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Yorodumi- PDB-2o45: Structure of the 23S rRNA of the large ribosomal subunit from Dei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2o45 | ||||||
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Title | Structure of the 23S rRNA of the large ribosomal subunit from Deinococcus Radiodurans in complex with the macrolide RU-69874 | ||||||
Components | 23S rRNA | ||||||
Keywords | RNA / Ribosome / macrolides / tunnel | ||||||
Function / homology | Chem-RU6 / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) Function and homology information | ||||||
Biological species | Deinococcus radiodurans (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å | ||||||
Authors | Baram, D. / Pyetan, E. / Auerbach-Nevo, T. / Yonath, A. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Chemical Parameters Influencing Fine Tuning in the Binding of Macrolide Antibiotics to the Ribosomal Tunnel Authors: Baram, D. / Pyetan, E. / Auerbach-Nevo, T. / Yonath, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2o45.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2o45.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 2o45.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2o45_validation.pdf.gz | 498.2 KB | Display | wwPDB validaton report |
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Full document | 2o45_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 2o45_validation.xml.gz | 118.5 KB | Display | |
Data in CIF | 2o45_validation.cif.gz | 183.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o4/2o45 ftp://data.pdbj.org/pub/pdb/validation_reports/o4/2o45 | HTTPS FTP |
-Related structure data
Related structure data | 1nkwS S: Starting model for refinement |
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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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Details | The large ribosomal subunit of Deinococcus radiodurans and Ru-69874 |
-Components
#1: RNA chain | Mass: 933405.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) |
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#2: Chemical | ChemComp-RU6 / ( |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 6.54 Å3/Da / Density % sol: 81.18 % |
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Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction |
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Diffraction source |
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Detector | Detector: CCD | ||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength | Relative weight: 1 | ||||||||||||
Reflection | Resolution: 3.6→30 Å / Num. obs: 226136 / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Rmerge(I) obs: 0.177 |
-Processing
Software | Name: CNS / Version: 1.1 / Classification: refinement | ||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry - 1nkw Resolution: 3.6→8 Å / σ(F): 1.5 / σ(I): 2 /
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Refinement step | Cycle: LAST / Resolution: 3.6→8 Å
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