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- PDB-7u2h: 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: 7u2h | |||||||||||||||
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Title | Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Gly-NH-tRNAgly, aminoacylated P-site fMet-NH-tRNAmet, and deacylated E-site tRNAgly at 2.55A resolution | |||||||||||||||
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Function / homology | ![]() large ribosomal subunit / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Syroegin, E.A. / Aleksandrova, E.V. / Polikanov, Y.S. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for the inability of chloramphenicol to inhibit peptide bond formation in the presence of A-site glycine. Authors: Syroegin, E.A. / Aleksandrova, E.V. / Polikanov, Y.S. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 7.6 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 | ![]() 7u2iC ![]() 7u2jC ![]() 6xhwS 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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2 | ![]()
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Unit cell |
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Components
-RNA chain , 7 types, 14 molecules 1A2A1B2B1a2a1v2v1w2w1x2x1y2y
#1: RNA chain | ![]() Mass: 948007.562 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) ![]() ![]() ![]() ![]() #53: RNA chain | Mass: 7922.840 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic 24-nt M-G-Stop mRNA / Source: (synth.) ![]() ![]() #54: RNA chain | Mass: 23802.225 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Aminoacylated Glycyl-tRNAgly / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #55: RNA chain | Mass: 25005.125 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Aminoacylated Formyl-Methionyl-tRNAmet / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #56: RNA chain | Mass: 23746.158 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Deacylated tRNAgly / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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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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-Non-polymers , 5 types, 6865 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/HOH.gif)
#57: Chemical | ChemComp-MG / #58: Chemical | #59: Chemical | ChemComp-ZN / #60: Chemical | ![]() #61: 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: 3.3 Å3/Da / Density % sol: 63.05 % / 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, 0.1 M Tris-HCl, pH 7.6, 2.5% PEG20000, 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: Jul 10, 2020 / Details: S/N E-32-0124 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.55→146.3 Å / Num. obs: 1896410 / % possible obs: 99.5 % / Redundancy: 10.072 % / Biso Wilson estimate: 55.31 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.268 / Rrim(I) all: 0.283 / Χ2: 1 / Net I/σ(I): 6.98 / Num. measured all: 19099952 / Scaling rejects: 11646 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6XHW Resolution: 2.55→146.3 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.76 / 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: 138.71 Å2 / Biso mean: 58.4404 Å2 / Biso min: 10.22 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.55→146.3 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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