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Yorodumi- PDB-4wro: Complex of 70S ribosome with tRNA-Phe and mRNA with C-A mismatch ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wro | |||||||||
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Title | Complex of 70S ribosome with tRNA-Phe and mRNA with C-A mismatch in the second position in the A-site | |||||||||
Components |
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Keywords | RIBOSOME / translation / mismatch | |||||||||
Function / homology | Function and homology information large ribosomal subunit / ribosomal small subunit assembly / ribosomal large subunit assembly / small ribosomal subunit / transferase activity / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding ...large ribosomal subunit / ribosomal small subunit assembly / ribosomal large subunit assembly / small ribosomal subunit / transferase activity / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Thermus thermophilus HB8 (bacteria) Escherichia coli K-12 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å | |||||||||
Authors | Rozov, A. / Demeshkina, N. / Yusupov, M. / Yusupova, G. | |||||||||
Citation | Journal: Nat Commun / Year: 2015 Title: Structural insights into the translational infidelity mechanism. Authors: Rozov, A. / Demeshkina, N. / Westhof, E. / Yusupov, M. / Yusupova, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wro.cif.gz | 6.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4wro.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4wro.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wro_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4wro_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 4wro_validation.xml.gz | 429.4 KB | Display | |
Data in CIF | 4wro_validation.cif.gz | 668.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wr/4wro ftp://data.pdbj.org/pub/pdb/validation_reports/wr/4wro | HTTPS FTP |
-Related structure data
Related structure data | 4wq1C 4wqrC 4wr6C 4wraC 4wsdC 4wsmC 4wt1C 4wu1C 4wzdC 4wzoC 3tve 3tvf 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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2 |
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Unit cell |
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-Components
-RNA chain , 7 types, 14 molecules 131G1L3L3K2L2K4L4K141H1K1J16
#1: RNA chain | Mass: 493958.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 155076 #2: RNA chain | Mass: 24635.887 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) #3: RNA chain | Mass: 24849.951 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) #4: RNA chain | Mass: 9802.024 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus HB8 (bacteria) #5: RNA chain | Mass: 948539.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 48268 #26: RNA chain | | Mass: 24633.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) #27: RNA chain | Mass: 39540.617 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382 |
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-30S ribosomal protein ... , 20 types, 23 molecules 1E122E223E324E5E6E7E8E1I2I3I4I5I6I7I8I9IAIBI1F
#6: Protein | Mass: 29317.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80371 #7: Protein | Mass: 26751.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80372 #8: Protein | Mass: 24373.447 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80373 #9: Protein | | Mass: 17583.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHQ5 #10: Protein | | Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SLP8 #11: Protein | | Mass: 18050.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P17291 #12: Protein | | Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHQ2, UniProt: A0A0M9AFS9*PLUS #13: Protein | | Mass: 14410.614 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80374 #14: Protein | | Mass: 11954.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHN7 #15: Protein | | Mass: 13737.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80376 #16: Protein | | Mass: 14637.384 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHN3 #17: Protein | | Mass: 14352.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80377 #18: Protein | | Mass: 7158.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHQ1, UniProt: A0A0N0BLP2*PLUS #19: Protein | | Mass: 10578.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SJ76 #20: Protein | | Mass: 10409.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SJH3 #21: Protein | | Mass: 12325.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHP7, UniProt: A0A0N0BLS5*PLUS #22: Protein | | Mass: 10258.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SLQ0 #23: Protein | | Mass: 10605.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHP2 #24: Protein | | Mass: 11736.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80380 #25: Protein/peptide | | Mass: 3350.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SIH3 |
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+50S ribosomal protein ... , 28 types, 28 molecules 1121314151615868788898A8B8C8D8E8F8G8H8I8J8K8L8M8N8O8P8Q8
-Non-polymers , 3 types, 3797 molecules
#56: Chemical | ChemComp-MG / #57: Chemical | ChemComp-ZN / #58: Water | ChemComp-HOH / | |
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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: 3.73 Å3/Da / Density % sol: 66.99 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: Tris-acetate, KSCN, PEG 550MME, PEG 20K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.05→200 Å / Num. obs: 1092032 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 63.8 % / Biso Wilson estimate: 96.907 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.325 / Rrim(I) all: 0.327 / Χ2: 1.08 / Net I/σ(I): 14.16 / Num. measured all: 69639588 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TVF, 3TVE Resolution: 3.05→151.956 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 3.05→151.956 Å
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