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Yorodumi- PDB-3pip: Crystal structure of the synergistic antibiotic pair lankamycin a... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 3pip | ||||||
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| Title | Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit | ||||||
Components |
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Keywords | RIBOSOME/ANTIBIOTIC / RIBOSOME / LARGE RIBOSOMAL SUBUNIT / 50S / RIBONUCLEOPROTEIN / RIBOSOMAL PROTEIN / RNA-BINDING / RRNA-BINDING / TRNA-BINDING / LANKAMYCIN / LANKACIDIN / MACROLIDE / RIBOSOME-ANTIBIOTIC complex | ||||||
| Function / homology | Function and homology informationlarge ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding ...large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / zinc ion binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
| Biological species | Deinococcus radiodurans R1 (radioresistant) Deinococcus radiodurans (radioresistant) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS REPLACEMENT / Resolution: 3.45 Å | ||||||
Authors | Belousoff, M.J. / Shapira, T. / Bashan, A. / Zimmerman, E. / Kinashi, H. / Rozenberg, H. / Yonath, A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011Title: Crystal structure of the synergistic antibiotic pair, lankamycin and lankacidin, in complex with the large ribosomal subunit. Authors: Belousoff, M.J. / Shapira, T. / Bashan, A. / Zimmerman, E. / Rozenberg, H. / Arakawa, K. / Kinashi, H. / Yonath, A. | ||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 3pip.cif.gz | 4.2 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb3pip.ent.gz | 3.5 MB | Display | PDB format |
| PDBx/mmJSON format | 3pip.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pi/3pip ftp://data.pdbj.org/pub/pdb/validation_reports/pi/3pip | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 3pioC ![]() 2zjrS S: Starting model for refinement C: citing same article ( |
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| Similar structure data |
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Links
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Assembly
| Deposited unit | ![]()
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| Unit cell |
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Components
-RNA chain , 2 types, 2 molecules XY
| #1: RNA chain | Mass: 933405.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Deinococcus radiodurans R1 (radioresistant)References: GenBank: AE000513.1 |
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| #2: RNA chain | Mass: 39605.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Deinococcus radiodurans R1 (radioresistant)References: GenBank: AE000513.1 |
+50S ribosomal protein ... , 28 types, 28 molecules ABCDEFGHIJKLMNOPQRSTUVWZ1234
-Non-polymers , 5 types, 84 molecules 








| #31: Chemical | ChemComp-LC2 / | ||||
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| #32: Chemical | ChemComp-LMA / | ||||
| #33: Chemical | ChemComp-MG / #34: Chemical | ChemComp-K / #35: Chemical | ChemComp-NA / |
-Details
| Has protein modification | Y |
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-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 8 |
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Sample preparation
| Crystal | Density Matthews: 4.4 Å3/Da / Density % sol: 72.07 % |
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| Crystal grow | Details: VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S. |
-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA |
| Detector | Type: PSI PILATUS 6M / Detector: PIXEL |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Relative weight: 1 |
| Reflection | Resolution: 3.45→19.998 Å / Num. obs: 260194 / % possible obs: 84.3 % / Observed criterion σ(I): 0.2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.216 / Rsym value: 0.096 / Net I/σ(I): 5.6 |
| Reflection shell | Resolution: 3.45→3.57 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 1.4 / % possible all: 85.6 |
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Processing
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| Refinement | Method to determine structure: ISOMORPHOUS REPLACEMENT Starting model: PDB ENTRY 2ZJR Resolution: 3.45→19.998 Å / SU ML: 0.52 / σ(F): 0.58 / Stereochemistry target values: ML
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| Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.01 Å2 / ksol: 0.21 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters |
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| Refinement step | Cycle: LAST / Resolution: 3.45→19.998 Å
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| Refine LS restraints |
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| LS refinement shell |
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| Refinement TLS params. | Method: refined / Origin x: 44.1537 Å / Origin y: 126.6952 Å / Origin z: 108.9806 Å
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| Refinement TLS group | Selection details: ALL |
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Deinococcus radiodurans R1 (radioresistant)
X-RAY DIFFRACTION
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