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Yorodumi- PDB-5fdv: Crystal structure of the Pyrrhocoricin antimicrobial peptide boun... -
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-Basic information
Entry | Database: PDB / ID: 5fdv | ||||||
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Title | Crystal structure of the Pyrrhocoricin 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 dormancy process / negative regulation of translational elongation / primary metabolic process / ribosomal small subunit binding / negative regulation of translational initiation / response to cold / cytosolic small ribosomal subunit / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding ...dormancy process / negative regulation of translational elongation / primary metabolic process / ribosomal small subunit binding / negative regulation of translational initiation / response to cold / cytosolic small ribosomal subunit / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / defense response to bacterium / ribonucleoprotein complex / translation / mRNA binding / innate immune response / zinc ion binding / extracellular region / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus HB8 (bacteria) Escherichia coli K-12 (bacteria) Pyrrhocoris apterus (insect) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Seefeldt, A.C. / Graf, M. / Perebaskine, N. / Nguyen, F. / Arenz, S. / Mardirossian, M. / Scocchi, M. / Wilson, D.N. / Innis, C.A. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2016 Title: Structure of the mammalian antimicrobial peptide Bac7(1-16) bound within the exit tunnel of a bacterial ribosome. Authors: Seefeldt, A.C. / Graf, M. / Perebaskine, N. / Nguyen, F. / Arenz, S. / Mardirossian, M. / Scocchi, M. / 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 | 5fdv.cif.gz | 7.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5fdv.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 5fdv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/5fdv ftp://data.pdbj.org/pub/pdb/validation_reports/fd/5fdv | HTTPS FTP |
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-Related structure data
Related structure data | 5f8kC 5fduC 4y4oS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-RNA chain , 3 types, 6 molecules 1A2A1B2B1a2a
#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: 55771382 #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: 55771382 |
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+50S ribosomal protein ... , 29 types, 58 molecules 1D2D1E2E1F2F1G2G1H2H1I2I1N2N1O2O1P2P1Q2Q1R2R1S2S1T2T1U2U1V2V...
-30S ribosomal protein ... , 20 types, 40 molecules 1b2b1c2c1d2d1e2e1f2f1g2g1h2h1i2i1j2j1k2k1l2l1m2m1n2n1o2o1p2p...
#34: 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: P80371 #35: 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: P80372 #36: 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: P80373 #37: 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: Q5SHQ5 #38: 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: Q5SLP8 #39: 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: P17291 #40: 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: Q5SHQ2, UniProt: A0A0M9AFS9*PLUS #41: 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 #42: 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: Q5SHN7 #43: 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: P80376 #44: 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: Q5SHN3 #45: 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: P80377 #46: 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: Q5SHQ1, UniProt: A0A0N0BLP2*PLUS #47: 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: Q5SJ76 #48: 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: Q5SJH3 #49: 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 #50: 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: Q5SLQ0 #51: 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: Q5SHP2 #52: 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 #53: Protein/peptide | Mass: 2831.295 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: rpsU, TTHA1396 / Plasmid: pGS21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5SIH3 |
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-Protein / Protein/peptide , 2 types, 4 molecules 2x1x1y2y
#33: Protein | Mass: 10964.620 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0AD49 #54: Protein/peptide | Mass: 1796.098 Da / Num. of mol.: 2 / Fragment: UNP residues 1-16 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) Pyrrhocoris apterus (insect) / References: UniProt: P37362 |
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-Non-polymers , 5 types, 6981 molecules
#55: Chemical | ChemComp-MG / #56: Chemical | ChemComp-ZN / #57: Chemical | #58: Chemical | ChemComp-A / | #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: 3.42 Å3/Da / Density % sol: 63.99 % |
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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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.987 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→50 Å / Num. obs: 1428776 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 13.8 % / Biso Wilson estimate: 64.57 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.172 / Rrim(I) all: 0.178 / Χ2: 0.967 / Net I/σ(I): 15.99 / Num. measured all: 19712065 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Y4O Resolution: 2.8→49.812 Å / FOM work R set: 0.8317 / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.43 / 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: 149.28 Å2 / Biso mean: 60.09 Å2 / Biso min: 8.77 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8→49.812 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 / % reflection obs: 100 %
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