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Yorodumi- PDB-1ond: THE CRYSTAL STRUCTURE OF THE 50S LARGE RIBOSOMAL SUBUNIT FROM DEI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ond | ||||||
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Title | THE CRYSTAL STRUCTURE OF THE 50S LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH TROLEANDOMYCIN MACROLIDE ANTIBIOTIC | ||||||
Components |
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Keywords | RIBOSOME / RIBOSOMES / TRNA / MACROLIDE / ANTIBIOTIC / EXIT-TUNNEL L22 / BLOCKAGE | ||||||
Function / homology | Function and homology information large ribosomal subunit / cytosolic large ribosomal subunit / rRNA binding / structural constituent of ribosome / translation / metal ion binding Similarity search - Function | ||||||
Biological species | Deinococcus radiodurans (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Berisio, R. / Schluenzen, F. / Harms, J. / Bashan, A. / Auerbach, T. / Baram, D. / Yonath, A. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2003 Title: Structural insight into the role of the ribosomal tunnel in cellular regulation Authors: Berisio, R. / Schluenzen, F. / Harms, J. / Bashan, A. / Auerbach, T. / Baram, D. / 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ond.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1ond.ent.gz | 1004.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ond.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/1ond ftp://data.pdbj.org/pub/pdb/validation_reports/on/1ond | HTTPS FTP |
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-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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-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: Protein | Mass: 15190.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXJ7 |
#3: Protein | Mass: 6810.017 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: P49228 |
#4: Chemical | ChemComp-TAO / |
Compound details | THE ENTRY CONTAINS ONLY A PART OF THE CRYSTAL ASYMMETRIC |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 4 Å3/Da / Density % sol: 64 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Method: evaporation / Details: EVAPORATION | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7.8 / Method: vapor diffusionDetails: Harms, J.M., (2001) Cell (Cambridge,Mass.), 107, 679. | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 15, 2002 | |||||||||||||||
Radiation | Monochromator: SI111 OR SI311 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 3.4→20 Å / Num. all: 291247 / Num. obs: 291247 / % possible obs: 88.1 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 2.4 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 5.4 | |||||||||||||||
Reflection shell | Resolution: 3.4→3.46 Å / Redundancy: 2 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 1.4 / Num. unique all: 13839 / % possible all: 84.5 | |||||||||||||||
Reflection | *PLUS Highest resolution: 3.4 Å / Lowest resolution: 20 Å | |||||||||||||||
Reflection shell | *PLUS % possible obs: 84.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NKW Resolution: 3.4→8 Å / Rfactor Rfree error: 0.003 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER / Details: The protein chains contain CA only.
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.4→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.4→8 Å | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3.4 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.31 / Rfactor Rwork: 0.262 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.0073 |