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- PDB-1zrw: solution structure of spinigerin in H20/TFE 10% -

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Basic information

Entry
Database: PDB / ID: 1zrw
Titlesolution structure of spinigerin in H20/TFE 10%
Componentsspinigerin
KeywordsANTIMICROBIAL PROTEIN / ANTIBIOTIC / helical peptide in TFE
Function / homologydefense response to fungus / killing of cells of another organism / defense response to bacterium / extracellular region / Spinigerin
Function and homology information
MethodSOLUTION NMR / molecular dynamics
AuthorsLandon, C. / Meudal, H. / Boulanger, N. / Bulet, P. / Vovelle, F.
Citation
Journal: Biopolymers / Year: 2006
Title: Solution structures of stomoxyn and spinigerin, two insect antimicrobial peptides with an alpha-helical conformation.
Authors: Landon, C. / Meudal, H. / Boulanger, N. / Bulet, P. / Vovelle, F.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: Insect immunity. Constitutive expression of a cysteine-rich antifungal and a linear antibacterial peptide in a termite insect
Authors: Lamberty, M. / Zachary, D. / Lanot, R. / Bordereau, C. / Robert, A. / Hoffmann, J.A. / Bulet, P.
History
DepositionMay 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 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: 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 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: spinigerin


Theoretical massNumber of molelcules
Total (without water)3,0091
Polymers3,0091
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)30 / 100structures with the least restraint violations
RepresentativeModel #1representative conformer

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Components

#1: Protein/peptide spinigerin


Mass: 3008.799 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: solid-phase synthesis (Fmoc). Sequence occurs naturally in Pseudacanthotermes spiniger
References: UniProt: P82357

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D TOCSY
1312D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 1.5mM spinigerin / Solvent system: 90% H2O, 10% TFE
Sample conditionspH: 5.7 / Pressure: ambiant / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Bcollection
NMRPipe2002.044.17.08Delaglioprocessing
NMRView5.0.16Johnsondata analysis
ARIA1.1Lingestructure solution
CNS1.1Brungerstructure solution
CNS1.1Brungerrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: representative conformer
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 30

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