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- PDB-1iyc: Solution structure of antifungal peptide, scarabaecin -

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Basic information

Entry
Database: PDB / ID: 1iyc
TitleSolution structure of antifungal peptide, scarabaecin
Componentsscarabaecin
KeywordsANTIFUNGAL PROTEIN / antifungal peptide / antimicrobial peptide / beetle / chitin-binding
Function / homologyChitin binding domain superfamily / chitin binding / defense response to fungus / killing of cells of another organism / defense response to Gram-negative bacterium / extracellular region / Scarabaecin
Function and homology information
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsHemmi, H. / Ishibashi, J. / Tomie, T. / Yamakawa, M.
CitationJournal: J.BIOL.CHEM. / Year: 2003
Title: Structural Basis for New Pattern of Conserved Amino Acid Residues Related to Chitin-binding in the Antifungal Peptide from the Coconut Rhinoceros Beetle Oryctes rhinoceros
Authors: Hemmi, H. / Ishibashi, J. / Tomie, T. / Yamakawa, M.
History
DepositionAug 5, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 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: 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
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
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: scarabaecin


Theoretical massNumber of molelcules
Total (without water)4,0881
Polymers4,0881
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #2lowest energy

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Components

#1: Protein/peptide scarabaecin


Mass: 4087.745 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in the coconut rhinoceros beetle.
References: UniProt: Q86SC0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQF-COSY
131E-COSY
141TOCSY
151ROESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 3mM Scarabaecin; 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
Sample conditionspH: 2.4 / Pressure: ambient / Temperature: 298 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 AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
Sparky3.105Goddard and Knellerdata analysis
Felix2000MSIprocessing
X-PLOR3.851Brungerrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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