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- PDB-6q08: Synoeca peptide was isolated from the venom of wasp synoeca surinama. -
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Open data
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Basic information
Entry | Database: PDB / ID: 6q08 | ||||||
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Title | Synoeca peptide was isolated from the venom of wasp synoeca surinama. | ||||||
![]() | Synoeca peptide | ||||||
![]() | ANTIMICROBIAL PROTEIN / Antimicrobial / peptide structure | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
![]() | Alves, E.S. / Rodrigues, L.V. / Liao, L.M. | ||||||
![]() | ![]() Title: NMR STRUCTURE OF THE ANTIMICROBIAL PEPTIDE ISOLATED FROM THE VENOM OF WASP Synoeca Surinama. Authors: Alves, E.S.F. / Rodrigues, L.V. / Liao, L.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 48.4 KB | Display | ![]() |
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PDB format | ![]() | 32.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.5 KB | Display | ![]() |
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Full document | ![]() | 505.6 KB | Display | |
Data in XML | ![]() | 10.5 KB | Display | |
Data in CIF | ![]() | 11.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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NMR ensembles |
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Components
#1: Protein/peptide | Mass: 1598.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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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 mM synoeca, 100 mM [U-98% 2H] SDS-D25, 5 % v/v [U-98% 2H] DSS, 90 % v/v H2O, 10 % [U-99% 2H] D2O, 90% H2O/10% D2O Details: A solution containing 1 mM of peptide was prepared in 300 mM of SDS-d25, 90:10 H2O/D2O and 5% of DSS, and the pH adjusted for 7. Label: Synoeca / Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||
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Sample |
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Sample conditions | Details: A solution containing 1 mM of peptide was prepared in 300 mM of SDS-d25, 90:10 H2O/D2O and 5% of DSS (4,4-dimethyl-4-silapentane-1-sulfonic acid), and the pH adjusted for 7. Ionic strength: neutal Not defined / Label: synoeca / pH: 7 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 4 Details: In the final structure calculation of synoeca-MP, 176 unique NOEs and 24 dihedral angles were used as restraints | ||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 10 |