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- PDB-1nwy: COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1nwy | ||||||
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Title | COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN | ||||||
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![]() | RIBOSOME / AZITHROMYCIN / MACROLIDE / KETOLIDE / 50S / RIBOSOMAL | ||||||
Function / homology | ![]() large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome ...large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schluenzen, F. / Harms, J. / Franceschi, F. / Hansen, H.A.S. / Bartels, H. / Zarivach, R. / Yonath, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.5 MB | Display | ![]() |
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PDB format | ![]() | 1.1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 693.7 KB | Display | ![]() |
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Full document | ![]() | 888.8 KB | Display | |
Data in XML | ![]() | 59 KB | Display | |
Data in CIF | ![]() | 130.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1nwxC ![]() 1lnr 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 09
#1: RNA chain | Mass: 933405.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: RNA chain | Mass: 39911.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
+Ribosomal protein ... , 28 types, 28 molecules ABCDEFGHIJKLMNOPQRSUWXYZ1234
-Protein / Non-polymers , 2 types, 3 molecules T![](data/chem/img/ZIT.gif)
![](data/chem/img/ZIT.gif)
#22: Protein | Mass: 25415.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#32: Chemical |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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 |