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Yorodumi- PDB-4w29: 70S ribosome translocation intermediate containing elongation fac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4w29 | |||||||||
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Title | 70S ribosome translocation intermediate containing elongation factor EFG/GDP/fusidic acid, mRNA, and tRNAs trapped in the AP/AP pe/E chimeric hybrid state. | |||||||||
Components |
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Keywords | RIBOSOME/Antibiotic / Chimeric hybrid state ribosome / translocation intermediate / EF-G / mRNA / tRNA / ribosome-antibiotic complex | |||||||||
Function / homology | Function and homology information translation elongation factor activity / large ribosomal subunit rRNA binding / large ribosomal subunit / regulation of translation / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome ...translation elongation factor activity / large ribosomal subunit rRNA binding / 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 / GTPase activity / GTP binding / zinc ion binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Thermus thermophilus (bacteria) Thermus thermophilus HB27 (bacteria) Escherichia coli (E. coli) Escherichia coli str. K-12 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å | |||||||||
Authors | Zhou, J. / Lancaster, L. / Donohue, J.P. / Noller, H.F. | |||||||||
Citation | Journal: Science / Year: 2014 Title: How the ribosome hands the A-site tRNA to the P site during EF-G-catalyzed translocation. Authors: Zhou, J. / Lancaster, L. / Donohue, J.P. / Noller, H.F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4w29.cif.gz | 7.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4w29.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4w29.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w2/4w29 ftp://data.pdbj.org/pub/pdb/validation_reports/w2/4w29 | HTTPS FTP |
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-Related structure data
Related structure data | 3f1e 3f1f S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-30S ribosomal protein ... , 19 types, 38 molecules ABCBACCCADCDAECEAFCFAGCGAHCHAICIAJCJAKCKALCLAMCMANCNAOCOAPCP...
#1: Protein | Mass: 27116.385 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: P62662 #2: Protein | Mass: 22975.588 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: P62663 #3: Protein | Mass: 24242.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: P62664 #4: Protein | Mass: 16460.193 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: P62665 #5: Protein | Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: P62666 #6: Protein | Mass: 17919.775 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: P62667 #7: Protein | Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: P62668 #8: Protein | Mass: 14279.419 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 #9: Protein | Mass: 11398.308 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: P62653 #10: Protein | Mass: 12606.369 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: P62654 #11: Protein | Mass: 13875.388 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: P61941 #12: Protein | Mass: 14207.666 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: P62655 #13: Protein | Mass: 7027.529 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: P62656 #14: Protein | Mass: 10447.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: P62657 #15: Protein | Mass: 9995.546 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: P62238 #16: Protein | Mass: 11880.098 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 #17: Protein | Mass: 8155.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: P62659 #18: Protein | Mass: 9006.486 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: P62660 #19: Protein | Mass: 10921.086 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 |
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-Protein , 1 types, 2 molecules AYCY
#20: Protein | Mass: 76510.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: Q72I01 |
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-RNA chain , 6 types, 12 molecules AACAAWCWAVCVAXCXBADABBDB
#21: RNA chain | Mass: 490593.469 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: GenBank: 46197919 #22: RNA chain | Mass: 24728.689 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1151176235 #23: RNA chain | Mass: 11747.178 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: in-vitro transcription / Source: (synth.) Escherichia coli str. K-12 (bacteria) #24: RNA chain | Mass: 24608.742 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1154835240 #59: RNA chain | Mass: 936302.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: GenBank: 46197919 #60: RNA chain | Mass: 38553.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: GenBank: 46197919 |
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+50S ribosomal protein ... , 34 types, 70 molecules BCDCBDDDBEDEBFDFBGDGBHDHBJDJBKDKBNDNBODOBPDPBQDQBRDRBSDSBTDT...
-Non-polymers , 4 types, 12 molecules
#61: Chemical | #62: Chemical | #63: Chemical | ChemComp-NMY / #64: Chemical | |
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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: 4.01 Å3/Da / Density % sol: 69.3 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
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Detector | Date: Oct 12, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→357 Å / Num. obs: 482241 / Redundancy: 3.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3F1E, 3F1F Resolution: 3.8→49.98 Å / SU ML: 1.39 / Phase error: 43.35 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.8→49.98 Å
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Refine LS restraints |
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LS refinement shell |
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