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Open data
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Basic information
Entry | Database: PDB / ID: 1xc0 | ||||||
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Title | Twenty Lowest Energy Structures of Pa4 by Solution NMR | ||||||
![]() | Pardaxin P-4 | ||||||
![]() | SIGNALING PROTEIN / Bend-helix-bend-helix motif | ||||||
Function / homology | Pardaxin / Pardaxin / other organism cell membrane / monoatomic ion transport / toxin activity / extracellular region / membrane / Pardaxin P-4![]() | ||||||
Method | SOLUTION NMR / extended structure; random simulated annealing; molecular dynamics | ||||||
![]() | Porcelli, F. / Buck, B. / Lee, D.-K. / Hallock, K.J. / Ramamoorthy, A. / Veglia, G. | ||||||
![]() | ![]() Title: Structure and orientation of pardaxin determined by NMR experiments in model membranes Authors: Porcelli, F. / Buck, B. / Lee, D.-K. / Hallock, K.J. / Ramamoorthy, A. / Veglia, G. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 207.5 KB | Display | ![]() |
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PDB format | ![]() | 174.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 338.3 KB | Display | ![]() |
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Full document | ![]() | 450 KB | Display | |
Data in XML | ![]() | 21.5 KB | Display | |
Data in CIF | ![]() | 33.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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: Pardaxins naturally occur in sole fish of genus Pardachirus. Pa4 was synthesized using standard 9-fluorenylmethoxycarbonyl-based solid-pahse methods with an ABI 431A peptide synthesizer. ...Details: Pardaxins naturally occur in sole fish of genus Pardachirus. Pa4 was synthesized using standard 9-fluorenylmethoxycarbonyl-based solid-pahse methods with an ABI 431A peptide synthesizer. Crude peptide was purified by reversed-phase HPLC References: UniProt: P81861 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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Sample preparation
Details | Contents: ~1.5 mg of lyophilized Pa4 in 20 mM PBS (pH 6.5),300 mM d31-DPC and 10% D2O. Sample pH was adjusted to ~4.5 with NaOH. Solvent system: 90% water and 10% D2O |
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Sample conditions | pH: 4.5 / Temperature: 303 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz |
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Processing
NMR software |
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Refinement | Method: extended structure; random simulated annealing; molecular dynamics Software ordinal: 1 / Details: 335 NOEs; 13 H-bonds | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 350 / Conformers submitted total number: 20 |