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Yorodumi- PDB-1j5a: STRUCTURAL BASIS FOR THE INTERACTION OF ANTIBIOTICS WITH THE PEPT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j5a | |||||||||
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Title | STRUCTURAL BASIS FOR THE INTERACTION OF ANTIBIOTICS WITH THE PEPTIDYL TRANSFERASE CENTER IN EUBACTERIA | |||||||||
Components |
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Keywords | RIBOSOME / 50S / 23S / 5S / ANTIBIOTICS / CLARITHROMYCIN / PEPTIDYL TRANSFERASE CENTER | |||||||||
Function / homology | Function and homology information large ribosomal subunit / cytosolic large ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / metal ion binding Similarity search - Function | |||||||||
Biological species | Deinococcus radiodurans (radioresistant) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.5 Å | |||||||||
Authors | Schluenzen, F. / Zarivach, R. / Harms, J. / Bashan, A. / Tocilj, A. / Albrecht, R. / Yonath, A. / Franceschi, F. | |||||||||
Citation | 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 | 1j5a.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1j5a.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 1j5a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j5/1j5a ftp://data.pdbj.org/pub/pdb/validation_reports/j5/1j5a | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-RNA chain , 1 types, 1 molecules A
#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: 15805042 |
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-RIBOSOMAL PROTEIN ... , 3 types, 3 molecules KLM
#2: Protein | Mass: 22308.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXK1 |
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#3: Protein | Mass: 15190.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXJ7 |
#4: Protein | Mass: 6810.017 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: P49228 |
-Non-polymers , 2 types, 3 molecules
#5: Chemical | ChemComp-CTY / |
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#6: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4 Å3/Da / Density % sol: 64 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: ethanol, dimethylhexanediol, MgCl2, KCl, Hepes, NH4Cl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.033 |
Detector | Type: SBC / Detector: CCD / Date: Jul 1, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. all: 260808 / Num. obs: 260808 / % possible obs: 85.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 3.5→3.63 Å / % possible all: 78.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 3.5→50 Å / σ(F): 0 Details: The coordinates of four chains of the 50s subunit and clarithromycin were deposited. The number of non-hydrogen atoms used in refinement is more than specified in REMARK 3: 26069 protein ...Details: The coordinates of four chains of the 50s subunit and clarithromycin were deposited. The number of non-hydrogen atoms used in refinement is more than specified in REMARK 3: 26069 protein atoms, 62115 nucleic acid atoms, and 123 heterogen atoms were used in refinement.
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Refinement step | Cycle: LAST / Resolution: 3.5→50 Å
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Refine LS restraints |
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