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- PDB-1mm0: Solution structure of termicin, an antimicrobial peptide from the... -

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Basic information

Entry
Database: PDB / ID: 1mm0
TitleSolution structure of termicin, an antimicrobial peptide from the termite Pseudacanthotermes spiniger
ComponentsTermicin
KeywordsANTIMICROBIAL PROTEIN / Termite / Cytein-rich / Antimicrobial peptide / Insect defensin / CSab motif
Function / homologyTermicin / Antifungal peptide termicin / Knottin, scorpion toxin-like superfamily / defense response to fungus / killing of cells of another organism / defense response to bacterium / extracellular region / Termicin
Function and homology information
Biological speciesPseudacanthotermes spiniger (cockroach)
MethodSOLUTION NMR / molecular dynamics
AuthorsDa Silva, P. / Jouvensal, L. / Lamberty, M. / Bulet, P. / Caille, A. / Vovelle, F.
CitationJournal: PROTEIN SCI. / Year: 2003
Title: Solution structure of termicin, an antimicrobial peptide from the termite Pseudacanthotermes spiniger
Authors: Da Silva, P. / Jouvensal, L. / Lamberty, M. / Bulet, P. / Caille, A. / Vovelle, F.
History
DepositionSep 2, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 13, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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 1.4Oct 23, 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: Termicin


Theoretical massNumber of molelcules
Total (without water)4,2281
Polymers4,2281
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 / 50structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Termicin


Mass: 4227.878 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudacanthotermes spiniger (cockroach)
Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P82321
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 2mM Termicin; 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
Sample conditionspH: 3.9 / Pressure: ambient / Temperature: 300 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
VNMR6.1processing
XEASY6001Bartels et al.data analysis
ARIA1.1Linge et aldata analysis
CNS1.1Brunger et alrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: the structures are based on a total of 834 restraints, 796 NOE-derived distance constraints, 26 dihedral angle restraints, 12 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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