+Open data
-Basic information
Entry | Database: PDB / ID: 4v6a | |||||||||
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Title | Structure of EF-P bound to the 70S ribosome. | |||||||||
Components |
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Keywords | RIBOSOME / translation / elongation factor / initiation / L1-stalk | |||||||||
Function / homology | Function and homology information translation elongation factor activity / large ribosomal subunit / regulation of translation / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome ...translation elongation factor activity / large ribosomal subunit / regulation of translation / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Thermus thermophilus HB8 (bacteria) Escherichia coli (E. coli) Thermus thermophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å | |||||||||
Authors | Stanley, R.E. / Blaha, G. | |||||||||
Citation | Journal: Science / Year: 2009 Title: Formation of the first peptide bond: the structure of EF-P bound to the 70S ribosome. Authors: Blaha, G. / Stanley, R.E. / Steitz, T.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v6a.cif.gz | 7.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v6a.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v6a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v6/4v6a ftp://data.pdbj.org/pub/pdb/validation_reports/v6/4v6a | HTTPS FTP |
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-Related structure data
Related structure data | 2j00 2j01 S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-RNA chain , 5 types, 10 molecules AACAAWCWAXCXBADABBDB
#1: RNA chain | Mass: 489961.031 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: 55771382 #23: RNA chain | Mass: 24802.785 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: metY / Plasmid: plppMet / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: GenBank: 253976232 #24: RNA chain | Mass: 1594.032 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemical synthesis #25: RNA chain | Mass: 947895.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: 55771382 #26: RNA chain | Mass: 39494.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: 55771382 |
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-30S ribosomal protein ... , 20 types, 40 molecules ABCBACCCADCDAECEAFCFAGCGAHCHAICIAJCJAKCKALCLAMCMANCNAOCOAPCP...
#2: Protein | Mass: 29317.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80371 #3: Protein | Mass: 26751.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80372 #4: Protein | Mass: 24373.447 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80373 #5: Protein | Mass: 17583.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ5 #6: Protein | Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SLP8 #7: Protein | Mass: 18050.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P17291 #8: Protein | Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ2, UniProt: A0A0M9AFS9*PLUS #9: Protein | Mass: 14410.614 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80374 #10: Protein | Mass: 11954.968 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHN7 #11: Protein | Mass: 13737.868 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80376 #12: Protein | Mass: 14637.384 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHN3 #13: Protein | Mass: 14338.861 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80377 #14: Protein | Mass: 7158.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ1, UniProt: A0A0N0BLP2*PLUS #15: Protein | Mass: 10578.407 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SJ76 #16: Protein | Mass: 10409.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SJH3 #17: Protein | Mass: 12325.655 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP7, UniProt: A0A0N0BLS5*PLUS #18: Protein | Mass: 10258.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SLQ0 #19: Protein | Mass: 10605.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP2 #20: Protein | Mass: 11736.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80380 #21: Protein/peptide | Mass: 3350.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SIH3 |
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-Protein , 1 types, 2 molecules AVCV
#22: Protein | Mass: 20247.010 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: AT-62 / Gene: efp, TTHA1125 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(AI) / References: UniProt: Q76G20 |
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+50S ribosomal protein ... , 30 types, 60 molecules BCDCBDDDBEDEBFDFBGDGBHDHBIDIBNDNBODOBPDPBQDQBRDRBSDSBTDTBUDU...
-Non-polymers , 2 types, 1056 molecules
#57: Chemical | ChemComp-MG / #58: Chemical | ChemComp-ZN / |
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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: 3.26 Å3/Da / Density % sol: 62.28 % |
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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 pH 7.6, 2.5 % Peg 20K, 7-12% MPD, 0.5 mM BME, vapor diffusion, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2008 |
Radiation | Monochromator: Kohzu HLD8-24 monochromator / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Highest resolution: 3.1 Å / Num. obs: 989777 / % possible obs: 92.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 71.4 Å2 / Rmerge(I) obs: 0.258 |
Reflection shell | Resolution: 3.1→3.18 Å / Rmerge(I) obs: 0.012 / Mean I/σ(I) obs: 0.8 / Num. measured obs: 93519 / Num. unique all: 1048227 / Num. unique obs: 38341 / % possible all: 49.6 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entries: 2j00, 2j01 Highest resolution: 3.1 Å / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.752 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber / Details: weighted least square procedure
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Displacement parameters | Biso max: 205.18 Å2 / Biso mean: 71.935 Å2 / Biso min: 6.18 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 3.1 Å
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Refine LS restraints |
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