[English] 日本語
Yorodumi- PDB-1p9x: THE CRYSTAL STRUCTURE OF THE 50S LARGE RIBOSOMAL SUBUNIT FROM DEI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p9x | ||||||
---|---|---|---|---|---|---|---|
Title | THE CRYSTAL STRUCTURE OF THE 50S LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH TELITHROMYCIN KETOLIDE ANTIBIOTIC | ||||||
Components | 23S RIBOSOMAL RNA | ||||||
Keywords | RIBOSOME / RIBOSOMES / TRNA / KETOLIDE / MACROLIDE / ANTIBIOTIC / EXIT-TUNNEL / BLOCKAGE | ||||||
Function / homology | TELITHROMYCIN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) Function and homology information | ||||||
Biological species | Deinococcus radiodurans (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Berisio, R. / Harms, J. / Schluenzen, F. / Zarivach, R. / Hansen, H.A. / Fucini, P. / Yonath, A. | ||||||
Citation | Journal: J.Bacteriol. / Year: 2003 Title: Structural insight into the antibiotic action of telithromycin against resistant mutants Authors: Berisio, R. / Harms, J. / Schluenzen, F. / Zarivach, R. / Hansen, H.A. / Fucini, P. / Yonath, A. #1: Journal: Nature / Year: 2001 Title: Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Centre in Eubacteria Authors: Schlunzen, F. / Zarivach, R. / Harms, J. / Bashan, A. / Tocilj, A. / Albrecht, R. / Yonath, A. / Franceschi, F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1p9x.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1p9x.ent.gz | 1013.4 KB | Display | PDB format |
PDBx/mmJSON format | 1p9x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/1p9x ftp://data.pdbj.org/pub/pdb/validation_reports/p9/1p9x | HTTPS FTP |
---|
-Related structure data
Related structure data | 1nkwS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-Components
#1: RNA chain | Mass: 933405.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: GenBank: 6460405 |
---|---|
#2: Chemical | ChemComp-TEL / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 10 |
---|
-Sample preparation
Crystal | Density Matthews: 4 Å3/Da / Density % sol: 64 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 273 K / Method: evaporation / pH: 7 / Details: pH 7., EVAPORATION, temperature 273K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7.8 / Method: vapor diffusion / Details: Harms, J., (2001) Cell, 107, 679. | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| ||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 15, 2002 | ||||||||||||||||||
Radiation |
| ||||||||||||||||||
Radiation wavelength |
| ||||||||||||||||||
Reflection | Resolution: 3.4→20 Å / Num. obs: 273922 / % possible obs: 82.7 % / Observed criterion σ(I): -1 / Redundancy: 3.4 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.181 / Net I/σ(I): 3.4 | ||||||||||||||||||
Reflection shell | Resolution: 3.4→3.46 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 1.5 / % possible all: 70.1 | ||||||||||||||||||
Reflection | *PLUS Highest resolution: 3.4 Å / Lowest resolution: 20 Å / Redundancy: 3.4 % | ||||||||||||||||||
Reflection shell | *PLUS Highest resolution: 3.4 Å / % possible obs: 70.1 % / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.5 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NKW Resolution: 3.4→15 Å / Rfactor Rfree error: 0.003 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→15 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3.4 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.34 / Rfactor Rwork: 0.28 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |