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Yorodumi- PDB-4v9j: 70S ribosome translocation intermediate GDPNP-II containing elong... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v9j | |||||||||
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Title | 70S ribosome translocation intermediate GDPNP-II containing elongation factor EFG/GDPNP, mRNA, and tRNA bound in the pe*/E state. | |||||||||
Components |
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Keywords | RIBOSOME/ANTIBIOTIC / GDPNP / chimeric hybrid state ribosome / translocation intermediate / EF-G / mRNA / tRNA / RIBOSOME-ANTIBIOTIC complex | |||||||||
Function / homology | Function and homology information ribosome disassembly / translation elongation factor activity / 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 ...ribosome disassembly / translation elongation factor activity / 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 / GTPase activity / mRNA binding / GTP binding / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Thermus thermophilus (bacteria) Escherichia coli (E. coli) Streptomyces (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.86 Å | |||||||||
Authors | Zhou, J. / Lancaster, L. / Donohue, J.P. / Noller, H.F. | |||||||||
Citation | Journal: Science / Year: 2013 Title: Crystal structures of EF-G-ribosome complexes trapped in intermediate states of translocation. Authors: Zhou, J. / Lancaster, L. / Donohue, J.P. / Noller, H.F. | |||||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED | |||||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v9j.cif.gz | 7.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v9j.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v9j_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 4v9j_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 4v9j_validation.xml.gz | 654.9 KB | Display | |
Data in CIF | 4v9j_validation.cif.gz | 967.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v9/4v9j ftp://data.pdbj.org/pub/pdb/validation_reports/v9/4v9j | HTTPS FTP |
-Related structure data
Related structure data | 4v9kC 4v9lC 4v9mC 2wri 2wrj 3f1e 3f1f 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
-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 (bacteria) / Strain: HB27 / References: UniProt: P62662 #2: Protein | Mass: 22975.588 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62663 #3: Protein | Mass: 24242.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62664 #4: Protein | Mass: 16460.193 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62665 #5: Protein | Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62666 #6: Protein | Mass: 17919.775 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62667 #7: Protein | Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62668 #8: Protein | Mass: 14298.466 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62669 #9: Protein | Mass: 11398.308 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62653 #10: Protein | Mass: 12606.369 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62654 #11: Protein | Mass: 13875.388 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P61941 #12: Protein | Mass: 14207.666 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62655 #13: Protein | Mass: 7027.529 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62656 #14: Protein | Mass: 10447.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62657 #15: Protein | Mass: 9995.546 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62238 #16: Protein | Mass: 11879.112 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62658 #17: Protein | Mass: 8155.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62659 #18: Protein | Mass: 9006.486 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62660 #19: Protein | Mass: 10907.060 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62661 |
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-RNA chain , 5 types, 10 molecules AACAAVCVAWCWBBDBBADA
#20: RNA chain | Mass: 490593.469 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 #21: RNA chain | Mass: 5907.628 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 #22: RNA chain | Mass: 24728.689 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) #59: RNA chain | Mass: 38553.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 #60: RNA chain | Mass: 936302.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 |
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+50S ribosomal protein ... , 34 types, 70 molecules BCDCBDDDBEDEBFDFBGDGBHDHBJDJBKDKBODOBPDPBQDQBRDRBSDSBTDTBUDU...
-Protein / Protein/peptide , 2 types, 4 molecules AYCYAUCU
#23: Protein | Mass: 76547.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72I01 #24: Protein/peptide | |
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-Non-polymers , 2 types, 4 molecules
#61: Chemical | #62: Chemical | |
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-Details
Sequence details | E. COLI NUMBERING IS USED FOR 5S, 16S, AND 23S RIBOSOMAL RNA. |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 5 |
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-Sample preparation
Crystal | Density Matthews: 4.04 Å3/Da / Density % sol: 69.54 % |
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Crystal grow | Details: 2.9% PEG20000, 2.8% PPG P400, 5.1% PEG550 MME, 200 mM potassium thiocyanate, Tris acetate |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 3.86→40 Å / Num. obs: 462446 / % possible obs: 96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.5 / Redundancy: 3.8 % / Rsym value: 0.336 / Net I/σ(I): 5.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 3F1E, 3F1F, 2WRI, AND 2WRJ Resolution: 3.86→40 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3.86→40 Å
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Refine LS restraints |
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