+Open data
-Basic information
Entry | Database: PDB / ID: 4v7l | |||||||||
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Title | The structures of viomycin bound to the 70S ribosome. | |||||||||
Components |
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Keywords | RIBOSOME/ANTIBIOTIC / Anti-tuberculosis antibiotic / 70S / ribosome / tRNA / mRNA / tuberactinomycin / viomycin / RIBOSOME-Antibiotic complex | |||||||||
Function / homology | Function and homology information large ribosomal subunit / regulation of translation / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation ...large ribosomal subunit / regulation of translation / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) Thermus thermophilus (bacteria) Streptomyces puniceus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å | |||||||||
Authors | Stanley, R.E. / Blaha, G. | |||||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2010 Title: The structures of the anti-tuberculosis antibiotics viomycin and capreomycin bound to the 70S ribosome. Authors: Stanley, R.E. / Blaha, G. / Grodzicki, R.L. / Strickler, M.D. / Steitz, T.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v7l.cif.gz | 7.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v7l.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v7l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/4v7l ftp://data.pdbj.org/pub/pdb/validation_reports/v7/4v7l | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-RNA chain , 7 types, 14 molecules AACAAVCVAWCWAXCXAYCYBADABBDB
#1: RNA chain | Mass: 489961.031 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: AP008226.1 #22: RNA chain | Mass: 9684.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: mRNA #23: RNA chain | Mass: 24060.287 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: A-site tRNA Gln / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: DH1 / Gene: EcDH1_R0066, glnV glnX, Pecwa_R0066 / Plasmid: pRS3 / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / References: GenBank: CP001637.1 #24: RNA chain | Mass: 24802.785 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: P-site tRNA fMet / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: DH1 / Gene: metY, Pecwa_R0068 / Plasmid: plppMet / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: GenBank: CP001790.1, GenBank: CP001637.1 #25: RNA chain | Mass: 24077.270 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: E-site tRNA Gln / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: DH1 / Gene: EcDH1_R0066, glnV glnX, Pecwa_R0066 / Plasmid: pRS3 / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / References: GenBank: CP001637.1 #27: RNA chain | Mass: 947895.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: AP008226.1 #28: RNA chain | Mass: 39494.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: AP008226.1 |
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-30S ribosomal protein ... , 20 types, 40 molecules ABCBACCCADCDAECEAFCFAGCGAHCHAICIAJCJAKCKALCLAMCMANCNAOCOAPCP...
#2: Protein | Mass: 29317.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80371 #3: Protein | Mass: 26751.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80372 #4: Protein | Mass: 24373.447 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80373 #5: Protein | Mass: 17583.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ5 #6: Protein | Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SLP8 #7: Protein | Mass: 18050.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P17291 #8: Protein | Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ2, UniProt: A0A0M9AFS9*PLUS #9: Protein | Mass: 14410.614 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80374 #10: Protein | Mass: 11954.968 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHN7 #11: Protein | Mass: 13737.868 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80376 #12: Protein | Mass: 14637.384 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHN3 #13: Protein | Mass: 14338.861 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80377 #14: Protein | Mass: 7158.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ1, UniProt: A0A0N0BLP2*PLUS #15: Protein | Mass: 10578.407 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SJ76 #16: Protein | Mass: 10409.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SJH3 #17: Protein | Mass: 12325.655 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP7, UniProt: A0A0N0BLS5*PLUS #18: Protein | Mass: 10258.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SLQ0 #19: Protein | Mass: 10605.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP2 #20: Protein | Mass: 11736.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80380 #21: Protein/peptide | Mass: 3350.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SIH3 |
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-Protein/peptide , 1 types, 2 molecules AZCZ
#26: Protein/peptide |
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+50S ribosomal protein ... , 30 types, 60 molecules BCDCBDDDBEDEBFDFBGDGBHDHBIDIBNDNBODOBPDPBQDQBRDRBSDSBTDTBUDU...
-Non-polymers , 2 types, 973 molecules
#59: Chemical | ChemComp-MG / #60: Chemical | ChemComp-ZN / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.29 Å3/Da / Density % sol: 62.56 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion / pH: 7.6 Details: 0.1-0.2 M Arginine-HCL, 0.1 M Tris pH 7.6, 2.5% Peg 20K, 7-12% MPD, 0.5 mM BME, vapor diffusion, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Kohzu HLD8-24 monochromator / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→50 Å / Num. obs: 1121164 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 80.997 Å2 / Rmerge(I) obs: 0.307 / Net I/σ(I): 3.86 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→50 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.807
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Displacement parameters | Biso max: 200 Å2 / Biso mean: 94.291 Å2 / Biso min: 16.65 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→50 Å
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