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Yorodumi- PDB-5hcq: Crystal structure of antimicrobial peptide Oncocin d15-19 bound t... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 5hcq | ||||||||||||
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| Title | Crystal structure of antimicrobial peptide Oncocin d15-19 bound to the Thermus thermophilus 70S ribosome | ||||||||||||
Components |
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Keywords | Ribosome/Antibiotic / Oncocin d15-19 / antimicrobial peptide / antibiotic / 70S ribosome / inhibition of translation / peptidyl transferase inhibitors / 50S ribosomal subunit / peptide exit tunnel / Ribosome-Antibiotic Complex | ||||||||||||
| Function / homology | Function and homology informationlarge ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding ...large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
| Biological species | ![]() ![]() Thermus thermophilus HB8 (bacteria)![]() Thermus thermophilus (bacteria) Enterobacteria phage T4 (virus) Oncopeltus fasciatus (milkweed bug) | ||||||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.801 Å | ||||||||||||
Authors | Gagnon, M.G. / Roy, R.N. / Lomakin, I.B. / Florin, T. / Mankin, A.S. / Steitz, T.A. | ||||||||||||
| Funding support | United States, 3items
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Citation | Journal: Nucleic Acids Res. / Year: 2016Title: Structures of proline-rich peptides bound to the ribosome reveal a common mechanism of protein synthesis inhibition. Authors: Gagnon, M.G. / Roy, R.N. / Lomakin, I.B. / Florin, T. / Mankin, A.S. / Steitz, T.A. | ||||||||||||
| 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 | 5hcq.cif.gz | 7.4 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb5hcq.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 5hcq.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 5hcq_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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| Full document | 5hcq_full_validation.pdf.gz | 1.7 MB | Display | |
| Data in XML | 5hcq_validation.xml.gz | 626.5 KB | Display | |
| Data in CIF | 5hcq_validation.cif.gz | 988.2 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hc/5hcq ftp://data.pdbj.org/pub/pdb/validation_reports/hc/5hcq | HTTPS FTP |
-Related structure data
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Links
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Assembly
| Deposited unit | ![]()
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| Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
-RNA chain , 5 types, 10 molecules 1A2A1B2B1a2a1v2v1x2x
| #1: RNA chain | Mass: 947895.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382#2: RNA chain | Mass: 39188.371 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382#32: RNA chain | Mass: 493652.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382#53: RNA chain | Mass: 7804.735 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: IDT-Synthesized 24-nt M-F-Stop mRNA / Source: (synth.) Enterobacteria phage T4 (virus)#54: RNA chain | Mass: 24846.902 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Initiator Methionine tRNA / Source: (gene. exp.) ![]() ![]() |
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+50S ribosomal protein ... , 29 types, 58 molecules 1D2D1E2E1F2F1G2G1H2H1I2I1N2N1O2O1P2P1Q2Q1R2R1S2S1T2T1U2U1V2V...
-30S ribosomal protein ... , 20 types, 40 molecules 1b2b1c2c1d2d1e2e1f2f1g2g1h2h1i2i1j2j1k2k1l2l1m2m1n2n1o2o1p2p...
| #33: 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 #34: 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 #35: 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 #36: 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 #37: 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 #38: 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 #39: 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 #40: 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 #41: 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 #42: 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 #43: Protein | Mass: 14637.384 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 #44: 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 #45: 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 #46: 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 #47: 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 #48: 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 #49: 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 #50: 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 #51: 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 #52: 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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-Protein/peptide , 1 types, 2 molecules 1z2z
| #55: Protein/peptide | Mass: 1692.015 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: GenScript-Synthesized peptide Oncocin d15-19 / Source: (synth.) Oncopeltus fasciatus (milkweed bug) |
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-Non-polymers , 4 types, 6496 molecules 






| #56: Chemical | ChemComp-MG / #57: Chemical | ChemComp-ZN / #58: Chemical | #59: 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: 2.95 Å3/Da / Density % sol: 58.35 % / Description: Long needles |
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| Crystal grow | Temperature: 292 K / Method: vapor diffusion Details: 0.15M Arginine-HCl, 0.1M Tris-HCl pH 7.3-7.6, 2.6-2.9% PEG-20K, 9-10% MPD, 0.5 mM BME PH range: 7.3-7.6 |
-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: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 13, 2015 / Details: S/N 60-0112-F | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Reflection | Resolution: 2.8→50 Å / Num. all: 1431810 / Num. obs: 1426619 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 5.021 % / Biso Wilson estimate: 57.75 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.161 / Rrim(I) all: 0.18 / Χ2: 0.972 / Net I/σ(I): 10.8 / Num. measured all: 7162802 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.801→49.923 Å / FOM work R set: 0.8126 / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.22 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso max: 154.67 Å2 / Biso mean: 60.09 Å2 / Biso min: 7.48 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: final / Resolution: 2.801→49.923 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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About Yorodumi




Thermus thermophilus HB8 (bacteria)
Enterobacteria phage T4 (virus)
Oncopeltus fasciatus (milkweed bug)
X-RAY DIFFRACTION
United States, 3items
Citation











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