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- PDB-1zuf: Solution Structure of DLP-4 -

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Basic information

Entry
Database: PDB / ID: 1zuf
TitleSolution Structure of DLP-4
ComponentsDefensin-like peptide 2/4
KeywordsTOXIN / helix / antiparallel beta-sheet
Function / homology
Function and homology information


toxin activity / extracellular region
Similarity search - Function
Defensin-like peptide / Defensin-like peptide family / Anthopleurin-A / Myotoxin/Anemone neurotoxin domain superfamily / Anthopleurin-A / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Defensin-like peptide 2/4
Similarity search - Component
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsTorres, A.M. / Tsampazi, C. / Geraghty, D.P. / Bansal, P.S. / Alewood, P.F. / Kuchel, P.W.
Citation
Journal: Biochem.J. / Year: 2005
Title: D-amino acid residue in a defensin-like peptide from platypus venom: effect on structure and chromatographic properties.
Authors: Torres, A.M. / Tsampazi, C. / Geraghty, D.P. / Bansal, P.S. / Alewood, P.F. / Kuchel, P.W.
#1: Journal: Biochem.J. / Year: 2000
Title: Defensin-like peptide-2 from platypus venom: member of a class of peptides with a distinct structural fold
Authors: Torres, A.M. / de Plater, G.M. / Doverskog, M. / Birinyi-Strachan, L.C. / Nicholson, G.M. / Gallagher, C.H. / Kuchel, P.W.
History
DepositionMay 31, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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 1.4Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Defensin-like peptide 2/4


Theoretical massNumber of molelcules
Total (without water)5,1221
Polymers5,1221
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)20 / 500structures with the lowest energy
RepresentativeModel #17closest to the average

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Components

#1: Protein/peptide Defensin-like peptide 2/4 / DLP-4


Mass: 5121.899 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized / References: UniProt: P82140
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

DetailsContents: 1mM DLP-4 / Solvent system: 90% H2O/10% D2O
Sample conditionspH: 3.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1Brukerprocessing
XEASY1.3.13Bartels, C., Xia, T., Billeter, M., Guntert, P., Wuthrich, K.data analysis
INFITSzyperski, I. Guntert, P., Otting, G., Wuthrich, K.data analysis
NOAHMumenthaler, C., Guntert, P., Braun, W., Wuthrich, K.structure solution
DYANA1.5Guntert, P., Mumenthaler, C., Wuthrich, K.structure solution
CNS1.1Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grossee-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T., Warren, G.L.structure solution
CNS1.1refinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
Details: The structures are based on a total of 451 restraints, 432 are NOE-derived distance constraints, 7 dihedral angle restraints, 12 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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