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Open data
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Basic information
Entry | Database: PDB / ID: 1nji | ||||||
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Title | Structure of chloramphenicol bound to the 50S ribosomal subunit | ||||||
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![]() | RIBOSOME / 50S / antibiotic / chloramphenicol / LSU | ||||||
Function / homology | ![]() ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / mRNA splicing, via spliceosome / 5S rRNA binding ...ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / mRNA splicing, via spliceosome / 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 / DNA repair / nucleotide binding / mRNA binding / DNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hansen, J.L. / 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
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 322.5 KB | Display | |
Data in CIF | ![]() | 509.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1k73C ![]() 1kc8C ![]() 1n8rC ![]() 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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1 |
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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 / Details: cultured cells / Source: (natural) ![]() |
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#2: RNA chain | Mass: 39318.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) ![]() |
+50S ribosomal protein ... , 27 types, 27 molecules CDEFGHJKLMNOPQRSTUVWXYZ1234
-Protein , 1 types, 1 molecules I
#9: Protein | Mass: 37213.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) ![]() |
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-Non-polymers , 7 types, 8099 molecules ![](data/chem/img/MG.gif)
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![](data/chem/img/CD.gif)
![](data/chem/img/HOH.gif)
#31: Chemical | ChemComp-MG / #32: Chemical | #33: Chemical | ChemComp-NA / #34: Chemical | ChemComp-CL / #35: Chemical | ChemComp-CLM / | #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: 3.13 Å3/Da / Density % sol: 60.74 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: PEG 6000, KCl, MgCl2, NH4Cl, Na Acetate, pH 5.8, VAPOR DIFFUSION, SITTING DROP at 291K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 7.1 / 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: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 22, 2002 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.92→50 Å / Num. all: 393891 / Num. obs: 393074 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 38.5 Å2 / Rmerge(I) obs: 0.246 / Rsym value: 0.246 / Net I/σ(I): 8.88 |
Reflection shell | Resolution: 2.92→2.97 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.965 / Mean I/σ(I) obs: 1.5 / Num. unique all: 19931 / Rsym value: 0.965 / % possible all: 97.1 |
Reflection | *PLUS Highest resolution: 3 Å / % possible obs: 96.4 % / Redundancy: 5 % |
Reflection shell | *PLUS Highest resolution: 3 Å / Lowest resolution: 3.1 Å / % possible obs: 96.5 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1JJ2 Resolution: 3→50 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 233703.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 24.06 Å2 / ksol: 0.307 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.11 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Highest resolution: 3 Å / Rfactor Rfree: 0.201 / Rfactor Rwork: 0.175 | ||||||||||||||||||||||||||||||||||||
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 |