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Yorodumi- PDB-4zer: Crystal structure of the Onc112 antimicrobial peptide bound to th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zer | ||||||
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Title | Crystal structure of the Onc112 antimicrobial peptide bound to the Thermus thermophilus 70S ribosome | ||||||
Components |
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Keywords | RIBOSOME / bacterial ribosome / proline-rich antimicrobial peptide / antibiotics / protein biosynthesis | ||||||
Function / homology | Function and homology information endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / large ribosomal subunit / 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 ...endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / large ribosomal subunit / 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 / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) Thermus thermophilus HB8 (bacteria) Oncopeltus fasciatus (milkweed bug) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Seefeldt, A.C. / Nguyen, F. / Antunes, S. / Perebaskine, N. / Graf, M. / Arenz, S. / Inampudi, K.K. / Douat, C. / Guichard, G. / Wilson, D.N. / Innis, C.A. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2015 Title: The proline-rich antimicrobial peptide Onc112 inhibits translation by blocking and destabilizing the initiation complex. Authors: Seefeldt, A.C. / Nguyen, F. / Antunes, S. / Perebaskine, N. / Graf, M. / Arenz, S. / Inampudi, K.K. / Douat, C. / Guichard, G. / Wilson, D.N. / Innis, C.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zer.cif.gz | 7.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4zer.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4zer.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zer_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4zer_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 4zer_validation.xml.gz | 627.1 KB | Display | |
Data in CIF | 4zer_validation.cif.gz | 970.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/4zer ftp://data.pdbj.org/pub/pdb/validation_reports/ze/4zer | HTTPS FTP |
-Related structure data
Related structure data | 4y4oS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-RNA chain , 5 types, 10 molecules 1A2A1B2B1a2a1x2xAB
#1: RNA chain | Mass: 948007.562 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382 #2: RNA chain | Mass: 38882.207 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 48271 #32: RNA chain | Mass: 493863.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 155076 #53: RNA chain | Mass: 24541.719 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Plasmid: pBS / Production host: Escherichia coli (E. coli) / References: GenBank: 745369752 #55: RNA chain | Mass: 8754.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) |
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+50S ribosomal protein ... , 29 types, 58 molecules 1D2D1E2E1F2F1G2G1H2H1I2I1N2N1O2O1P2P1Q2Q1R2R1S2S1T2T1U2U1V2V...
-30S ribosomal protein ... , 20 types, 40 molecules 1b2b1c2c1d2d1e2e1f2f1g2g1h2h1i2i1j2j1k2k1l2l1m2m1n2n1o2o1p2p...
#33: Protein | Mass: 26646.852 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P62662, UniProt: P80371*PLUS #34: Protein | Mass: 22862.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P62663, UniProt: P80372*PLUS #35: Protein | Mass: 24242.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P62664, UniProt: P80373*PLUS #36: Protein | Mass: 16144.848 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P62665, UniProt: Q5SHQ5*PLUS #37: Protein | Mass: 11917.675 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P62666, UniProt: Q5SLP8*PLUS #38: Protein | Mass: 17919.775 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P62667, UniProt: P17291*PLUS #39: Protein | Mass: 15737.372 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P62668, UniProt: P0DOY9*PLUS #40: Protein | Mass: 14279.419 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80374 #41: Protein | Mass: 11169.997 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P62653, UniProt: Q5SHN7*PLUS #42: Protein | Mass: 12032.662 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P62654, UniProt: P80376*PLUS #43: Protein | Mass: 13650.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P61941, UniProt: Q5SHN3*PLUS #44: Protein | Mass: 13237.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P62655, UniProt: P80377*PLUS #45: Protein | Mass: 7027.529 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P62656, UniProt: P0DOY6*PLUS #46: Protein | Mass: 10447.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P62657, UniProt: Q5SJ76*PLUS #47: Protein | Mass: 9795.354 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P62238, UniProt: Q5SJH3*PLUS #48: Protein | Mass: 11722.904 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHP7, UniProt: A0A0N0BLS5*PLUS #49: Protein | Mass: 7897.451 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P62659, UniProt: Q5SLQ0*PLUS #50: Protein | Mass: 9455.995 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P62660, UniProt: Q5SHP2*PLUS #51: Protein | Mass: 10876.067 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80380 #52: Protein/peptide | Mass: 2831.295 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SIH3 |
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-Protein/peptide , 1 types, 2 molecules 1y2y
#54: Protein/peptide | Mass: 2396.837 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) Oncopeltus fasciatus (milkweed bug) |
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-Non-polymers , 8 types, 6187 molecules
#56: Chemical | ChemComp-MG / #57: Chemical | #58: Chemical | #59: Chemical | ChemComp-ARG / | #60: Chemical | ChemComp-ZN / #61: Chemical | #62: Chemical | ChemComp-K / | #63: 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: 3.48 Å3/Da / Density % sol: 64.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: Tris-HCl, PEG 20000, MPD, Arginine |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Highest resolution: 3.1 Å / Num. obs: 1050694 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 71.92 Å2 / Rmerge F obs: 0.989 / Rmerge(I) obs: 0.22 / Rrim(I) all: 0.255 / Χ2: 0.882 / Net I/σ(I): 5.47 / Num. measured all: 3999403 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Y4O Resolution: 3.1→49.723 Å / FOM work R set: 0.7952 / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.02 / 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: 104.27 Å2 / Biso mean: 61.14 Å2 / Biso min: 13.27 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.1→49.723 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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