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- PDB-3cce: Structure of Anisomycin resistant 50S Ribosomal Subunit: 23S rRNA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3cce | ||||||
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Title | Structure of Anisomycin resistant 50S Ribosomal Subunit: 23S rRNA mutation U2535A | ||||||
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![]() | RIBOSOME / 23S rRNA mutation U2535A | ||||||
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 | ![]() ![]() | ||||||
![]() | Blaha, G. / Gurel, G. | ||||||
![]() | ![]() Title: Mutations outside the anisomycin-binding site can make ribosomes drug-resistant. Authors: Blaha, G. / Gurel, G. / Schroeder, S.J. / 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 | ![]() | 674 KB | Display | ![]() |
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Full document | ![]() | 896.1 KB | Display | |
Data in XML | ![]() | 133.8 KB | Display | |
Data in CIF | ![]() | 258.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3cc2C ![]() 3cc4C ![]() 3cc7C ![]() 3ccjC ![]() 3cclC ![]() 3ccmC ![]() 3ccqC ![]() 3ccrC ![]() 3ccsC ![]() 3ccuC ![]() 3ccvC ![]() 3cd6C 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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1 |
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Unit cell |
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Components
+50S ribosomal protein ... , 29 types, 29 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZ123
-RNA chain , 2 types, 2 molecules 09
#30: RNA chain | Mass: 946470.562 Da / Num. of mol.: 1 / Mutation: G2099A, U2535A / Source method: isolated from a natural source / Source: (natural) ![]() |
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#31: RNA chain | Mass: 39303.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 7 types, 8128 molecules ![](data/chem/img/MG.gif)
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![](data/chem/img/NA.gif)
![](data/chem/img/CD.gif)
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![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
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![](data/chem/img/NA.gif)
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#32: Chemical | ChemComp-MG / #33: Chemical | ChemComp-CL / #34: Chemical | ChemComp-SR / #35: Chemical | ChemComp-NA / #36: Chemical | ChemComp-CD / #37: Chemical | #38: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE SEQUENCE OF CHAIN 0 MATCHES TO GB ENTRY AY596297 BETWEEN 2634210 AND 2637132, WITH G2099A AND ...THE SEQUENCE OF CHAIN 0 MATCHES TO GB ENTRY AY596297 BETWEEN 2634210 AND 2637132, WITH G2099A AND U2535A MUTATIONS. THE SEQUENCE OF CHAIN Z MATCHES TO REFSEQ ENTRY YP_136287. |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.43 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: sitting drop / pH: 5.8 Details: PEG6000, KCL, NH4CL, MGCl2, pH 5.80, sitting drop, temperature 292K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC / Detector: CCD / Date: Sep 18, 2005 Details: 54-pole harmonic emission undulator, a vertically focusing mirror and a horizontally focusing monochromator |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→50 Å / Num. obs: 462394 / % possible obs: 99.1 % / Redundancy: 4.8 % / Biso Wilson estimate: 55.1 Å2 / Rmerge(I) obs: 0.107 |
Reflection shell | Resolution: 2.75→2.96 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 1.74 / % possible all: 90.3 |
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Processing
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Refinement | Resolution: 2.75→49.33 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 173653.03 / 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: 36.47 Å2 / ksol: 0.308367 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.75→49.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.92 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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