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- PDB-3cc4: 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: 3cc4 | ||||||
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Title | Co-crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit | ||||||
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![]() | RIBOSOME / wild type / large ribosomal subunit / Haloarcula marismortui / co-crystal / anisomycin | ||||||
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. #1: ![]() Title: Structures of five antibiotics bound at the peptidyl transferase center of the large ribosomal subunit. Authors: Hansen, J.L. / 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 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 299.1 KB | Display | |
Data in CIF | ![]() | 481.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3cc2C ![]() 3cc7C ![]() 3cceC ![]() 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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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: 946463.500 Da / Num. of mol.: 1 / 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 , 8 types, 8122 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SR.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ANM.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SR.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ANM.gif)
![](data/chem/img/HOH.gif)
#32: Chemical | ChemComp-MG / #33: Chemical | ChemComp-CL / #34: Chemical | ChemComp-SR / #35: Chemical | ChemComp-NA / #36: Chemical | ChemComp-CD / #37: Chemical | #38: Chemical | ChemComp-ANM / | #39: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE SEQUENCE OF CHAIN 0 MATCHES TO GB ENTRY AY596297 BETWEEN 2634210 AND 2637132. THE SEQUENCE OF ...THE SEQUENCE OF CHAIN 0 MATCHES TO GB ENTRY AY596297 BETWEEN 2634210 AND 2637132. 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: 3.07 Å3/Da / Density % sol: 59.98 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: sitting drop / pH: 5.8 Details: PEG6000, KCL, NH4CL, MGCl2, pH 5.8, 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 QUANTUM 315 / 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: 2.7→50 Å / Num. obs: 492663 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.106 / Χ2: 1.06 / Net I/σ(I): 9.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Resolution: 2.7→49.85 Å / Rfactor Rfree error: 0.004 / FOM work R set: 0.825 / Data cutoff high absF: 128938.109 / 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: 29.663 Å2 / ksol: 0.303 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→49.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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