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- PDB-1q3j: Solution structure of ALO3: a new knottin-type antifungal peptide... -

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Basic information

Entry
Database: PDB / ID: 1q3j
TitleSolution structure of ALO3: a new knottin-type antifungal peptide from the insect Acrocinus longimanus
ComponentsALO3
KeywordsANTIFUNGAL PROTEIN / knottin / cystine-knot
Function / homologyGurmarin/antimicrobial peptide / Antifungal peptide / Gurmarin/antifungal peptide / Antimicrobial peptide, C6 type, conserved site / Plant C6 type antimicrobial peptide (AMP) signature. / defense response to fungus / killing of cells of another organism / extracellular region / Antimicrobial peptide Alo-3
Function and homology information
MethodSOLUTION NMR / simulated annealing with torsion angle space
AuthorsBarbault, F. / Landon, C. / Guenneugues, M. / Meyer, J.P. / Schott, V. / Dimarrcq, J.L. / Vovelle, F.
CitationJournal: Biochemistry / Year: 2003
Title: Solution structure of Alo-3: a new knottin-type antifungal peptide from the insect Acrocinus longimanus.
Authors: Barbault, F. / Landon, C. / Guenneugues, M. / Meyer, J.P. / Schott, V. / Dimarcq, J.L. / Vovelle, F.
History
DepositionJul 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 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 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALO3


Theoretical massNumber of molelcules
Total (without water)3,8811
Polymers3,8811
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)10 / 100structures with the lowest energy and the least restraint violations
RepresentativeModel #4lowest energy

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Components

#1: Protein/peptide ALO3


Mass: 3881.415 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. The sequence of the peptide is naturally found in Acrocinus longimanus (giant harlequin beetle).
References: UniProt: P83653
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
121DQF-COSY
2312D TOCSY
1412D NOESY
1522D TOCSY
162kinetics exchange
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
1peptide at 1.2mM, acetate buffer at 40mM, 90% H2O, 10% D2O90% H2O/10% D2O
2peptide at 1.2mM, acetate buffer at 40mM, 100% D2O100% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
15.2ambient 293 K
25.2ambient 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.2Delaglio, F.processing
NMRView5Johnson, B.A.data analysis
ARIA1.1Nilges, M.structure solution
CNS1.1Brunger, A.T.structure solution
MOLMOL2k1Koradi, R.data analysis
CNS1.1Brunger, A.T.refinement
RefinementMethod: simulated annealing with torsion angle space / Software ordinal: 1
Details: Determination of disulfide pattern was done using ambiguous disulfide restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy and the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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