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- PDB-4tue: Crystal structure of ASL-SufJ bound to Codon ACC-U on the Ribosome -
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Open data
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Basic information
Entry | Database: PDB / ID: 4tue | |||||||||
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Title | Crystal structure of ASL-SufJ bound to Codon ACC-U on the Ribosome | |||||||||
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![]() | RIBOSOME / Protein biosynthesis / RNA / tRNA / transfer RNA / 30S / 50S / 70S / 16S / 23S / ribosomal subunit / mRNA frameshift | |||||||||
Function / homology | ![]() large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit ...large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Fagan, C.E. / Dunham, C.M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into translational recoding by frameshift suppressor tRNASufJ. Authors: Fagan, C.E. / Maehigashi, T. / Dunkle, J.A. / Miles, S.J. / Dunham, C.M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 13.8 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 3.2 MB | Display | |
Data in XML | ![]() | 710.1 KB | Display | |
Data in CIF | ![]() | 1018.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-RNA chain , 7 types, 14 molecules QAXAQVXVQXXXQYXYRAYARBYBZ5Z6
#1: RNA chain | Mass: 493958.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #22: RNA chain | Mass: 24802.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #23: RNA chain | Mass: 8155.996 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA oligonucleotide / Source: (synth.) synthetic construct (others) #24: RNA chain | Mass: 5764.468 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA oligonucleotide / Source: (synth.) synthetic construct (others) #25: RNA chain | Mass: 947895.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #26: RNA chain | Mass: 39494.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #56: RNA chain | Mass: 1098.880 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA oligonucleotide / Source: (synth.) synthetic construct (others) |
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-30S ribosomal protein ... , 20 types, 40 molecules QBXBQCXCQDXDQEXEQFXFQGXGQHXHQIXIQJXJQKXKQLXLQMXMQNXNQOXOQPXP...
#2: Protein | Mass: 29317.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 26751.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | Mass: 24373.447 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #5: Protein | Mass: 17583.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Protein | Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #7: Protein | Mass: 18050.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein | Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #9: Protein | Mass: 14410.614 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #10: Protein | Mass: 11954.968 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #11: Protein | Mass: 13737.868 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #12: Protein | Mass: 14637.384 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #13: Protein | Mass: 14338.861 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #14: Protein | Mass: 7158.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #15: Protein | Mass: 10578.407 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #16: Protein | Mass: 10409.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #17: Protein | Mass: 12325.655 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #18: Protein | Mass: 10258.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #19: Protein | Mass: 10605.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #20: Protein | Mass: 11736.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #21: Protein/peptide | Mass: 3350.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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+50S ribosomal protein ... , 29 types, 58 molecules RDYDREYERFYFRGYGRHYHRIYIRNYNROYORPYPRQYQRRYRRSYSRTYTRUYURVYV...
-Non-polymers , 3 types, 891 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/PAR.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/PAR.gif)
![](data/chem/img/ZN.gif)
#57: Chemical | ChemComp-MG / #58: Chemical | #59: Chemical | ChemComp-ZN / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 4% PEG 20k, 4% PEG550 MME, 0.1M TRIS-ACETATE, 0.2M KSCN, 10mM MgCl |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300HS / Detector: CCD / Date: Jun 22, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 3.5→50 Å / Num. obs: 732004 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 103.62 Å2 / Rmerge F obs: 0.99 / Rmerge(I) obs: 0.231 / Rrim(I) all: 0.254 / Χ2: 0.963 / Net I/σ(I): 5.69 / Num. measured all: 4247078 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Resolution: 3.5→49.802 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.41 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 434.11 Å2 / Biso mean: 103.8186 Å2 / Biso min: 5.62 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.5→49.802 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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