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- PDB-2g9p: NMR structure of a novel antimicrobial peptide, latarcin 2a, from... -

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Basic information

Entry
Database: PDB / ID: 2g9p
TitleNMR structure of a novel antimicrobial peptide, latarcin 2a, from spider (Lachesana tarabaevi) venom
Componentsantimicrobial peptide Latarcin 2a
KeywordsANTIMICROBIAL PROTEIN / helix-hinge-helix
Function / homologyLatarcin precursor / Latarcin precursor / defense response to fungus / toxin activity / killing of cells of another organism / defense response to bacterium / extracellular region / M-zodatoxin-Lt2a
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics, refinement in implicit membrane model (water, octanol, water slab)
AuthorsDubovskii, P.V. / Volynsky, P.E. / Polyansky, A.A. / Chupin, V.V. / Efremov, R.G. / Arseniev, A.S.
CitationJournal: Biochemistry / Year: 2006
Title: Spatial structure and activity mechanism of a novel spider antimicrobial peptide.
Authors: Dubovskii, P.V. / Volynsky, P.E. / Polyansky, A.A. / Chupin, V.V. / Efremov, R.G. / Arseniev, A.S.
History
DepositionMar 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE The sequence of the protein has not been deposited into any sequence database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: antimicrobial peptide Latarcin 2a


Theoretical massNumber of molelcules
Total (without water)2,9131
Polymers2,9131
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 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide antimicrobial peptide Latarcin 2a


Mass: 2912.610 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence can be naturally found in spider (Lachesana tarabaevi) venom
References: UniProt: Q1ELU1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
2322D TOCSY
2422D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.7 mM Ltc2a; 102 mM SDS-d25, 95% H2O, 5% D2O95% H2O/5% D2O
21.7 mM Ltc2a; 102 mM SDS-d25, 100 % D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1no salt 6.8ambient 318 K
2no salt 6.8ambient 318 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY6001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1.C.Varian, Cocollection
XwinNMR3.1.aBruker, GMBhcollection
CYANA1.0.6.Herrmann T., Guentert P., Wuethrich K.structure solution
FANMEMvon Freyberg, B., Braun, W., Nolde, D.E., Volynsky, P.E., Arseniev, A.S., Efremov, R.G.refinement
XEASY40300000Bartels, C., Xia, T., Billeter, M., Guentert, P., Wuetrich, K.data analysis
MOLMOL2K.1Koradi, R., Billetr, M., Wuetrich, K.data analysis
RefinementMethod: torsion angle dynamics, refinement in implicit membrane model (water, octanol, water slab)
Software ordinal: 1
Details: In total, 222 distance and 123 torsion angles constraints were used for structure calculation
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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