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Yorodumi- PDB-3pio: Crystal structure of the synergistic antibiotic pair lankamycin a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pio | ||||||
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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 / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome ...large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / 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: 3.2473 Å | ||||||
Authors | Belousoff, M.J. / Shapira, T. / Bashan, A. / Zimmerman, E. / Arakawa, K. / 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 | 3pio.cif.gz | 4.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3pio.ent.gz | 3.4 MB | Display | PDB format |
PDBx/mmJSON format | 3pio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pi/3pio ftp://data.pdbj.org/pub/pdb/validation_reports/pi/3pio | HTTPS FTP |
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-Related structure data
Related structure data | 3pipC 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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Details | BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. BIOMOLECULE: 1 AUTHOR DETERMINED BIOLOGICAL UNIT: 30-MERIC APPLY THE FOLLOWING TO CHAINS: X, Y, A, B, C, D, E, F, G, AND CHAINS: H, I, J, K, L, M, N, O, P, AND CHAINS: Q, R, S, T, U, V, W, Z, 1, AND CHAINS: 2, 3, 4, 5, 6 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 |
-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 , 4 types, 212 molecules
#31: Chemical | ChemComp-LMA / | ||||
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#32: Chemical | ChemComp-MG / #33: Chemical | ChemComp-NA / #34: Chemical | ChemComp-K / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 4.46 Å3/Da / Density % sol: 72.4 % |
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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: ESRF / Beamline: ID23-2 / Wavelength: 0.873 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Details: MICROFOCUS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 3.2473→19.995 Å / Num. obs: 353603 / % possible obs: 93.3 % / Observed criterion σ(I): 0.1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.178 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 3.2473→3.36 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.2 / % possible all: 34 |
-Processing
Software |
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Refinement | Method to determine structure: ISOMORPHOUS REPLACEMENT Starting model: PDB ENTRY 2ZJR Resolution: 3.2473→19.995 Å / SU ML: 0.41 / σ(F): 0.61 / Phase error: 32.06 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.04 Å / VDW probe radii: 0.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42 Å2 / ksol: 0.24 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.2473→19.995 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: 44.3174 Å / Origin y: 127.3391 Å / Origin z: 109.4249 Å
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Refinement TLS group | Selection details: ALL |