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- PDB-1v28: Solution structure of paralytic peptide of the wild Silkmoth, Ant... -

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Basic information

Entry
Database: PDB / ID: 1v28
TitleSolution structure of paralytic peptide of the wild Silkmoth, Antheraea yamamai
ComponentsParalytic Peptide
KeywordsTOXIN / Paralytic peptide / antheraea yamamai / single beta sheet / ENF family
Function / homologyParalytic/GBP/PSP peptide / Paralytic/GBP/PSP peptide / cytokine activity / extracellular space / Paralytic peptide 2
Function and homology information
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsKawaguchi, K. / Ying, A. / Suzuki, K. / Kumaki, Y. / Demura, M. / Nitta, K.
CitationJournal: To be Published
Title: Structural characterization of paralytic peptide of the wild Silkmoth Antheraea yamamai by NMR
Authors: Kawaguchi, K. / Ying, A. / Suzuki, K. / Kumaki, Y. / Demura, M. / Nitta, K.
History
DepositionOct 9, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Nov 13, 2024Group: Data collection / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_spectrometer
Item: _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Paralytic Peptide


Theoretical massNumber of molelcules
Total (without water)2,4411
Polymers2,4411
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 100structures with the lowest energy
RepresentativeModel #11lowest energy

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Components

#1: Protein/peptide Paralytic Peptide


Mass: 2440.757 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic construct / References: UniProt: P30254*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D TOCSY
1312D NOESY
142E-COSY
1522D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
13mM Paralytic peptide; pH 4.4(pH was adjusted by HCl and NaOH); 90% H2O, 10% D2O90% H2O/10% D2O
23mM Paralytic peptide; pH 4.4(pH was adjusted by HCl and NaOH); 99% D2O99% D2O
Sample conditionspH: 4.4 / Pressure: ambient / Temperature: 293 K

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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 DRXBrukerDRX6001
JEOL AlphaJEOLAlpha6002

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Processing

NMR softwareName: X-PLOR / Version: 3.851 / Developer: Michael Nilges, John Kuszewski, Axel T. Brunger / Classification: refinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 189 restraints, 165 are NOE-derived distance constraints, 12 dihedral angle restraints, 12 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 25

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