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- PDB-1ozz: NMR structure of antifungal defensin ARD1 from Archaeoprepona demophon -

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Basic information

Entry
Database: PDB / ID: 1ozz
TitleNMR structure of antifungal defensin ARD1 from Archaeoprepona demophon
Componentsdefensin ARD1
KeywordsANTIFUNGAL PROTEIN / ALPHA-BETA PROTEIN / CSAB MOTIF (CYSTEINE STABILIZED ALPHA-HELIX BETA-SHEET MOTIF)
Function / homology
Function and homology information


antifungal humoral response / defense response / killing of cells of another organism / innate immune response / extracellular region
Similarity search - Function
Invertebrate defensins family profile. / Defensin, invertebrate/fungal / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesArchaeoprepona demophon (one-spotted prepona)
MethodSOLUTION NMR / molecular dynamics
AuthorsLandon, C. / Guenneugues, M. / Barbault, F. / Legrain, M. / Menin, L. / Schott, V. / Vovelle, F. / Dimarcq, J.L.
CitationJournal: Protein Sci. / Year: 2004
Title: Lead optimization of antifungal peptides with 3D NMR structures analysis.
Authors: Landon, C. / Barbault, F. / Legrain, M. / Menin, L. / Guenneugues, M. / Schott, V. / Vovelle, F. / Dimarcq, J.L.
History
DepositionApr 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE AT THE TIME OF PROCESSING, NO SEQUENCE DATABASE REFERENCE WAS AVAILABLE FOR THIS SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: defensin ARD1


Theoretical massNumber of molelcules
Total (without water)4,8091
Polymers4,8091
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 #1lowest energy

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Components

#1: Protein/peptide defensin ARD1


Mass: 4809.409 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoprepona demophon (one-spotted prepona)
Plasmid: pEM2 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P84156
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: homonuclear 2D DQF-COSY, TOCSY, NOESY
NMR detailsText: determined using standard 2D homonuclear techniques

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Sample preparation

DetailsContents: 2mM ARD1, 40mM Na acetate buffer / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 40mM Na acetate buffer / pH: 4.3 / 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 spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMRcollection
NMRPipeDelaglioprocessing
NMRView5.0.3Johnsondata analysis
ARIA1.1Lingestructure solution
CNX2000.1Brungerstructure solution
CNX2000.1Brungerrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
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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