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- PDB-1p8b: SOLUTION STRUCTURE OF PA1B, A 37-AMINO ACID INSECTICIDAL PROTEIN ... -

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Basic information

Entry
Database: PDB / ID: 1p8b
TitleSOLUTION STRUCTURE OF PA1B, A 37-AMINO ACID INSECTICIDAL PROTEIN EXTRACTED FROM PEA SEEDS (PISUM SATIVUM)
ComponentsPea Albumin 1, subunit b
KeywordsPLANT PROTEIN / inhibitor cystine-knot
Function / homologyAlbumin I / Albumin I chain b / Albumin I chain a / Albumin I chain a / nutrient reservoir activity / toxin activity / Albumin-1 B / Albumin-1 F
Function and homology information
Biological speciesPisum sativum (garden pea)
MethodSOLUTION NMR / Torsion angle simulated annealing, molecular dynamics in explicit solvent
AuthorsJouvensal, L. / Quillien, L. / Ferrasson, E. / Rahbe, Y. / Gueguen, J. / Vovelle, F.
Citation
Journal: Biochemistry / Year: 2003
Title: PA1b, an insecticidal protein extracted from pea seeds (Pisum sativum): 1H-2-D NMR study and molecular modeling
Authors: Jouvensal, L. / Quillien, L. / Ferrasson, E. / Rahbe, Y. / Gueguen, J. / Vovelle, F.
#1: Journal: EUR.J.BIOCHEM. / Year: 2003
Title: Characterization of a high affinity binding site for the pea albumin 1b entomotoxin in the weevil Sitophilus
Authors: Gressent, F. / Rahioui, I. / Rahbe, Y.
#2: Journal: Patent / Year: 1999
Title: Use of a polypeptide derived from a PA1b legume albumen as insecticide
Authors: Delobel, B. / Grenier, A.M. / Gueguen, J. / Ferrasson, E. / Mbaiguinam, M.
History
DepositionMay 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations
Category: citation / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.pdbx_database_id_patent
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pea Albumin 1, subunit b


Theoretical massNumber of molelcules
Total (without water)3,7491
Polymers3,7491
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Pea Albumin 1, subunit b / PA1b / Albumin A1b / Leginsulin


Mass: 3749.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: isolated from pea seeds / Source: (natural) Pisum sativum (garden pea) / Strain: cv. Frilene / References: UniProt: P62927, UniProt: P62931*PLUS
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
1212D TOCSY
131DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 2.1mM PA1b; 0.02% NaN3; 50% H2O, 50% TFE-d2 / Solvent system: 50% H20, 50% TFE-d2
Sample conditionspH: 4.8 / Pressure: ambient / Temperature: 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 spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.1Delaglioprocessing
XEASY6001Bartelsdata analysis
CNS1.1Brungerstructure solution
ARIA1.1Lingestructure solution
ARIA1.1Lingerefinement
RefinementMethod: Torsion angle simulated annealing, molecular dynamics in explicit solvent
Software ordinal: 1
Details: The structures are based on 858 NOE-derived distance restraints, 15 dihedral angle restraints and 7 hydrogen bond restraints
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 15

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