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Yorodumi- PDB-3pip: Crystal structure of the synergistic antibiotic pair lankamycin a... -
+Open data
-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 information large ribosomal subunit / large ribosomal subunit rRNA binding / 5S rRNA binding / transferase activity / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding ...large ribosomal subunit / large ribosomal subunit rRNA binding / 5S rRNA binding / transferase activity / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA 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: 2011 Title: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-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
Summary document | 3pip_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 3pip_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 3pip_validation.xml.gz | 253.4 KB | Display | |
Data in CIF | 3pip_validation.cif.gz | 348.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pi/3pip ftp://data.pdbj.org/pub/pdb/validation_reports/pi/3pip | HTTPS FTP |
-Related structure data
Related structure data | 3pioC 2zjrS S: Starting model for refinement C: citing same article (ref.) |
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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
-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 |
-Processing
Software |
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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 |