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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 | |||||||||
Components |
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Keywords | 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 | Function and homology informationtranslation 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 / small ribosomal subunit rRNA binding ...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 / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / viral translational frameshifting / mRNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
| Biological species | ![]() ![]() Thermus thermophilus HB8 (bacteria)![]() Thermus thermophilus (bacteria)synthetic construct (others) | |||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.09997551079 Å | |||||||||
Authors | Hoffer, E.D. / Dunham, C.M. | |||||||||
| Funding support | United States, 2items
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Citation | Journal: Cell Rep / Year: 2016Title: 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: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 5dfe.cif.gz | 16.2 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb5dfe.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 5dfe.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 5dfe_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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| Full document | 5dfe_full_validation.pdf.gz | 2.5 MB | Display | |
| Data in XML | 5dfe_validation.xml.gz | 725.9 KB | Display | |
| Data in CIF | 5dfe_validation.cif.gz | 1 MB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/5dfe ftp://data.pdbj.org/pub/pdb/validation_reports/df/5dfe | HTTPS FTP |
-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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| 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) ![]() Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382#5: RNA chain | Mass: 39494.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382#35: RNA chain | Mass: 493864.625 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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-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) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)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) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)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) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)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) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)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) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)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) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)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) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)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) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)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) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)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) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)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) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)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) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)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) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)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) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)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) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)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) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)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) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)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) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)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) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)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) ![]() Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)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: X-RAY DIFFRACTION / Number of used crystals: 2 |
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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: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 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: molecular replacement |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting 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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About Yorodumi





Thermus thermophilus HB8 (bacteria)
X-RAY DIFFRACTION
United States, 2items
Citation



















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