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Yorodumi- PDB-4l71: Crystal Structure of Frameshift Suppressor tRNA SufA6 Bound to Co... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 4l71 | |||||||||
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| Title | Crystal Structure of Frameshift Suppressor tRNA SufA6 Bound to Codon CCC-A on the Ribosome | |||||||||
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Keywords | RIBOSOME / Protein biosynthesis / ribosomes / RNA / tRNA / transfer RNA / 30S / 70S / 16S / 23S / ribosomal subunit | |||||||||
| Function / homology | Function and homology informationlarge ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit ...large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
| Biological species | ![]() Thermus thermophilus HB8 (bacteria)![]() Thermus thermophilus (bacteria)![]() Synthetic (others) | |||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.90000100875 Å | |||||||||
Authors | Maehigashi, T. / Dunkle, J.A. / Dunham, C.M. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014Title: Structural insights into +1 frameshifting promoted by expanded or modification-deficient anticodon stem loops. Authors: Maehigashi, T. / Dunkle, J.A. / Miles, S.J. / Dunham, C.M. | |||||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 4l71.cif.gz | 6.4 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb4l71.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 4l71.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 4l71_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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| Full document | 4l71_full_validation.pdf.gz | 3.9 MB | Display | |
| Data in XML | 4l71_validation.xml.gz | 826.6 KB | Display | |
| Data in CIF | 4l71_validation.cif.gz | 1.1 MB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l7/4l71 ftp://data.pdbj.org/pub/pdb/validation_reports/l7/4l71 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 1vvjC ![]() 4l47C ![]() 4lelC ![]() 4lfzC ![]() 4lntC ![]() 4lskC ![]() 4lt8C ![]() 4p70C ![]() 3i9d ![]() 3i9e S: Starting model for refinement 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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Components
-RNA chain , 7 types, 14 molecules QAXARAYARBYBQVXVQXXXQYXYZ6Z8
| #1: RNA chain | Mass: 493958.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382#22: RNA chain | Mass: 948240.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382#23: RNA chain | Mass: 39494.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382#53: RNA chain | Mass: 24802.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #54: RNA chain | Mass: 8155.012 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA oligonucleotide / Source: (synth.) Synthetic (others) #55: RNA chain | Mass: 5818.518 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA oligonucleotide / Source: (synth.) Synthetic (others) #56: RNA chain | Mass: 1098.880 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA oligonucleotide / Source: (synth.) Synthetic (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) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80371 #3: Protein | Mass: 26751.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80372 #4: Protein | Mass: 24373.447 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80373 #5: Protein | Mass: 17583.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ5 #6: Protein | Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P62666, UniProt: Q5SLP8*PLUS #7: Protein | Mass: 18050.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P17291 #8: Protein | Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P0DOY9 #9: Protein | Mass: 14410.614 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80374 #10: Protein | Mass: 11954.968 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN7 #11: Protein | Mass: 13737.868 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80376 #12: Protein | Mass: 14637.384 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN3 #13: Protein | Mass: 14338.861 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80377 #14: Protein | Mass: 7158.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P0DOY6 #15: Protein | Mass: 10578.407 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJ76 #16: Protein | Mass: 10409.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJH3 #17: Protein | Mass: 12325.655 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P0DOY7 #18: Protein | Mass: 10258.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() Thermus thermophilus (bacteria) / Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: P62659#19: Protein | Mass: 10605.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP2 #20: Protein | Mass: 11736.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80380 #21: Protein/peptide | Mass: 3350.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SIH3 |
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+50S ribosomal protein ... , 29 types, 58 molecules RDYDREYERFYFRGYGRHYHRIYIRNYNROYORPYPRQYQRRYRRSYSRTYTRUYURVYV...
-Non-polymers , 3 types, 684 molecules 




| #57: Chemical | ChemComp-MG / #58: Chemical | #59: Chemical | ChemComp-ZN / |
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-Details
| Has protein modification | Y |
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-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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Sample preparation
| Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.82 % |
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| Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 Details: 4% PEG 20k, 4% PEG550 MME, 0.1M TRIS-ACETATE, 0.2M KSCN, 10mM MgCl, pH 7.0, vapor diffusion, temperature 293K |
-Data collection
| Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 20, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Reflection | Resolution: 3.7→49.676 Å / Num. all: 612965 / Num. obs: 612965 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 85.008 Å2 / Rmerge(I) obs: 0.313 / Net I/σ(I): 4.51 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Reflection shell | Rmerge(I) obs: 0.014 / Diffraction-ID: 1
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Processing
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| Refinement | Method to determine structure: FOURIER SYNTHESISStarting model: PDB ENTRY 3I9D AND 3I9E Resolution: 3.90000100875→49.6753690821 Å / SU ML: 0.561846974021 / σ(F): 1.99156751478 / Phase error: 26.5129643394 / Stereochemistry target values: PHENIX
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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 mean: 6.62923505921 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: LAST / Resolution: 3.90000100875→49.6753690821 Å
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| Refine LS restraints |
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| LS refinement shell |
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Thermus thermophilus HB8 (bacteria)
X-RAY DIFFRACTION
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