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Open data
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Basic information
Entry | Database: PDB / ID: 5dfe | |||||||||
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Title | 70S termination complex containing E. coli RF2 | |||||||||
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![]() | RIBOSOME / PROTEIN BIOSYNTHESIS / RIBOSOMES / RNA / tRNA / TRANSFER RNA / 30S / 50S / 70S / 16S / 23S / RIBOSOMAL SUBUNIT / RF2 / RELEASE FACTOR 2 / PEPTIDE CHAIN TERMINATION / RELEASE FACTOR / BACTERIAL PROTEINS / CODON / MOLECULAR PEPTIDE CHAIN TERMINATION / TRANSLATIONAL | |||||||||
Function / homology | ![]() translation release factor activity, codon specific / translational termination / large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit ...translation release factor activity, codon specific / translational termination / large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / viral translational frameshifting / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Hoffer, E.D. / Dunham, C.M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Uniformity of Peptide Release Is Maintained by Methylation of Release Factors. Authors: Pierson, W.E. / Hoffer, E.D. / Keedy, H.E. / Simms, C.L. / Dunham, C.M. / Zaher, H.S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 16.2 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5czpC ![]() 5j30C ![]() 5j3cC ![]() 4y4oS C: citing same article ( 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 , 5 types, 10 molecules QVXVQXXXYARAYBRBXAQA
#1: RNA chain | Mass: 24802.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: RNA chain | Mass: 8196.021 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA oligonucleotide / Source: (synth.) synthetic construct (others) #4: RNA chain | Mass: 948035.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #5: RNA chain | Mass: 39494.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #35: RNA chain | Mass: 493864.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Protein , 1 types, 2 molecules QYXY
#3: Protein | Mass: 42991.402 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: prfB, supK, b2891, JW5847 / Plasmid: pETDUET / Production host: ![]() ![]() |
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+50S ribosomal protein ... , 29 types, 58 molecules YDRDYEREYFRFYGRGYHRHYIRIYNRNYOROYPRPYQRQYRRRYSRSYTRTYURUYVRV...
-30S ribosomal protein ... , 20 types, 40 molecules XBQBXCQCXDQDXEQEXFQFXGQGXHQHXIQIXJQJXKQKXLQLXMQMXNQNXOQOXPQP...
#36: Protein | Mass: 29317.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80371 #37: Protein | Mass: 26751.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80372 #38: Protein | Mass: 24373.447 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80373 #39: Protein | Mass: 17583.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ5 #40: Protein | Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLP8 #41: Protein | Mass: 18050.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P17291 #42: Protein | Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ2, UniProt: A0A0M9AFS9*PLUS #43: Protein | Mass: 14410.614 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80374 #44: Protein | Mass: 11954.968 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN7 #45: Protein | Mass: 13737.868 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80376 #46: Protein | Mass: 14683.476 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN3 #47: Protein | Mass: 14338.861 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80377 #48: Protein | Mass: 7158.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ1, UniProt: A0A0N0BLP2*PLUS #49: Protein | Mass: 10578.407 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJ76 #50: Protein | Mass: 10409.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJH3 #51: Protein | Mass: 12325.655 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP7, UniProt: A0A0N0BLS5*PLUS #52: Protein | Mass: 10258.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLQ0 #53: Protein | Mass: 10605.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP2 #54: Protein | Mass: 11736.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80380 #55: Protein/peptide | Mass: 3350.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SIH3 |
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-Non-polymers , 3 types, 2527 molecules 




#56: Chemical | ChemComp-MG / #57: Chemical | ChemComp-ZN / #58: Chemical | |
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-Details
Has protein modification | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal |
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Crystal grow |
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Kohzu HLD8-24 monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.09997551079→49.9 Å / Num. obs: 1057161 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 12.7 % / Biso Wilson estimate: 65.1513074296 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.269 / Net I/av σ(I): 8.98 / Net I/σ(I): 8.98 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4Y4O Resolution: 3.09997551079→49.8846320819 Å / SU ML: 0.35301417503 / Cross valid method: FREE R-VALUE / σ(F): 1.36291542291 / Phase error: 20.0734461834
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 77.0700635802 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.09997551079→49.8846320819 Å
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Refine LS restraints |
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LS refinement shell |
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