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- PDB-1p0a: NMR structure of ETD135, mutant of the antifungal defensin ARD1 f... -

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Basic information

Entry
Database: PDB / ID: 1p0a
TitleNMR structure of ETD135, mutant of the 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 13, 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. ...SEQUENCE AT THE TIME OF PROCESSING, NO SEQUENCE DATABASE REFERENCE WAS AVAILABLE FOR THIS SEQUENCE. THERE IS A A36L MUTATION COMPARED TO THE WILD TYPE 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)4,8511
Polymers4,8511
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: 4851.489 Da / Num. of mol.: 1 / Mutation: A36L
Source method: isolated from a genetically manipulated source
Details: ETD135 mutant
Source: (gene. exp.) Archaeoprepona demophon (one-spotted prepona)
Plasmid: pEM35 / 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 ETD135, 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
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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