+Open data
-Basic information
Entry | Database: PDB / ID: 5m9u | ||||||
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Title | Spatial structure of antimicrobial peptide arenicin-1 mutant V8R | ||||||
Components | Arenicin-1 | ||||||
Keywords | ANTIMICROBIAL PROTEIN / STRUCTURE FROM CYANA 3.97 | ||||||
Function / homology | BRICHOS domain / BRICHOS domain / BRICHOS domain profile. / defense response to fungus / killing of cells of another organism / defense response to bacterium / Arenicin-1 Function and homology information | ||||||
Biological species | Arenicola marina (lugworm) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Myshkin, M.Y. / Shenkarev, Z.O. / Panteleev, P.V. / Ovchinnikova, T.V. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2017 Title: Dimerization of the antimicrobial peptide arenicin plays a key role in the cytotoxicity but not in the antibacterial activity. Authors: Panteleev, P.V. / Myshkin, M.Y. / Shenkarev, Z.O. / Ovchinnikova, T.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m9u.cif.gz | 155.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m9u.ent.gz | 129.4 KB | Display | PDB format |
PDBx/mmJSON format | 5m9u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m9/5m9u ftp://data.pdbj.org/pub/pdb/validation_reports/m9/5m9u | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 2824.409 Da / Num. of mol.: 1 / Mutation: V8R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arenicola marina (lugworm) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5SC60 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution / Contents: 1.8 mM [U-99% 15N] arenicin-1 V8R, 95% H2O/5% D2O / Label: 15N_sample / Solvent system: 95% H2O/5% D2O |
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Sample | Conc.: 1.8 mM / Component: arenicin-1 V8R / Isotopic labeling: [U-99% 15N] |
Sample conditions | Ionic strength: 0 Not defined / Label: conditions_1 / pH: 4.5 / Pressure: 1 atm / Temperature: 293 K |
-NMR measurement
NMR spectrometer | Type: Bruker AvanceI / Manufacturer: Bruker / Model: AvanceI / Field strength: 700 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 200 / Conformers submitted total number: 20 |