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- PDB-2mcx: Solid-state NMR structure of piscidin 3 in aligned 1:1 phosphatid... -
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Basic information
Entry | Database: PDB / ID: 2mcx | ||||||
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Title | Solid-state NMR structure of piscidin 3 in aligned 1:1 phosphatidylethanolamine/phosphoglycerol lipid bilayers | ||||||
![]() | Piscidin-3 | ||||||
![]() | ANTIMICROBIAL PROTEIN / antimicrobial peptide / cationic / amphipathic / histidine rich / helical / lipid bilayers / bacterial cell membrane mimic | ||||||
Function / homology | ![]() regulation of defense response to virus / killing of cells of another organism / defense response to bacterium / innate immune response / lipid binding / extracellular region / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | SOLID-STATE NMR / simulated annealing | ||||||
Model details | lowest energy, model1 | ||||||
![]() | Fu, R. / Tian, Y. / Perrin Jr., B.S. / Grant, C.V. / Wieczorek, W.E. / Pastor, R.W. / Cotten, M.L. | ||||||
![]() | ![]() Title: High-resolution structures and orientations of antimicrobial peptides piscidin 1 and piscidin 3 in fluid bilayers reveal tilting, kinking, and bilayer immersion. Authors: Perrin, B.S. / Tian, Y. / Fu, R. / Grant, C.V. / Chekmenev, E.Y. / Wieczorek, W.E. / Dao, A.E. / Hayden, R.M. / Burzynski, C.M. / Venable, R.M. / Sharma, M. / Opella, S.J. / Pastor, R.W. / Cotten, M.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 67.4 KB | Display | ![]() |
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PDB format | ![]() | 52.5 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 367.9 KB | Display | ![]() |
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Full document | ![]() | 409.5 KB | Display | |
Data in XML | ![]() | 6.6 KB | Display | |
Data in CIF | ![]() | 9.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2mcuC ![]() 2mcvC ![]() 2mcwC C: citing same article ( |
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Similar structure data | |
Other databases |
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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: 2495.952 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic construct Source: (synth.) ![]() References: UniProt: P0C006 |
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-Experimental details
-Experiment
Experiment | Method: SOLID-STATE NMR |
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NMR experiment | Type: 15N 1H solid-state de-HETCOR |
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Sample preparation
Details | Type: bicelle Contents: 15-20 mM [15N]-A12G17 PISCIDIN 3, 300-400 mM 1:1 (MOLAR) 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-PHOSPHATIDYLETHANOLAMINE/1-PALMITOYL-2-OLEOYL-SN-GLYCERO-PHOSPHOGLYCEROL, 40 mM PHOSPHATE BUFFER WITH 100% H2O Label: sample_1 / Solvent system: 100% H2O | ||||||||||||||||||||||||
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Sample conditions | pH: 6.0 / Pressure: ambient / Temperature: 305 K |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: Structures were calculated using a simulated annealing protocol within Xplor-NIH with torsion angle molecular dynamics in the presence of experimentally determined restraints. Solid-state ...Details: Structures were calculated using a simulated annealing protocol within Xplor-NIH with torsion angle molecular dynamics in the presence of experimentally determined restraints. Solid-state NMR experiments on static oriented lipid bilayer samples allowed for the measurements of anisotropic backbone 15N chemical shifts and 15N-1H dipolar couplings, which were used as the experimental restraints. The initial structure was an alpha helix with ideal phi/psi angles (-61/-45). The calculations also included the Xplor-NIH potential for knowledge-based torsion angles and the routine terms ANGL, BOND and IMPR. A total of 100 structures were generated and the 10 lowest energy structures were accepted for analysis and representation. By convention, the bilayer normal for all of the oriented samples is aligned along the z-axis of the calculated structures. | |||||||||
NMR representative | Selection criteria: lowest energy | |||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 10 |