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Yorodumi- PDB-4v83: Crystal structure of a complex containing domain 3 from the PSIV ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v83 | |||||||||
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Title | Crystal structure of a complex containing domain 3 from the PSIV IGR IRES RNA bound to the 70S ribosome. | |||||||||
Components |
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Keywords | RIBOSOME / 70S / IGR / IRES / PSIV / CrPV | |||||||||
Function / homology | Function and homology information large ribosomal subunit rRNA binding / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation ...large ribosomal subunit rRNA binding / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Thermus thermophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | |||||||||
Authors | Zhu, J. / Korostelev, A. / Costantino, D. / Noller, H.F. / Kieft, J.S. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Crystal structures of complexes containing domains from two viral internal ribosome entry site (IRES) RNAs bound to the 70S ribosome. Authors: Zhu, J. / Korostelev, A. / Costantino, D.A. / Donohue, J.P. / Noller, H.F. / Kieft, J.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v83.cif.gz | 7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v83.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v83.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/4v83 ftp://data.pdbj.org/pub/pdb/validation_reports/v8/4v83 | HTTPS FTP |
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-Related 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
-RNA chain , 4 types, 8 molecules AACAAVCVBADABBDB
#1: RNA chain | Mass: 489042.562 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: GenBank: AE017221.1 #22: RNA chain | Mass: 11183.638 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 #23: RNA chain | Mass: 936302.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: GenBank: AE017221.1 #24: RNA chain | Mass: 38553.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: GenBank: AE017221.1 |
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-30S ribosomal protein ... , 20 types, 40 molecules ABCBACCCADCDAECEAFCFAGCGAHCHAICIAJCJAKCKALCLAMCMANCNAOCOAPCP...
#2: Protein | Mass: 26987.271 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62662 #3: Protein | Mass: 22862.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62663 #4: Protein | Mass: 24242.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62664 #5: Protein | Mass: 16460.193 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62665 #6: Protein | Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62666 #7: Protein | Mass: 17919.775 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62667 #8: Protein | Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62668 #9: Protein | Mass: 14298.466 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62669 #10: Protein | Mass: 11299.176 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62653 #11: Protein | Mass: 12606.369 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62654 #12: Protein | Mass: 13804.311 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P61941 #13: Protein | Mass: 13237.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62655 #14: Protein | Mass: 7027.529 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62656 #15: Protein | Mass: 10447.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62657 #16: Protein | Mass: 9924.469 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62238 #17: Protein | Mass: 11721.919 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62658 #18: Protein | Mass: 8155.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62659 #19: Protein | Mass: 8949.435 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62660 #20: Protein | Mass: 10907.060 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62661 #21: Protein/peptide | Mass: 2960.475 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62613 |
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+50S ribosomal protein ... , 29 types, 58 molecules BCDCBDDDBEDEBFDFBGDGBHDHBIDIBJDJBKDKBLDLBMDMBNDNBODOBPDPBQDQ...
-Non-polymers , 2 types, 2661 molecules
#54: Chemical | ChemComp-MG / #55: 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: 3.51 Å3/Da / Density % sol: 64.97 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 7 Details: 100 mM Tris-OAc, pH 7.0, 200 mM KSCN, 3.6-5% PEG20,000, 6-14% MPD, vapor diffusion, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 30, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→60 Å / Num. obs: 743704 / Biso Wilson estimate: 106.18 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→49.999 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.46 / σ(F): 1.33 / Phase error: 25.18 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.895 Å2 / ksol: 0.219 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 428.94 Å2 / Biso mean: 149.8145 Å2 / Biso min: 32.26 Å2
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Refinement step | Cycle: LAST / Resolution: 3.5→49.999 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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