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Yorodumi- PDB-4v8n: The crystal structure of agmatidine tRNA-Ile2 bound to the 70S ri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v8n | |||||||||
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Title | The crystal structure of agmatidine tRNA-Ile2 bound to the 70S ribosome in the A and P site. | |||||||||
Components |
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Keywords | RIBOSOME / AGMATIDINE / TRNA / TRNAILE2 | |||||||||
Function / homology | Function and homology information 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 ...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 / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | THERMUS THERMOPHILUS (bacteria) HALOARCULA MARISMORTUI (Halophile) ESCHERICHIA COLI (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | |||||||||
Authors | Voorhees, R.M. / Mandal, D. / Neubauer, C. / Koehrer, C. / RajBhandary, U.L. / Ramakrishnan, V. | |||||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2013 Title: The Structural Basis for Specific Decoding of Aua by Isoleucine tRNA on the Ribosome Authors: Voorhees, R.M. / Mandal, D. / Neubauer, C. / Koehrer, C. / Rajbhandary, U.L. / Ramakrishnan, V. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "QA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "QA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v8n.cif.gz | 7.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v8n.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v8n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v8n_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 4v8n_full_validation.pdf.gz | 3.8 MB | Display | |
Data in XML | 4v8n_validation.xml.gz | 887.8 KB | Display | |
Data in CIF | 4v8n_validation.cif.gz | 1.2 MB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/4v8n ftp://data.pdbj.org/pub/pdb/validation_reports/v8/4v8n | HTTPS FTP |
-Related structure data
Related structure data | 2j00 S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-RNA chain , 6 types, 14 molecules AACAAVAYCVCYAWCWAXCXBADABBDB
#1: RNA chain | Mass: 493958.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: CHAIN A (16S RNA) HAS E.COLI NUMBERING, BASED ON A STRUCTURAL ALIGNMENT WITH THE CORRESPONDING E. COLI STRUCTURE IN 2AVY. Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: GenBank: 55979969 #22: RNA chain | Mass: 25213.094 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) #23: RNA chain | Mass: 25096.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) #24: RNA chain | Mass: 7858.840 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI (E. coli) #35: RNA chain | Mass: 947935.438 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: CHAIN A (23S RNA) HAS E.COLI RESIDUE NUMBERING, BASED ON A STRUCTURAL ALIGNMENT WITH THE CORRESPONDING E. COLI STRUCTURE IN 2AW4 Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: GenBank: 55979969 #36: RNA chain | Mass: 39540.617 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: GenBank: 55979969 |
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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 - MRC - MSAW1 / 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 - MRC - MSAW1 / 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 - MRC - MSAW1 / 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 - MRC - MSAW1 / 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 - MRC - MSAW1 / 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 - MRC - MSAW1 / 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 - MRC - MSAW1 / 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 - MRC - MSAW1 / 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 - MRC - MSAW1 / 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 - MRC - MSAW1 / References: UniProt: P80376 #12: Protein | Mass: 14920.754 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / 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 - MRC - MSAW1 / 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 - MRC - MSAW1 / 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 - MRC - MSAW1 / 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 - MRC - MSAW1 / 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 - MRC - MSAW1 / 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 - MRC - MSAW1 / 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 - MRC - MSAW1 / 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 - MRC - MSAW1 / 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 - MRC - MSAW1 / References: UniProt: Q5SIH3 |
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+50S RIBOSOMAL PROTEIN ... , 31 types, 62 molecules B0D0B1D1B2D2B3D3B4D4B5D5B6D6B7D7B8D8B9D9BCDCBDDDBEDEBFDFBGDG...
-Non-polymers , 1 types, 4 molecules
#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: 62.26 % / Description: NONE |
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Crystal grow | pH: 7.1 Details: 0.1 M TRIS-ACETATE PH 7, 0.2 M KSCN, 3.5-5.5% (W/V) PEG 20K, AND 3.5-5.5% (W/V) PEG 550 MONOMETHYL ETHER |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9771 |
Detector | Type: ADSC / Detector: CCD / Date: Nov 2, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9771 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 1046021 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 57.8 Å2 / Rmerge(I) obs: 0.02 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 3.1→3.2 Å / Redundancy: 2.3 % / Rmerge(I) obs: 1.2 / Mean I/σ(I) obs: 1.1 / % possible all: 76.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2J00 2j00 Resolution: 3.1→50 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT / Bsol: 33.5293 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 101.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.1→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.29 Å / Rfactor Rfree error: 0.004 / Total num. of bins used: 6
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Xplor file |
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