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- PDB-5f8k: Crystal structure of the Bac7(1-16) antimicrobial peptide bound t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5f8k | ||||||
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Title | Crystal structure of the Bac7(1-16) antimicrobial peptide bound to the Thermus thermophilus 70S ribosome | ||||||
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![]() | RIBOSOME / bacterial ribosome / proline-rich antimicrobial peptide / antibiotics / protein biosynthesis | ||||||
Function / homology | ![]() lipopolysaccharide binding / large ribosomal subunit / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 ...lipopolysaccharide binding / large ribosomal subunit / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / defense response to Gram-negative bacterium / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / defense response to Gram-positive bacterium / structural constituent of ribosome / ribonucleoprotein complex / translation / innate immune response / mRNA binding / extracellular space / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() synthetic construct (others) ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Seefeldt, A.C. / Graf, M. / Perebaskine, N. / Nguyen, F. / Arenz, S. / Mardirossian, M. / Scocchi, M. / Wilson, D.N. / Innis, C.A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 7.6 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 646.8 KB | Display | |
Data in CIF | ![]() | 1005.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5fduC ![]() 5fdvC ![]() 4y4oS S: Starting model for refinement C: citing same article ( |
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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 1A2A1B2B1a2a1v2v1x2x
#1: RNA chain | Mass: 948007.562 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() #2: RNA chain | Mass: 38882.207 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() #32: RNA chain | Mass: 493558.438 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() #53: RNA chain | Mass: 935.620 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) synthetic construct (others) #54: RNA chain | Mass: 24541.719 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source 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: 26646.852 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() #34: Protein | Mass: 22862.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() #35: Protein | Mass: 24242.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() #36: Protein | Mass: 16144.848 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() #37: Protein | Mass: 11917.675 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() #38: Protein | Mass: 17919.775 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() #39: Protein | Mass: 15737.372 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() #40: Protein | Mass: 14279.419 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() #41: Protein | Mass: 11169.997 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() #42: Protein | Mass: 12032.662 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() #43: Protein | Mass: 13650.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() #44: Protein | Mass: 13237.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() #45: Protein | Mass: 7027.529 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() #46: Protein | Mass: 10447.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() #47: Protein | Mass: 9795.354 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() #48: Protein | Mass: 11722.904 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() #49: Protein | Mass: 7897.451 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() #50: Protein | Mass: 9455.995 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() #51: Protein | Mass: 10876.067 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() #52: Protein/peptide | Mass: 2831.295 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Protein/peptide , 1 types, 2 molecules 1y2y
#55: Protein/peptide | Mass: 2084.570 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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-Non-polymers , 5 types, 7565 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
#56: Chemical | ChemComp-MG / #57: Chemical | ChemComp-ZN / #58: Chemical | #59: Chemical | #60: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.39 Å3/Da / Density % sol: 63.75 % |
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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: 90 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 18, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Highest resolution: 2.8 Å / Num. obs: 1422951 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 42.03 Å2 / Rmerge F obs: 0.957 / Rmerge(I) obs: 0.512 / Rrim(I) all: 0.545 / Χ2: 0.853 / Net I/σ(I): 5.71 / Num. measured all: 11868574 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4Y4O Resolution: 2.8→48.625 Å / FOM work R set: 0.7657 / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.71 / 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: 120.12 Å2 / Biso mean: 44.05 Å2 / Biso min: 3.54 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8→48.625 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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