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Yorodumi- PDB-2kns: Helical Hairpin Structure of Pardaxin in Lipopolysaccharide Micel... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kns | ||||||
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Title | Helical Hairpin Structure of Pardaxin in Lipopolysaccharide Micelles: Studied by NMR Spectroscopy | ||||||
Components | Pardaxin P-4 | ||||||
Keywords | ANTIMICROBIAL PROTEIN / Pardaxin / Pa4 / LPS / trNOE / antimicrobial peptide / STD NMR / Ion transport / Porin / Secreted / Toxin / Transmembrane / Transport | ||||||
Function / homology | Pardaxin / Pardaxin / other organism cell membrane / monoatomic ion transport / toxin activity / extracellular region / membrane / Pardaxin P-4 Function and homology information | ||||||
Biological species | Pardachirus marmoratus (finless sole) | ||||||
Method | SOLUTION NMR / distance geometry | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Bhunia, A. / Bhattacharjya, S. / Ramamoorthy, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: NMR structure of pardaxin, a pore-forming antimicrobial peptide, in lipopolysaccharide Micelles: Mechanism of outer membrane permeabilization Authors: Bhunia, A. / Domadia, P.N. / Torres, J. / Hallock, K.J. / Ramamoorthy, A. / Bhattacharjya, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kns.cif.gz | 216.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kns.ent.gz | 188.2 KB | Display | PDB format |
PDBx/mmJSON format | 2kns.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/2kns ftp://data.pdbj.org/pub/pdb/validation_reports/kn/2kns | HTTPS FTP |
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-Related structure data
Similar structure data |
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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: 3325.851 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Standard F-moc solid phase peptide synthesis / Source: (synth.) Pardachirus marmoratus (finless sole) / References: UniProt: P81861 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined based on NOE |
-Sample preparation
Details | Contents: 0.5mM Pardaxin-1; 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 0.5 mM / Component: Pardaxin-1 |
Sample conditions | pH: 4.5 / Temperature: 288 K |
-NMR measurement
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz |
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-Processing
NMR software | Name: DYANA / Version: 1.5 / Developer: Guntert, Braun and Wuthrich / Classification: refinement |
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Refinement | Method: distance geometry / Software ordinal: 1 |
NMR representative | Selection criteria: lowest energy |
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1 |