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Yorodumi- PDB-5wis: 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: 5wis | |||||||||||||||||||||
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| Title | Crystal structure of the Thermus thermophilus 70S ribosome in complex with methymycin and bound to mRNA and A-, P- and E-site tRNAs at 2.7A resolution | |||||||||||||||||||||
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Keywords | RIBOSOME / macrolide / antibiotic / inhibitor / inhibition of translation / peptidyl transferase center | |||||||||||||||||||||
| Function / homology | Function and homology informationlarge ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit ...large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||||||||||||||
| Biological species | ![]() ![]() Thermus thermophilus HB8 (bacteria)![]() Thermus thermophilus (bacteria) Enterobacteria phage T4 (virus) | |||||||||||||||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.703 Å | |||||||||||||||||||||
Authors | Almutairi, M.M. / Svetlov, M.S. / Hansen, D.A. / Khabibullina, N.F. / Klepacki, D. / Kang, H.Y. / Sherman, D.H. / Vazquez-Laslop, N. / Polikanov, Y.S. / Mankin, A.S. | |||||||||||||||||||||
| Funding support | United States, Saudi Arabia, 6items
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Citation | Journal: Nucleic Acids Res. / Year: 2017Title: Co-produced natural ketolides methymycin and pikromycin inhibit bacterial growth by preventing synthesis of a limited number of proteins. Authors: Almutairi, M.M. / Svetlov, M.S. / Hansen, D.A. / Khabibullina, N.F. / Klepacki, D. / Kang, H.Y. / Sherman, D.H. / Vazquez-Laslop, N. / Polikanov, Y.S. / Mankin, A.S. | |||||||||||||||||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 5wis.cif.gz | 7.8 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb5wis.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 5wis.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 5wis_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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| Full document | 5wis_full_validation.pdf.gz | 2 MB | Display | |
| Data in XML | 5wis_validation.xml.gz | 659.3 KB | Display | |
| Data in CIF | 5wis_validation.cif.gz | 1 MB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/5wis ftp://data.pdbj.org/pub/pdb/validation_reports/wi/5wis | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 5witC ![]() 4y4pS S: Starting model for refinement C: citing same article ( |
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| Similar structure data |
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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 , 6 types, 14 molecules 1A2A1B2B1a2a1v2v1w1y2w2y1x2x
| #1: RNA chain | Mass: 948035.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() Thermus thermophilus HB8 (bacteria) / 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 HB8 (bacteria) / 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 HB8 (bacteria) / References: GenBank: 55771382#53: RNA chain | Mass: 7804.735 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthesized 24-nt M-F-Stop mRNA / Source: (synth.) Enterobacteria phage T4 (virus)#54: RNA chain | Mass: 24645.881 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Phenylalanine tRNA / Source: (gene. exp.) ![]() ![]() #55: RNA chain | Mass: 24846.902 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Initiator Methionine tRNA / 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) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80371 #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: P80372 #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: P80373 #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: Q5SHQ5 #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: Q5SLP8 #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: P17291 #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: P0DOY9 #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: Q5SHN7 #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: P80376 #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: Q5SHN3 #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: P80377 #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: P0DOY6 #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: Q5SJ76 #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: Q5SJH3 #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: Q5SLQ0 #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: Q5SHP2 #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: Q5SIH3 |
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-Non-polymers , 6 types, 7960 molecules 










| #56: Chemical | ChemComp-MG / #57: Chemical | #58: Chemical | #59: Chemical | ChemComp-ZN / #60: Chemical | #61: Water | ChemComp-HOH / | |
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-Details
| Has protein modification | Y |
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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: 2.93 Å3/Da / Density % sol: 58.02 % / 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: Mar 26, 2016 / 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→255.767 Å / Num. obs: 1561494 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.408 % / Biso Wilson estimate: 52.18 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.142 / Rrim(I) all: 0.168 / Χ2: 1.005 / Net I/σ(I): 8.22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Reflection shell | Diffraction-ID: 1
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: 4Y4P Resolution: 2.703→255.767 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.53
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| Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso max: 133.22 Å2 / Biso mean: 59.2544 Å2 / Biso min: 8.28 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: final / Resolution: 2.703→255.767 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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About Yorodumi




Thermus thermophilus HB8 (bacteria)
Enterobacteria phage T4 (virus)
X-RAY DIFFRACTION
United States,
Saudi Arabia, 6items
Citation





















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