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Yorodumi- PDB-6cfk: Crystal structure of the Thermus thermophilus 70S ribosome in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cfk | ||||||||||||||||||
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Title | Crystal structure of the Thermus thermophilus 70S ribosome in complex with D-histidyl-CAM and bound to protein Y (YfiA) at 2.7A resolution | ||||||||||||||||||
Components |
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Keywords | ribosome/inhibitor / Chloramphenicol / antibiotic / inhibitor / ribosome / 70S / ribosome structure / inhibition of translation / peptidyl transferase center / ribosome-inhibitor complex | ||||||||||||||||||
Function / homology | Function and homology information dormancy process / negative regulation of translational elongation / primary metabolic process / ribosomal small subunit binding / negative regulation of translational initiation / response to cold / cytosolic small ribosomal subunit / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding ...dormancy process / negative regulation of translational elongation / primary metabolic process / ribosomal small subunit binding / negative regulation of translational initiation / response to cold / cytosolic small ribosomal subunit / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Escherichia coli (E. coli) Thermus thermophilus (bacteria) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||||||||||||||
Authors | Tereshchenkov, A.G. / Dobosz-Bartoszek, M. / Osterman, I.A. / Marks, J. / Sergeeva, V.A. / Kasatsky, P. / Komarova, E.S. / Stavrianidi, A.N. / Rodin, I.A. / Konevega, A.L. ...Tereshchenkov, A.G. / Dobosz-Bartoszek, M. / Osterman, I.A. / Marks, J. / Sergeeva, V.A. / Kasatsky, P. / Komarova, E.S. / Stavrianidi, A.N. / Rodin, I.A. / Konevega, A.L. / Sergiev, P.V. / Sumbatyan, N.V. / Mankin, A.S. / Bogdanov, A.A. / Polikanov, Y.S. | ||||||||||||||||||
Funding support | United States, Russian Federation, 5items
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Citation | Journal: J. Mol. Biol. / Year: 2018 Title: Binding and Action of Amino Acid Analogs of Chloramphenicol upon the Bacterial Ribosome. Authors: Tereshchenkov, A.G. / Dobosz-Bartoszek, M. / Osterman, I.A. / Marks, J. / Sergeeva, V.A. / Kasatsky, P. / Komarova, E.S. / Stavrianidi, A.N. / Rodin, I.A. / Konevega, A.L. / Sergiev, P.V. / ...Authors: Tereshchenkov, A.G. / Dobosz-Bartoszek, M. / Osterman, I.A. / Marks, J. / Sergeeva, V.A. / Kasatsky, P. / Komarova, E.S. / Stavrianidi, A.N. / Rodin, I.A. / Konevega, A.L. / Sergiev, P.V. / Sumbatyan, N.V. / Mankin, A.S. / Bogdanov, A.A. / Polikanov, Y.S. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cfk.cif.gz | 7.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6cfk.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6cfk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cf/6cfk ftp://data.pdbj.org/pub/pdb/validation_reports/cf/6cfk | HTTPS FTP |
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-Related structure data
Related structure data | 6cfjC 6cflC 4y4oS 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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Unit cell |
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-Components
-RNA chain , 3 types, 6 molecules 1A2A1B2B1a2a
#1: RNA chain | Mass: 948035.625 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: GenBank: 55771382 #2: RNA chain | Mass: 39188.371 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: GenBank: 55771382 #32: RNA chain | Mass: 493864.625 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: GenBank: 155076 |
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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) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P62662, UniProt: P80371*PLUS #34: 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: P62663, UniProt: P80372*PLUS #35: 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: P62664, UniProt: P80373*PLUS #36: 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: P27152, UniProt: Q5SHQ5*PLUS #37: 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: P23370, UniProt: Q5SLP8*PLUS #38: 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: P62667, UniProt: P17291*PLUS #39: 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: P24319, UniProt: P0DOY9*PLUS #40: 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 #41: 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: P80375, UniProt: Q5SHN7*PLUS #42: 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: P62654, UniProt: P80376*PLUS #43: Protein | Mass: 14683.476 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: P17293, UniProt: Q5SHN3*PLUS #44: 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: P62655, UniProt: P80377*PLUS #45: 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: P24320, UniProt: P0DOY6*PLUS #46: 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: P80378, UniProt: Q5SJ76*PLUS #47: 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: P62238, UniProt: Q5SJH3*PLUS #48: 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 #49: Protein | Mass: 10258.299 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: P62659, UniProt: Q5SLQ0*PLUS #50: 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: P80381, UniProt: Q5SHP2*PLUS #51: 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 #52: 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: P62612, UniProt: Q5SIH3*PLUS |
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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.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: raiA, yfiA, b2597, JW2578 / Plasmid: pGS21a-YFIA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: P0AD49 |
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-Non-polymers , 8 types, 8944 molecules
#54: Chemical | ChemComp-MG / #55: Chemical | #56: Chemical | #57: Chemical | ChemComp-MPD / ( #58: Chemical | #59: Chemical | ChemComp-ZN / #60: Chemical | #61: Water | ChemComp-HOH / | |
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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: 3.36 Å3/Da / Density % sol: 58.1 % / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 5, 2015 / Details: S/N 60-0112-F | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→121.919 Å / Num. obs: 1575457 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.389 % / Biso Wilson estimate: 52.56 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.146 / Rrim(I) all: 0.173 / Χ2: 0.939 / Net I/σ(I): 8.7 / Num. measured all: 5338935 / Scaling rejects: 1813 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Y4O Resolution: 2.7→121.919 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.34 / 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: 132.02 Å2 / Biso mean: 54.1721 Å2 / Biso min: 8.69 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.7→121.919 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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