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Yorodumi- PDB-1nwy: COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nwy | ||||||
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Title | COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN | ||||||
Components |
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Keywords | RIBOSOME / AZITHROMYCIN / MACROLIDE / KETOLIDE / 50S / RIBOSOMAL | ||||||
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 / translation / ribonucleoprotein complex / mRNA binding / RNA binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Deinococcus radiodurans (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.3 Å | ||||||
Authors | Schluenzen, F. / Harms, J. / Franceschi, F. / Hansen, H.A.S. / Bartels, H. / Zarivach, R. / Yonath, A. | ||||||
Citation | Journal: Structure / Year: 2003 Title: Structural basis for the antibiotic activity of ketolides and azalides. Authors: Schlunzen, F. / Harms, J.M. / Franceschi, F. / Hansen, H.A. / Bartels, H. / Zarivach, R. / Yonath, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nwy.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1nwy.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 1nwy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nwy_validation.pdf.gz | 693.7 KB | Display | wwPDB validaton report |
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Full document | 1nwy_full_validation.pdf.gz | 888.8 KB | Display | |
Data in XML | 1nwy_validation.xml.gz | 59 KB | Display | |
Data in CIF | 1nwy_validation.cif.gz | 130.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nw/1nwy ftp://data.pdbj.org/pub/pdb/validation_reports/nw/1nwy | HTTPS FTP |
-Related structure data
Related structure data | 1nwxC 1lnr 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 09
#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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#2: RNA chain | Mass: 39911.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: GenBank: 15805042 |
+Ribosomal protein ... , 28 types, 28 molecules ABCDEFGHIJKLMNOPQRSUWXYZ1234
-Protein / Non-polymers , 2 types, 3 molecules T
#22: Protein | Mass: 25415.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RX88 |
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#32: 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 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 291K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7.8 / Method: vapor diffusionDetails: Harms, J.M., (2001) Cell (Cambridge,Mass.), 107, 679. | |||||||||||||||||||||||||||||||||||
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: APS / Beamline: 19-ID / Wavelength: 1.0332 / Wavelength: 1.0332 Å |
Detector | Type: SBC / Detector: CCD / Date: Nov 14, 2001 |
Radiation | Monochromator: SI111 OR SI311 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→30 Å / Num. all: 330873 / Num. obs: 330873 / % possible obs: 86.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rsym value: 0.11 / Net I/σ(I): 9 |
Reflection shell | Resolution: 3.2→3.25 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.34 / % possible all: 83.4 |
Reflection | *PLUS Highest resolution: 3.2 Å / Lowest resolution: 30 Å / Rmerge(I) obs: 0.11 |
Reflection shell | *PLUS % possible obs: 83.4 % / Rmerge(I) obs: 0.339 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1LNR 1lnr Resolution: 3.3→15 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: THE STRUCTURE CONTAINS CA COORDINATES ONLY FOR THE PROTEIN CHAINS.
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Refinement step | Cycle: LAST / Resolution: 3.3→15 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 3.2 Å / Lowest resolution: 30 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |