XML | ![]() | 5.7 KB | Display | |
Data in CIF | ![]() | 7.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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 / Source: (synth.) synthetic construct (others) #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.51 % |
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Crystal grow | Temperature: 310 K / Method: vapor diffusion / pH: 6.4 / Details: MPF, Na Cacodylate, NaCl, KCl |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 26, 2004 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9357 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→32.82 Å / Num. obs: 4398 / % possible obs: 100 % / Redundancy: 3.59 % / Rmerge(I) obs: 0.16 / Χ2: 0.96 / Net I/σ(I): 4.8 / Num. measured all: 15897 / Scaling rejects: 120 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Bsol: 64.5977 Å2 | ||||||||||||||||||||||||
Displacement parameters | Biso max: 120.73 Å2 / Biso mean: 45.5528 Å2 / Biso min: 10.2 Å2
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Refinement step | Cycle: final / Resolution: 2.7→10 Å
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Refine LS restraints |
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Xplor file |
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