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- PDB-1kc8: Co-crystal Structure of Blasticidin S Bound to the 50S Ribosomal ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kc8 | ||||||
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Title | Co-crystal Structure of Blasticidin S Bound to the 50S Ribosomal Subunit | ||||||
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![]() | RIBOSOME / 50S subunit / blasticidin S / antibiotic / P-loop / P-site | ||||||
Function / homology | ![]() ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA / mRNA splicing, via spliceosome / 5S rRNA binding / large ribosomal subunit rRNA binding ...ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA / mRNA splicing, via spliceosome / 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 / DNA repair / mRNA binding / nucleotide binding / DNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hansen, J.L. / Ban, N. / Nissen, P. / Moore, P.B. / Steitz, T.A. | ||||||
![]() | ![]() Title: Structures of Five Antibiotics Bound at the Peptidyl Transferase Center of the Large Ribosomal Subunit Authors: Hansen, J. / Moore, P.B. / Steitz, T.A. #1: ![]() Title: The complete atomic structure of the large ribosomal subunit at 2.4 A resolution Authors: Ban, N. / Nissen, P. / Hansen, J. / Moore, P.B. / Steitz, T.A. #2: ![]() Title: The structural basis of ribosome activity in peptide bond synthesis Authors: Nissen, P. / Hansen, J. / Ban, N. / Moore, P.B. / Steitz, T.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 | ![]() | 2.5 MB | Display | ![]() |
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PDB format | ![]() | 1.9 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1k73C ![]() 1n8rC ![]() 1njiC ![]() 1jjkS 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
-RNA chain , 2 types, 2 molecules AB
#1: RNA chain | Mass: 946034.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: RNA chain | Mass: 39318.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
+RIBOSOMAL PROTEIN ... , 28 types, 28 molecules CDEFGHIJKLMNOPQRSTUVWXYZ1234
-Non-polymers , 7 types, 8114 molecules ![](data/chem/img/BLS.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/HOH.gif)
#31: Chemical | #32: Chemical | ChemComp-MG / #33: Chemical | #34: Chemical | ChemComp-NA / #35: Chemical | ChemComp-CL / #36: Chemical | ChemComp-CD / #37: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.17 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion / pH: 5.8 Details: PEG 6K, KCl, NH4Cl, MgCl2, NaOAc, pH 5.8, VAPOR DIFFUSION, temperature 292K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: back-extraction, vapor diffusion / Details: Ban, N., (2000) Science, 289, 905. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Sep 27, 2000 |
Radiation | Monochromator: Si-111 Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. all: 361295 / Num. obs: 361295 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 36.7 Å2 / Rmerge(I) obs: 0.166 / Rsym value: 0.166 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 6 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.5 / Num. unique all: 35812 / Rsym value: 0.78 / % possible all: 99.7 |
Reflection | *PLUS % possible obs: 94.5 % / Redundancy: 7.4 % |
Reflection shell | *PLUS Lowest resolution: 3.1 Å / % possible obs: 76.6 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NATIVE 1JJK Resolution: 3.01→19.99 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 185476.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 Stereochemistry target values: RNA and protein Brunger and Berman with 3' 2' endo possible Blasticidin S generated from BESGOV structure at CSD using xplo2d
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 24.8732 Å2 / ksol: 0.305814 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.01→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.01→3.11 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 3 Å / Lowest resolution: 3.1 Å |