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- PDB-1irr: Solution structure of paralytic peptide of the silkworm, Bombyx mori -

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Basic information

Entry
Database: PDB / ID: 1irr
TitleSolution structure of paralytic peptide of the silkworm, Bombyx mori
Componentsparalytic peptide
KeywordsCYTOKINE / single beta sheet
Function / homologyParalytic/GBP/PSP peptide / Paralytic/GBP/PSP peptide / Paralytic peptide
Function and homology information
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsMiura, K. / Kamimura, M. / Aizawa, T. / Kiuchi, M. / Hayakawa, Y. / Mizuguchi, M. / Kawano, K.
CitationJournal: peptides / Year: 2002
Title: Solution structure of paralytic peptide of silkworm, Bombyx mori
Authors: Miura, K. / Kamimura, M. / Aizawa, T. / Kiuchi, M. / Hayakawa, Y. / Mizuguchi, M. / Kawano, K.
History
DepositionOct 23, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)2,4671
Polymers2,4671
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)20 / 100structures with the lowest energy
RepresentativeModel #5lowest energy

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Components

#1: Protein/peptide paralytic peptide


Mass: 2466.793 Da / Num. of mol.: 1 / Fragment: residues 1-23 / Source method: obtained synthetically / Details: This sequence occurs naturally in silkworm. / References: UniProt: Q95YI2
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
1312D TOCSY
2422D NOESY
252DQF-COSY
2622D TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
14.0mM BmPP, 90% H2O, 10% D2O90% H2O/10% D2O
24.0mM BmPP, 100% D2O100% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
14.51 atm303 K
24.51 atm303 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 spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1Nilgesdata analysis
CNS1Brungerstructure solution
CNS1Brungerrefinement
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 200 restraints, 200 are NOE-derived unambiguous distance constraints, 72 are NOE-derived ambiguous distance constraints, 17 dihedral angle ...Details: the structures are based on a total of 200 restraints, 200 are NOE-derived unambiguous distance constraints, 72 are NOE-derived ambiguous distance constraints, 17 dihedral angle restraints,14 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: 20

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