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- PDB-4v5a: Structure of the Ribosome Recycling Factor bound to the Thermus t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4v5a | |||||||||
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Title | Structure of the Ribosome Recycling Factor bound to the Thermus thermophilus 70S ribosome with mRNA, ASL-Phe and tRNA-fMet | |||||||||
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![]() | RIBOSOME / RIBOSOMAL PROTEIN / RIBONUCLEOPROTEIN / TRNA-BINDING / RRNA-BINDING / METAL-BINDING / RRF / TRNA / MRNA / RECYCLING / PROTEIN BIOSYNTHESIS / RNA-BINDING / ZINC-FINGER / TRANSLATION | |||||||||
Function / homology | ![]() cytoplasmic translational termination / ribosomal large subunit binding / large ribosomal subunit / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding ...cytoplasmic translational termination / ribosomal large subunit binding / large ribosomal subunit / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Weixlbaumer, A. / Petry, S. / Dunham, C.M. / Selmer, M. / Kelley, A.C. / Ramakrishnan, V. | |||||||||
![]() | ![]() Title: Crystal structure of the ribosome recycling factor bound to the ribosome. Authors: Weixlbaumer, A. / Petry, S. / Dunham, C.M. / Selmer, M. / Kelley, A.C. / Ramakrishnan, V. | |||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 6.9 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 4.8 MB | Display | |
Data in XML | ![]() | 1 MB | Display | |
Data in CIF | ![]() | 1.4 MB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2j00 ![]() 2j01 ![]() 2j02 ![]() 2j03 S: Starting model for refinement |
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Similar structure data |
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Links
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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 , 6 types, 12 molecules AACAAVCVAWCWAXCXBADABBDB
#1: RNA chain | Mass: 493958.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: CHAIN A (16S RNA) HAS E.COLI NUMBERING, BASED ON A STRUCTURAL ALIGNMENT WITH THE CORRESPONDING E.COLI STRUCTURE IN 2AVY. Source: (natural) ![]() ![]() #22: RNA chain | Mass: 24485.539 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #23: RNA chain | Mass: 24816.811 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #24: RNA chain | Mass: 10087.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #35: RNA chain | Mass: 904824.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: CHAIN A (23S RNA) HAS E.COLI RESIDUE NUMBERING, BASED ON A STRUCTURAL ALIGNMENT WITH THE CORRESPONDING E. COLI STRUCTURE IN 2AW4 Source: (natural) ![]() ![]() #36: RNA chain | Mass: 39494.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-30S RIBOSOMAL PROTEIN ... , 20 types, 40 molecules ABCBACCCADCDAECEAFCFAGCGAHCHAICIAJCJAKCKALCLAMCMANCNAOCOAPCP...
#2: Protein | Mass: 29317.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 26751.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | Mass: 24373.447 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #5: Protein | Mass: 17583.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Protein | Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #7: Protein | Mass: 18050.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein | Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #9: Protein | Mass: 14429.661 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #10: Protein | Mass: 11954.968 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #11: Protein | Mass: 13737.868 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #12: Protein | Mass: 14920.754 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #13: Protein | Mass: 14338.861 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #14: Protein | Mass: 7158.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #15: Protein | Mass: 10578.407 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #16: Protein | Mass: 10409.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #17: Protein | Mass: 12325.655 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #18: Protein | Mass: 10258.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #19: Protein | Mass: 10605.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #20: Protein | Mass: 11736.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #21: Protein/peptide | Mass: 3350.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Protein , 1 types, 2 molecules AYCY
#25: Protein | Mass: 21029.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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+50S RIBOSOMAL PROTEIN ... , 29 types, 58 molecules B0D0B1D1B2D2B3D3B4D4B5D5B6D6B7D7B8D8BCDCBDDDBEDEBFDFBGDGBHDH...
-Non-polymers , 2 types, 1486 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/ZN.gif)
#57: Chemical | ChemComp-MG / #58: Chemical | ChemComp-ZN / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.65 % / Description: NONE |
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Crystal grow | pH: 7 / Details: COMPARE SELMER ET AL SCIENCE 2006, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC / Detector: CCD / Date: Nov 23, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97943 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. obs: 727953 / % possible obs: 96.7 % / Observed criterion σ(I): 1.6 / Redundancy: 6.2 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.3 / Net I/σ(I): 3.8 |
Reflection shell | Resolution: 3.5→3.7 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.6 / % possible all: 88.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 2J00, 2J01, 2J02, 2J03 Resolution: 3.5→20 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 19903003.23 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 2.47921 Å2 / ksol: 0.15 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 89.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.5→3.72 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
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Xplor file |
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