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Yorodumi- PDB-1jzx: Structural Basis for the Interaction of Antibiotics with the Pept... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jzx | ||||||
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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 / Clindamycin / Peptidyl transferase center | ||||||
Function / homology | Function and homology information large ribosomal subunit / cytosolic large ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / metal ion binding Similarity search - Function | ||||||
Biological species | Deinococcus radiodurans (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.1 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 | 1jzx.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1jzx.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 1jzx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jzx_validation.pdf.gz | 481.2 KB | Display | wwPDB validaton report |
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Full document | 1jzx_full_validation.pdf.gz | 654.6 KB | Display | |
Data in XML | 1jzx_validation.xml.gz | 51 KB | Display | |
Data in CIF | 1jzx_validation.cif.gz | 89.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jz/1jzx ftp://data.pdbj.org/pub/pdb/validation_reports/jz/1jzx | HTTPS FTP |
-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-CLY / |
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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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Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 1, 2001 |
Radiation | Monochromator: Si111 or Si311 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→35 Å / Num. all: 400661 / Num. obs: 400661 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 3.1→3.21 Å / % possible all: 82.2 |
Reflection | *PLUS Lowest resolution: 35 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.118 |
Reflection shell | *PLUS % possible obs: 82.2 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 3.1→35 Å / σ(F): 0 Details: The coordinates of four chains of the 50s subunit and clindamycin were deposited. The number of non-hydrogen atoms used in refinement is more than specified in REMARK 3: 26069 protein atoms, ...Details: The coordinates of four chains of the 50s subunit and clindamycin 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 103 heterogen atoms were used in refinement.
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Refinement step | Cycle: LAST / Resolution: 3.1→35 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS/REFMAC / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3.1 Å / Lowest resolution: 35 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.268 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |