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Yorodumi- PDB-4v4y: Crystal structure of the 70S Thermus thermophilus ribosome with t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v4y | |||||||||
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Title | Crystal structure of the 70S Thermus thermophilus ribosome with translocated and rotated Shine-Dalgarno Duplex. | |||||||||
Components |
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Keywords | RIBOSOME / SHINE-DALGARNO / POST-INITIATION | |||||||||
Function / homology | Function and homology information endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / large ribosomal subunit / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding ...endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / large ribosomal subunit / regulation of translation / 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 / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Thermus thermophilus (bacteria) Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.5 Å | |||||||||
Authors | Jenner, L. / Yusupova, G. / Rees, B. / Moras, D. / Yusupov, M. | |||||||||
Citation | Journal: Nature / Year: 2006 Title: Structural basis for messenger RNA movement on the ribosome. Authors: Yusupova, G. / Jenner, L. / Rees, B. / Moras, D. / Yusupov, M. | |||||||||
History |
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Remark 400 | COMPOUND THE COMPLETE ASYMMETRIC UNIT CONTAINS 30S AND 50S RIBOSOMAL SUBUNITS. THIS ENTRY 2HGP ...COMPOUND THE COMPLETE ASYMMETRIC UNIT CONTAINS 30S AND 50S RIBOSOMAL SUBUNITS. THIS ENTRY 2HGP CONTAINS 30S RIBOSOMAL SUBUNIT. THE 50S RIBOSOMAL SUBUNIT CAN BE FOUND IN PDB ENTRY 2HGQ. | |||||||||
Remark 999 | SEQUENCE THE TRNA SEQUENCES (MOL. B, C AND D) WERE TAKEN FROM SPRINZL : TRNA COMPILATION 2000 (HTTP: ...SEQUENCE THE TRNA SEQUENCES (MOL. B, C AND D) WERE TAKEN FROM SPRINZL : TRNA COMPILATION 2000 (HTTP://WWW.STAFF.UNI-BAYREUTH.DE/~BTC914/SEARCH/). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v4y.cif.gz | 3.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v4y.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v4y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/4v4y ftp://data.pdbj.org/pub/pdb/validation_reports/v4/4v4y | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-RNA chain , 5 types, 7 molecules AAA1ACADABBABB
#1: RNA chain | Mass: 493958.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: 155076 | ||||
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#2: RNA chain | Mass: 15565.702 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: solid-phase system (Dharmacon, Inc., Boulder, CO) | ||||
#3: RNA chain | Mass: 24485.539 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) #24: RNA chain | | Mass: 948280.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: 48268 #25: RNA chain | | Mass: 39846.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: 48271 |
-30S ribosomal protein ... , 20 types, 20 molecules AEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAX
#4: Protein | Mass: 29317.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80371 |
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#5: Protein | Mass: 26751.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80372 |
#6: Protein | Mass: 24373.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80373 |
#7: Protein | Mass: 17583.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P27152, UniProt: Q5SHQ5*PLUS |
#8: Protein | Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P23370, UniProt: Q5SLP8*PLUS |
#9: Protein | Mass: 18050.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P17291 |
#10: Protein | Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P24319, UniProt: P0DOY9*PLUS |
#11: Protein | Mass: 14410.614 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80374 |
#12: Protein | Mass: 11954.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80375, UniProt: Q5SHN7*PLUS |
#13: Protein | Mass: 13737.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80376 |
#14: Protein | Mass: 14637.384 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P17293, UniProt: Q5SHN3*PLUS |
#15: Protein | Mass: 14338.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80377 |
#16: Protein | Mass: 7158.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P24320, UniProt: P0DOY6*PLUS |
#17: Protein | Mass: 10578.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80378, UniProt: Q5SJ76*PLUS |
#18: Protein | Mass: 10409.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SJH3 |
#19: Protein | Mass: 12324.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P24321 |
#20: Protein | Mass: 10244.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80382 |
#21: Protein | Mass: 10605.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80381, UniProt: Q5SHP2*PLUS |
#22: Protein | Mass: 11736.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80380 |
#23: Protein/peptide | Mass: 3350.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P62612, UniProt: Q5SIH3*PLUS |
+50S ribosomal protein ... , 29 types, 29 molecules BCBDBEBFBGBHBKBLBMBNBOBPBQBRBSBTBUBVBWBXBYB1B2B3B4B5B6B7B8
-Protein , 1 types, 1 molecules BZ
#47: Protein | Mass: 9529.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60493 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 5.9 Å3/Da / Density % sol: 87.1 % | ||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98016 Å |
Detector | Type: MAR CCD 225 mm / Detector: CCD / Date: Nov 27, 2005 / Details: DYNAMICALLY BENDABLE MIRROR |
Radiation | Monochromator: Si (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98016 Å / Relative weight: 1 |
Reflection | Resolution: 5.5→300 Å / Num. all: 170516 / Num. obs: 169350 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.102 / Χ2: 1.086 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 5.5→5.59 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 8395 / Χ2: 1.142 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 5.5→300 Å / FOM work R set: 0.749 / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS / Bsol: 152 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 226.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 5.5→300 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50
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Xplor file |
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