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- PDB-5ndk: Crystal structure of aminoglycoside TC007 co-crystallized with 70... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ndk | ||||||
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Title | Crystal structure of aminoglycoside TC007 co-crystallized with 70S ribosome from Thermus thermophilus, three tRNAs and mRNA | ||||||
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![]() | RIBOSOME / translation / 3S / 50S / 70S / tRNA / mRNA / bacteria / RNA-protein complex / inhibitor / antibiotic / aminoglycoside | ||||||
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 | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Prokhorova, I. / Djumagulov, M. / Urzhumtsev, A. / Yusupov, M. / Yusupova, G. | ||||||
![]() | ![]() Title: Aminoglycoside interactions and impacts on the eukaryotic ribosome. Authors: Prokhorova, I. / Altman, R.B. / Djumagulov, M. / Shrestha, J.P. / Urzhumtsev, A. / Ferguson, A. / Chang, C.T. / Yusupov, M. / Blanchard, S.C. / Yusupova, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 6.8 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.1 MB | Display | ![]() |
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Full document | ![]() | 5.3 MB | Display | |
Data in XML | ![]() | 877.9 KB | Display | |
Data in CIF | ![]() | 1.2 MB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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 , 5 types, 14 molecules 131G1H14161JY1Y4W1X1V1W4X4V4
#1: RNA chain | Mass: 493997.312 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: GenBank: 55771382 #15: RNA chain | Mass: 948539.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: GenBank: 55771382 #26: RNA chain | Mass: 39540.617 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: GenBank: 55771382 #51: RNA chain | Mass: 7911.565 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #52: RNA chain | Mass: 24485.539 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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+50S ribosomal protein ... , 27 types, 54 molecules A865B5F81119L5P85815G8C5Q8M5B875L8H561696825H8D52129C885M8I5...
-30S ribosomal protein ... , 20 types, 40 molecules 2A2I8I8A222E8E823I3A3E329I9A1F1B4I4A4E42AIAA5I5A5E52BIBA6I6A...
#6: Protein | Mass: 13737.868 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P80376 #7: Protein | Mass: 12325.655 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: Q5SHP7, UniProt: P0DOY7*PLUS #8: Protein | Mass: 26751.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P80372 #9: Protein | Mass: 14410.614 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P80374 #13: Protein | Mass: 14637.384 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: Q5SHN3 #14: Protein | Mass: 24373.447 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P80373 #19: Protein | Mass: 10258.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: Q5SLQ0 #20: Protein/peptide | Mass: 3350.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: Q5SIH3 #24: Protein | Mass: 14338.861 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P80377 #25: Protein | Mass: 17583.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: Q5SHQ5 #29: Protein | Mass: 10605.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: Q5SHP2 #33: Protein | Mass: 7158.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: Q5SHQ1, UniProt: P0DOY6*PLUS #34: Protein | Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: Q5SLP8 #37: Protein | Mass: 11736.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P80380 #41: Protein | Mass: 10578.407 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: Q5SJ76 #42: Protein | Mass: 18050.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P17291 #44: Protein | Mass: 29317.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P80371 #48: Protein | Mass: 11954.968 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: Q5SHN7 #49: Protein | Mass: 10409.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: Q5SJH3 #50: Protein | Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: Q5SHQ2, UniProt: P0DOY9*PLUS |
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-Non-polymers , 4 types, 2908 molecules ![](data/chem/img/8UZ.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#53: Chemical | ChemComp-8UZ / #54: Chemical | ChemComp-MG / #55: Chemical | ChemComp-ZN / #56: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 4% PEG20K, 4% PEGMME 550, 100mM Tris/HAc, 200mM KSCN |
-Data collection
Diffraction | Mean temperature: 90 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 25, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.95→152.739 Å / Num. obs: 1204009 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 46.833 % / Biso Wilson estimate: 72.68 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.307 / Rrim(I) all: 0.31 / Χ2: 0.939 / Net I/σ(I): 16.04 / Num. measured all: 56386821 / Scaling rejects: 4433 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]()
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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: 242.32 Å2 / Biso mean: 78.5617 Å2 / Biso min: 20 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.95→152.739 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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