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- PDB-1k73: Co-crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit -
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Open data
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Basic information
Entry | Database: PDB / ID: 1k73 | ||||||
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Title | Co-crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit | ||||||
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![]() | RIBOSOME / 50S / anisomycin / antibiotic / Harloarcula marismortui | ||||||
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 / ribonucleoprotein complex / translation / DNA repair / nucleotide binding / mRNA binding / DNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hansen, J. / 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 | ![]() 1kc8C ![]() 1n8rC ![]() 1njiC ![]() 1jj2S 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, 8112 molecules ![](data/chem/img/ANM.gif)
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#31: Chemical | ChemComp-ANM / | ||||||||||
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#32: Chemical | ChemComp-MG / #33: Chemical | #34: Chemical | ChemComp-NA / #35: Chemical | ChemComp-CL / #36: Chemical | ChemComp-CD / #37: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.24 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: PEG 6K, 1.2 M KCl, 30 mm MgCl2, 0.5 M NH4Cl, 100 mM NaOAC, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: Jun 16, 2001 |
Radiation | 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: 360115 / Num. obs: 360115 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 38.7 Å2 / Rmerge(I) obs: 0.168 / Rsym value: 0.168 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 3→50 Å / Redundancy: 5 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2 / Rsym value: 0.77 / % possible all: 96.6 |
Reflection | *PLUS % possible obs: 90.9 % / Redundancy: 6 % |
Reflection shell | *PLUS Lowest resolution: 3.1 Å / % possible obs: 66.4 % / Mean I/σ(I) obs: 1.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1JJ2.pdb Resolution: 3.01→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 278574.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 25.4308 Å2 / ksol: 0.298296 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.01→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.11 Å / Rfactor Rfree error: 0.023 / 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 / Rfactor Rfree: 0.254 / Rfactor Rwork: 0.206 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 |