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Yorodumi- PDB-1ibk: STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT IN CO... -
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-Basic information
Entry | Database: PDB / ID: 1ibk | ||||||
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Title | STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT IN COMPLEX WITH THE ANTIBIOTIC PAROMOMYCIN | ||||||
Components |
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Keywords | RIBOSOME / 30S RIBOSOMAL SUBUNIT / ANTIBIOTIC / PAROMOMYCIN / AMINOGLYCOSIDE / DECODING | ||||||
Function / homology | Function and homology information endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome ...endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 3.31 Å | ||||||
Authors | Ogle, J.M. / Brodersen, D.E. / Clemons Jr., W.M. / Tarry, M.J. / Carter, A.P. / Ramakrishnan, V. | ||||||
Citation | 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. #1: 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. #2: 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 | 1ibk.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1ibk.ent.gz | 934.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ibk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ibk_validation.pdf.gz | 1019.8 KB | Display | wwPDB validaton report |
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Full document | 1ibk_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 1ibk_validation.xml.gz | 162.8 KB | Display | |
Data in CIF | 1ibk_validation.cif.gz | 229.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/1ibk ftp://data.pdbj.org/pub/pdb/validation_reports/ib/1ibk | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-RNA chain , 2 types, 2 molecules AX
#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: 1790.069 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
#3: Protein | Mass: 29317.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: EMBL: 13446664, UniProt: P80371*PLUS |
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#4: Protein | Mass: 26751.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: EMBL: 13446666, UniProt: P80372*PLUS |
#5: Protein | Mass: 24373.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80373 |
#6: Protein | Mass: 17583.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P27152, UniProt: Q5SHQ5*PLUS |
#7: 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 |
#8: Protein | Mass: 18050.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P17291 |
#9: 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 |
#10: Protein | Mass: 14429.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: EMBL: 13446668, UniProt: P80374*PLUS |
#11: Protein | Mass: 11954.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80375, UniProt: Q5SHN7*PLUS |
#12: 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 |
#13: 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 |
#14: 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 |
#15: Protein | Mass: 7158.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P24320, UniProt: P0DOY6*PLUS |
#16: Protein | Mass: 10578.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80378, UniProt: Q5SJ76*PLUS |
#17: Protein | Mass: 10409.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 12056104, UniProt: Q5SJH3*PLUS |
#18: Protein | Mass: 12324.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: EMBL: 673503, UniProt: P0DOY7*PLUS |
#19: Protein | Mass: 10244.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 6739549, UniProt: Q5SLQ0*PLUS |
#20: Protein | Mass: 10605.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80381, UniProt: Q5SHP2*PLUS |
#21: Protein | Mass: 11736.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 11125386, UniProt: P80380*PLUS |
#22: 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, 116 molecules
#23: Chemical | ChemComp-PAR / | ||
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#24: Chemical | ChemComp-MG / #25: Chemical | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 12 |
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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, AMMONIUM CHLORIDE, POTASSIUM CHLORIDE, MAGNESIUM ACETATE, SODIUM CACODYLATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 277K, pH 6.50 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 Details: Wimberly, B.T., (2000) Nature, 407, 327.,Trakhanov, S.D., (1987) FEBS Lett., 220, 319. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: APS / Beamline: 19-ID / Wavelength: 0.99187 / Wavelength: 0.99187 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Feb 24, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99187 Å / Relative weight: 1 |
Reflection | Resolution: 3.31→316.23 Å / Num. obs: 207340 / % possible obs: 97.8 % / Redundancy: 5.21 % / Biso Wilson estimate: 70.09 Å2 / Rsym value: 0.16 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 3.31→3.43 Å / Redundancy: 4.41 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.664 / % possible all: 98 |
Reflection | *PLUS Num. measured all: 1079968 / Rmerge(I) obs: 0.16 |
Reflection shell | *PLUS % possible obs: 98 % / Rmerge(I) obs: 0.664 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER / Resolution: 3.31→316.23 Å / Cross valid method: THROUGHOUT Stereochemistry target values: PROTEINS: ENGH & HUBER, RNA: PARKINSON AT AL.
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Solvent computation | Bsol: 300 Å2 / ksol: 0.354 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.56 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.31→316.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.31→3.43 Å / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5.03 % / Rfactor obs: 0.229 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.368 / Rfactor Rwork: 0.31 |