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Yorodumi- PDB-1n32: Structure of the Thermus thermophilus 30S ribosomal subunit bound... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n32 | ||||||
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Title | Structure of the Thermus thermophilus 30S ribosomal subunit bound to codon and near-cognate transfer RNA anticodon stem-loop mismatched at the first codon position at the a site with paromomycin | ||||||
Components |
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Keywords | RIBOSOME / 30S RIBOSOMAL SUBUNIT / A SITE / DECODING / NEAR-COGNATE / MISMATCH / WOBBLE / GU / G:U / TRANSFER RNA / TRNA / ANTICODON / STEM-LOOP / MESSENGER RNA / MRNA / CODON / ANTIBIOTIC / PAROMOMYCIN | ||||||
Function / homology | Function and homology information small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / zinc ion binding ...small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / zinc ion binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 3 Å | ||||||
Authors | Ogle, J.M. / Murphy IV, F.V. / Tarry, M.J. / Ramakrishnan, V. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2002 Title: Selection of tRNA by the Ribosome Requires a Transition from an Open to a Closed Form Authors: Ogle, J.M. / Murphy IV, F.V. / Tarry, M.J. / Ramakrishnan, V. #1: Journal: Science / Year: 2001 Title: Recognition of Cognate Transfer RNA by the 30S Ribosomal Subunit Authors: Ogle, J.M. / Brodersen, D.E. / Clemons Jr., W.M. / Tarry, M.J. / Carter, A.P. / Ramakrishnan, V. #2: Journal: Nature / Year: 2000 Title: Structure of the 30S Ribosomal Subunit Authors: Wimberly, B.T. / Brodersen, D.E. / Clemons Jr., W.M. / Morgan-Warren, R. / Carter, A.P. / Vonrhein, C. / Hartsch, T. / Ramakrishnan, V. #3: Journal: Nature / Year: 2000 Title: Functional Insights from the Structure of the 30S Ribosomal Subunit and its Interactions with Antibiotics Authors: Carter, A.P. / Clemons Jr., W.M. / Brodersen, D.E. / Wimberly, B.T. / Morgan-Warren, R. / Ramakrishnan, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n32.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1n32.ent.gz | 965.2 KB | Display | PDB format |
PDBx/mmJSON format | 1n32.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n3/1n32 ftp://data.pdbj.org/pub/pdb/validation_reports/n3/1n32 | HTTPS FTP |
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-Related structure data
Related structure data | 1n33C 1n34C 1n36C 1j5eS 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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1 |
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Unit cell |
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-Components
-RNA chain , 3 types, 3 molecules AYZ
#1: RNA chain | Mass: 493958.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 155076 |
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#2: RNA chain | Mass: 5460.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) |
#3: RNA chain | Mass: 1792.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) |
-30S RIBOSOMAL PROTEIN ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTV
#4: Protein | Mass: 29317.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 13446664, UniProt: P80371*PLUS |
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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) / References: GenBank: 13446666, UniProt: P80372*PLUS |
#6: Protein | Mass: 24242.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80373 |
#7: Protein | Mass: 17452.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / 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) / References: UniProt: P23370, UniProt: Q5SLP8*PLUS |
#9: Protein | Mass: 17919.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / 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) / References: UniProt: P24319, UniProt: P0DOY9*PLUS |
#11: Protein | Mass: 14429.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 13446668, UniProt: P80374*PLUS |
#12: Protein | Mass: 11823.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / 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) / References: GenBank: 4519421, UniProt: P80376*PLUS |
#14: Protein | Mass: 14920.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / 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) / References: GenBank: 4519420, UniProt: P80377*PLUS |
#16: Protein | Mass: 7027.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P24320, UniProt: P0DOY6*PLUS |
#17: Protein | Mass: 10447.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / 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) / References: UniProt: P80379, UniProt: Q5SJH3*PLUS |
#19: Protein | Mass: 12193.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P24321, UniProt: P0DOY7*PLUS |
#20: Protein | Mass: 10244.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: EMBL: 6739549, UniProt: Q5SLQ0*PLUS |
#21: Protein | Mass: 10474.269 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / 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) / References: EMBL: 11125386, UniProt: P80380*PLUS |
#23: Protein/peptide | Mass: 3218.835 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P32193, UniProt: Q5SIH3*PLUS |
-Non-polymers , 3 types, 161 molecules
#24: Chemical | ChemComp-PAR / | ||
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#25: Chemical | ChemComp-MG / #26: Chemical | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 10 |
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-Sample preparation
Crystal | Density Matthews: 4.17 Å3/Da / Density % sol: 70.5 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: MPD, NH4Cl, KCl, CaCl2, magnesium acetate, potassium-MES, sodium cacodylate, PH 6.5, VAPOR DIFFUSION, HANGING DROP AT 277K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Details: Clemons, W.M., (2001) J. Mol. Biol., 310, 827. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9797 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 5, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→141.42 Å / Num. obs: 272610 / % possible obs: 95.5 % / Redundancy: 3.52 % / Biso Wilson estimate: 75.175 Å2 / Rsym value: 0.128 / Net I/σ(I): 7 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 2.91 % / Mean I/σ(I) obs: 2 / Rsym value: 0.564 / % possible all: 80.1 |
Reflection | *PLUS Highest resolution: 3 Å / Lowest resolution: 500 Å / Num. measured all: 918025 / Rmerge(I) obs: 0.128 |
Reflection shell | *PLUS % possible obs: 80.1 % / Rmerge(I) obs: 0.564 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: 1J5E WITHOUT IONS AND PORTIONS AROUND THE SITE Resolution: 3→141.42 Å / Cross valid method: THROUGHOUT Stereochemistry target values: PROTEINS: ENGH & HUBER, RNA: PARKINSON AT AL.
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Solvent computation | Bsol: 96.8 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.51 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→141.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.11 Å / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Rfactor Rfree: 0.27 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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