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- PDB-5z1h: Crystal structure of the bacterial ribosomal decoding site in com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5z1h | ||||||||||||||||||||||||||||
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Title | Crystal structure of the bacterial ribosomal decoding site in complex with 6'-fluoro sisomicin | ||||||||||||||||||||||||||||
![]() | RNA (5'-R(*![]() RNA / rRNA / aminoglycoside | Function / homology | Chem-FSJ / RNA / RNA (> 10) | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() Kanazawa, H. / Hanessian, S. / Kondo, J. | Funding support | | ![]()
![]() ![]() Title: Structure-Based Design of a Eukaryote-Selective Antiprotozoal Fluorinated Aminoglycoside. Authors: Kanazawa, H. / Saavedra, O.M. / Maianti, J.P. / Young, S.A. / Izquierdo, L. / Smith, T.K. / Hanessian, S. / Kondo, J. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 37.4 KB | Display | ![]() |
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PDB format | ![]() | 24.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 762.1 KB | Display | ![]() |
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Full document | ![]() | 763.7 KB | Display | |
Data in XML | ![]() | 5.2 KB | Display | |
Data in CIF | ![]() | 6.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 7370.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-FSJ / ( | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2-Methyl-2,4-pentanediol, LiCl, spermine tetrahydrochloride, sodium cacodylate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 14, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→42.8 Å / Num. obs: 5052 / % possible obs: 99.7 % / Redundancy: 3.54 % / Biso Wilson estimate: 39.59 Å2 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.084 / Χ2: 0.92 / Net I/σ(I): 8.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Resolution: 2.4→42.8 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.44
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 241.24 Å2 / Biso mean: 41.16 Å2 / Biso min: 14.91 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→42.8 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4
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