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Yorodumi- PDB-2e5l: A snapshot of the 30S ribosomal subunit capturing mRNA via the Sh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2e5l | ||||||
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Title | A snapshot of the 30S ribosomal subunit capturing mRNA via the Shine- Dalgarno interaction | ||||||
Components |
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Keywords | RIBOSOME / 30S ribosomal subunit / mRNA capture / Shine-Dalgarno interaction / 5' untranslated region / translation initiation / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 Å | ||||||
Authors | Kaminishi, T. / Wilson, D.N. / Takemoto, C. / Harms, J.M. / Kawazoe, M. / Schluenzen, F. / Hanawa-Suetsugu, K. / Shirouzu, M. / Fucini, P. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Structure / Year: 2007 Title: A snapshot of the 30S ribosomal subunit capturing mRNA via the Shine-Dalgarno interaction Authors: Kaminishi, T. / Wilson, D.N. / Takemoto, C. / Harms, J.M. / Kawazoe, M. / Schluenzen, F. / Hanawa-Suetsugu, K. / Shirouzu, M. / Fucini, P. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2e5l.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2e5l.ent.gz | 929.2 KB | Display | PDB format |
PDBx/mmJSON format | 2e5l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/2e5l ftp://data.pdbj.org/pub/pdb/validation_reports/e5/2e5l | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-RNA chain , 2 types, 3 molecules A12
#1: RNA chain | Mass: 493345.969 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: 1962.277 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-30S ribosomal protein ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTV
#3: Protein | Mass: 26256.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80371 |
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#4: Protein | Mass: 26619.881 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80372 |
#5: Protein | Mass: 24242.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80373 |
#6: Protein | Mass: 17452.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SHQ5 |
#7: Protein | Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SLP8 |
#8: Protein | Mass: 17919.775 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: Q5SHQ2, 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: UniProt: P62669, UniProt: P80374*PLUS |
#11: Protein | Mass: 11823.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SHN7 |
#12: Protein | Mass: 13606.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80376 |
#13: Protein | Mass: 14506.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SHN3 |
#14: Protein | Mass: 14207.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80377 |
#15: Protein | Mass: 7027.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SHQ1, UniProt: P0DOY6*PLUS |
#16: Protein | Mass: 10447.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SJ76 |
#17: Protein | Mass: 10409.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SJH3 |
#18: 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 |
#19: Protein | Mass: 10113.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80382, UniProt: Q5SLQ0*PLUS |
#20: Protein | Mass: 10474.269 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SHP2 |
#21: Protein | Mass: 11590.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P62661, 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: Q5SIH3 |
-Non-polymers , 1 types, 2 molecules
#23: Chemical |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 6 |
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-Sample preparation
Crystal | Density Matthews: 4.8 Å3/Da / Density % sol: 74.2 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 10mM HEPES-KOH, 10mM MgCl2, 60mM NH4Cl, 6mM beta-mercaptoethanol, 11-12% MPD, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9801 Å |
Detector | Type: MAR CCD 225 mm / Detector: CCD / Date: Oct 1, 2005 / Details: Dynamically bendable mirror |
Radiation | Monochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→148.83 Å / Num. all: 221305 / Num. obs: 214963 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 87.687 Å2 / Rmerge(I) obs: 0.162 / Net I/σ(I): 7.48 |
Reflection shell | Resolution: 3.3→3.48 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.755 / Mean I/σ(I) obs: 2.5 / Num. measured obs: 190787 / Num. unique all: 30666 / % possible all: 95.2 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→148.83 Å / Rfactor Rfree error: 0.003 / FOM work R set: 0.718 / Data cutoff high absF: 27049244 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 104.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.3→148.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.42 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 10
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Xplor file |
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