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- PDB-1ueo: Solution structure of the [T8A]-Penaeidin-3 -

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Basic information

Entry
Database: PDB / ID: 1ueo
TitleSolution structure of the [T8A]-Penaeidin-3
ComponentsPenaeidin-3a
KeywordsANTIBIOTIC / helix / coil-helix-coil / proline-rich / cysteine-rich / disulfide bond
Function / homologyPenaeidin / Penaeidin / chitin binding / defense response to fungus / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / cytoplasm / Penaeidin-3a
Function and homology information
Biological speciesLitopenaeus vannamei (Pacific white shrimp)
MethodSOLUTION NMR / simulated annealing
AuthorsYang, Y. / Poncet, J. / Garnier, J. / Zatylny, C. / Bachere, E. / Aumelas, A.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Solution structure of the recombinant penaeidin-3, a shrimp antimicrobial peptide
Authors: Yang, Y. / Poncet, J. / Garnier, J. / Zatylny, C. / Bachere, E. / Aumelas, A.
History
DepositionMay 20, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Penaeidin-3a


Theoretical massNumber of molelcules
Total (without water)6,6771
Polymers6,6771
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 60structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Penaeidin-3a / Penaeidin-3


Mass: 6676.788 Da / Num. of mol.: 1 / Mutation: T8A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Litopenaeus vannamei (Pacific white shrimp)
Plasmid: pTG4812 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): TGY 48-1 / References: UniProt: P81058

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: DQF-COSY, TOCSY, NOESY
NMR detailsText: A 0.3ml solution of penaeidin-3 was used in a Shigemi tube. The 500 MHz spectrometer was equipped with a cryoprobe. This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7mM95% H2O/5% D2O
20.7mM99.98% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1ND 3.9 ambient 293 K
2ND 3.9 ambient 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2collection
Gifa4.4Delsuc, M.A.processing
X-PLOR3.8refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 552 NOE-derived distance constraints and 28 dihedral angle restraints. The arrangement of the three disulfide bonds was determined in this study.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 60 / Conformers submitted total number: 20

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