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- PDB-1i2v: NMR SOLUTION STRUCTURES OF AN ANTIFUNGAL AND ANTIBACTERIAL MUTANT... -

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Basic information

Entry
Database: PDB / ID: 1i2v
TitleNMR SOLUTION STRUCTURES OF AN ANTIFUNGAL AND ANTIBACTERIAL MUTANT OF HELIOMICIN
ComponentsDEFENSIN HELIOMICIN
KeywordsANTIMICROBIAL PROTEIN / alpha-beta protein / CSab motif (cysteine stabilized alpha-helix beta-sheet motif)
Function / homology
Function and homology information


defense response to fungus / 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 speciesHeliothis virescens (tobacco budworm)
MethodSOLUTION NMR / torsion angle dynamics (DYANA), energy minimisation (XPLOR)
AuthorsLamberty, M. / Caille, A. / Landon, C. / Tassin-Moindrot, S. / Hetru, C. / Bulet, P. / Vovelle, F.
CitationJournal: Biochemistry / Year: 2001
Title: Solution structures of the antifungal heliomicin and a selected variant with both antibacterial and antifungal activities.
Authors: Lamberty, M. / Caille, A. / Landon, C. / Tassin-Moindrot, S. / Hetru, C. / Bulet, P. / Vovelle, F.
History
DepositionFeb 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 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 HELIOMICIN


Theoretical massNumber of molelcules
Total (without water)4,7361
Polymers4,7361
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)18 / 40structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy, target function
RepresentativeModel #1lowest target function

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Components

#1: Protein/peptide DEFENSIN HELIOMICIN


Mass: 4736.310 Da / Num. of mol.: 1 / Mutation: K23L, R24L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Heliothis virescens (tobacco budworm) / Plasmid: PSEA2 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): TGY 48-1 / References: UniProt: P81544
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H DQF-COSY; TQF-COSY; TOCSY; NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 4 mM heliomicin-LL ; 40mM sodium acetate buffer / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 40mM sodium acetate buffer / pH: 4.3 / Pressure: ambient / Temperature: 293 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: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
UXNMRcollection
XEASYBartelsdata analysis
DYANAGuentertrefinement
X-PLORBrungerrefinement
RefinementMethod: torsion angle dynamics (DYANA), energy minimisation (XPLOR)
Software ordinal: 1
Details: the structures are based on a total of 120 intra-residue, 172 sequential, 108 medium range, 190 long range NOE-derived distance restraints, 9 distances restraints corresponding to the 3 ...Details: the structures are based on a total of 120 intra-residue, 172 sequential, 108 medium range, 190 long range NOE-derived distance restraints, 9 distances restraints corresponding to the 3 disulfide bridge, 100 dihedral angle restraints, and 13 distance restraints for hydrogen bonds
NMR representativeSelection criteria: lowest target function
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy, target function
Conformers calculated total number: 40 / Conformers submitted total number: 18

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