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- PDB-1njn: The crystal structure of the 50S Large ribosomal subunit from Dei... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1njn | ||||||
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Title | The crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with the antibiotic sparsomycin | ||||||
![]() | 23S ribosomal RNA | ||||||
![]() | RIBOSOME / Ribosomes / tRNA / puromycin / sparsomycin / peptidyl-transferase / peptide bond formation | ||||||
Function / homology | SPARSOMYCIN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000)![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Bashan, A. / Agmon, I. / Zarivatch, R. / Schluenzen, F. / Harms, J.M. / Berisio, R. / Bartels, H. / Hansen, H.A. / Yonath, A. | ||||||
![]() | ![]() Title: Structural basis of the ribosomal machinery for Peptide bond formation, translocation, and nascent chain progression Authors: Bashan, A. / Agmon, I. / Zarivatch, R. / Schluenzen, F. / Harms, J.M. / Berisio, R. / Bartels, H. / Franceschi, F. / Auerbach, T. / Hansen, H.A. / Kossoy, E. / Kessler, M. / 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 | ![]() | 1.3 MB | Display | ![]() |
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PDB format | ![]() | 1002 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.2 KB | Display | ![]() |
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Full document | ![]() | 581.1 KB | Display | |
Data in XML | ![]() | 49 KB | Display | |
Data in CIF | ![]() | 80.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1njmC ![]() 1njoC ![]() 1njpC ![]() 1nkwS C: citing same article ( S: Starting model for refinement |
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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
#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: Chemical | ChemComp-SPS / |
-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 | pH: 7.8 Details: ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, SPARSOMYCIN, pH 7.80 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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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: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 1, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9331 Å / Relative weight: 1 |
Reflection | Resolution: 3.7→40 Å / Num. obs: 206787 / % possible obs: 81.1 % / Observed criterion σ(I): -3 / Rsym value: 0.126 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 3.7→3.76 Å / Mean I/σ(I) obs: 1.7 / Rsym value: 0.37 / % possible all: 80 |
Reflection | *PLUS Lowest resolution: 40 Å / Rmerge(I) obs: 0.126 |
Reflection shell | *PLUS % possible obs: 80 % / Rmerge(I) obs: 0.37 |
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Processing
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Refinement | Method to determine structure: DIFFERENCE FOURIER MAPS Starting model: PDB ENTRY 1NKW Resolution: 3.7→15 Å / Rfactor Rfree error: 0.003 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 3.7→15 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor Rfree: 0.3117 / Rfactor Rwork: 0.271 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_d |