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Open data
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Basic information
Entry | Database: PDB / ID: 1ma2 | ||||||
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Title | Tachyplesin I Wild type peptide NMR Structure | ||||||
![]() | Tachyplesin I | ||||||
![]() | ANTIMICROBIAL PROTEIN / Tachyplesin / beta hairpin / disulfide bridge / anti-microbial peptide | ||||||
Function / homology | defense response to bacterium / extracellular region / Tachyplesin-1![]() | ||||||
Method | SOLUTION NMR / simulated annealing with complete cross validation | ||||||
Model type details | minimized average | ||||||
![]() | Laederach, A. / Andreotti, A.H. / Fulton, D.B. | ||||||
![]() | ![]() Title: Solution and micelle-bound structures of tachyplesin I and its active aromatic linear derivatives Authors: Laederach, A. / Andreotti, A.H. / Fulton, D.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 174.6 KB | Display | ![]() |
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PDB format | ![]() | 137.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 333.4 KB | Display | ![]() |
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Full document | ![]() | 510.2 KB | Display | |
Data in XML | ![]() | 11.1 KB | Display | |
Data in CIF | ![]() | 17.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 2274.807 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The peptide was chemically synthesized using Fmoc solid state synthesis. The sequence of the peptide is naturally found in Tachypleus tridentatus (Japanese horeshoe crab). References: UniProt: P14213 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: 2D experiments were collected both in pure D2O and 9:1 H2O:D2O. To resolve overlap, two temperatures were used, 277K and 298K, and NOE restraints from both temperatures were used in the refinement process. |
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Sample preparation
Details | Contents: Tachyplesin I peptide at 0.5 mM Solvent system: 90%/10% H2O/D2O and 99% D2O with 0.15% TFA, pH 3.0 | |||||||||||||||
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Sample conditions |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz |
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Processing
NMR software |
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Refinement | Method: simulated annealing with complete cross validation / Software ordinal: 1 | ||||||||||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 300 / Conformers submitted total number: 31 |