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Yorodumi- PDB-6mpf: Structure of the Thermus thermophilus 30S ribosomal subunit compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mpf | |||||||||||||||
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Title | Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a 2-thiocytidine (s2C32) and inosine (I34) modified anticodon stem loop (ASL) of Escherichia coli transfer RNA Arginine 1 (TRNAARG1) bound to an mRNA with an CGC-codon in the A-site and paromomycin | |||||||||||||||
Components |
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Keywords | RIBOSOME / 2-thiocytidine / inosine / transfer RNA / tRNA / 30S / translation / anticodon | |||||||||||||||
Function / homology | Function and homology information small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Thermus thermophilus HB8 (bacteria) Thermus thermophilus (bacteria) Escherichia coli (E. coli) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.33 Å | |||||||||||||||
Authors | Cantara, W.A. / DeMirci, H. / Agris, P.F. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: J.Mol.Biol. / Year: 2020 Title: A Structural Basis for Restricted Codon Recognition Mediated by 2-thiocytidine in tRNA Containing a Wobble Position Inosine. Authors: Vangaveti, S. / Cantara, W.A. / Spears, J.L. / DeMirci, H. / Murphy IV, F.V. / Ranganathan, S.V. / Sarachan, K.L. / Agris, P.F. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mpf.cif.gz | 2.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6mpf.ent.gz | 2.1 MB | Display | PDB format |
PDBx/mmJSON format | 6mpf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mp/6mpf ftp://data.pdbj.org/pub/pdb/validation_reports/mp/6mpf | HTTPS FTP |
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-Related structure data
Related structure data | 6dtiC 6mknC 6mpiC 1xnrS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-RNA chain , 3 types, 3 molecules AWX
#1: RNA chain | Mass: 489636.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus HB8 (strain HB8 / ATCC 27634 / DSM 579) (bacteria) |
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#22: RNA chain | Mass: 1239.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
#23: RNA chain | Mass: 3522.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
-30S ribosomal protein ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTV
#2: Protein | Mass: 26987.271 Da / Num. of mol.: 1 / 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 |
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#3: Protein | Mass: 22862.430 Da / Num. of mol.: 1 / 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: 24242.254 Da / Num. of mol.: 1 / 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: 16331.079 Da / Num. of mol.: 1 / 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.: 1 / 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: Q5SLP8 |
#7: Protein | Mass: 17919.775 Da / Num. of mol.: 1 / 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.: 1 / 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: 14279.419 Da / Num. of mol.: 1 / 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: 11299.176 Da / Num. of mol.: 1 / 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: 12606.369 Da / Num. of mol.: 1 / 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: 13804.311 Da / Num. of mol.: 1 / 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: 14207.666 Da / Num. of mol.: 1 / 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: 7027.529 Da / Num. of mol.: 1 / 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: 10447.213 Da / Num. of mol.: 1 / 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: 9924.469 Da / Num. of mol.: 1 / 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: 12194.460 Da / Num. of mol.: 1 / 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: 8497.198 Da / Num. of mol.: 1 / 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: Q5SLQ0 |
#19: Protein | Mass: 9203.743 Da / Num. of mol.: 1 / 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: 10921.086 Da / Num. of mol.: 1 / 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: 2960.475 Da / Num. of mol.: 1 / 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 |
-Non-polymers , 3 types, 106 molecules
#24: Chemical | ChemComp-PAR / | ||
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#25: Chemical | ChemComp-MG / #26: Chemical | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.53 Å3/Da / Density % sol: 72.87 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: MPD, NH4Cl, KCl, CaCl2, magnesium acetate, sodium cacodylate, pH 6.5 VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 277 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 17, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 3.33→49.563 Å / Num. obs: 375418 / % possible obs: 97.7 % / Redundancy: 3.1 % / Biso Wilson estimate: 118.39 Å2 / Net I/σ(I): 12.98 |
Reflection shell | Resolution: 3.33→3.449 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.42 / Num. unique obs: 20244 / CC1/2: 0.563 / % possible all: 97.82 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1XNR Resolution: 3.33→49.563 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 0.92 / Phase error: 20.58
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 271.14 Å2 / Biso mean: 119.6542 Å2 / Biso min: 30 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.33→49.563 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26
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