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- PDB-8t8b: Crystal structure of the Thermus thermophilus 70S ribosome in com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8t8b | |||||||||||||||||||||||||||
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Title | Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y, A-site aminoacyl-tRNA analog ACC-PMN, and P-site formyl-MAI-tripeptidyl-tRNA analog ACCA-IAMf at 2.65A resolution | |||||||||||||||||||||||||||
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![]() | RIBOSOME/RNA / 70S ribosome / peptidyl-tRNA / RNA-peptide conjugate / RNA modification / FT-ICR mass spectrometry / formylation / RIBOSOME / RIBOSOME-RNA complex | |||||||||||||||||||||||||||
Function / homology | ![]() dormancy process / negative regulation of translational elongation / ribosomal small subunit binding / negative regulation of translational initiation / response to cold / large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding ...dormancy process / negative regulation of translational elongation / ribosomal small subunit binding / negative regulation of translational initiation / response to cold / 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 / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||||||||
![]() | Thaler, J. / Syroegin, E.A. / Breuker, K. / Polikanov, Y.S. / Micura, R. | |||||||||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Practical Synthesis of N -Formylmethionylated Peptidyl-tRNA Mimics. Authors: Thaler, J. / Syroegin, E.A. / Breuker, K. / Polikanov, Y.S. / Micura, R. | |||||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 7.5 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8t8cC ![]() 7rqbS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-RNA chain , 4 types, 8 molecules 1A2A1B2B1a2a1w2w
#1: RNA chain | Mass: 948021.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: RNA chain | Mass: 39188.371 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #32: RNA chain | Mass: 493863.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #54: RNA chain | Mass: 1428.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic aminoacyl-tRNA-mimic ACC-PMN / Source: (synth.) ![]() ![]() |
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+50S ribosomal protein ... , 29 types, 58 molecules 1D2D1E2E1F2F1G2G1H2H1I2I1N2N1O2O1P2P1Q2Q1R2R1S2S1T2T1U2U1V2V...
-30S ribosomal protein ... , 20 types, 40 molecules 1b2b1c2c1d2d1e2e1f2f1g2g1h2h1i2i1j2j1k2k1l2l1m2m1n2n1o2o1p2p...
#33: Protein | Mass: 29317.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #34: Protein | Mass: 26751.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #35: Protein | Mass: 24373.447 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #36: Protein | Mass: 17583.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #37: Protein | Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #38: Protein | Mass: 18050.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #39: Protein | Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #40: Protein | Mass: 14410.614 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #41: Protein | Mass: 11954.968 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #42: Protein | Mass: 13737.868 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #43: Protein | Mass: 14683.476 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #44: Protein | Mass: 14338.861 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #45: Protein | Mass: 7158.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #46: Protein | Mass: 10578.407 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #47: Protein | Mass: 10409.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #48: Protein | Mass: 12325.655 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #49: Protein | Mass: 10258.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #50: Protein | Mass: 10605.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #51: Protein | Mass: 11736.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #52: Protein/peptide | Mass: 3350.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Protein , 1 types, 2 molecules 1y2y
#53: Protein | Mass: 12803.583 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: C-terminal His-tag / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-P-site Peptidyl-tRNA Analog ... , 2 types, 4 molecules 1x2x1v2v
#55: RNA chain | Mass: 1222.833 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: RNA part of the synthetic formylated peptidyl-tRNA mimic ACCA-IAMf Source: (synth.) ![]() ![]() #56: Protein/peptide | Mass: 361.457 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Peptide part of the synthetic formylated peptidyl-tRNA mimic ACCA-IAMf Source: (synth.) ![]() ![]() |
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-Non-polymers , 6 types, 8238 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/ARG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/ARG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/HOH.gif)
#57: Chemical | ChemComp-MG / #58: Chemical | ChemComp-MPD / ( #59: Chemical | #60: Chemical | ChemComp-ZN / #61: Chemical | #62: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 60.77 % / Description: Long needles |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion / pH: 7.6 Details: 0.1-0.2 M Arginine-HCl, 0.1M Tris-HCl pH 7.6, 2.5% PEG-20K, 7-12% MPD, 0.5 mM BME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 11, 2023 / Details: S/N E-32-0124 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.65→119.32 Å / Num. obs: 1585401 / % possible obs: 99 % / Redundancy: 6.151 % / Biso Wilson estimate: 69.847 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.19 / Rrim(I) all: 0.207 / Χ2: 1.187 / Net I/σ(I): 8.02 / Num. measured all: 9752234 / Scaling rejects: 10053 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7RQB Resolution: 2.65→119.32 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.78 / 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: 155.01 Å2 / Biso mean: 73.031 Å2 / Biso min: 23.17 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.65→119.32 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: 30
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