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- PDB-5m9u: Spatial structure of antimicrobial peptide arenicin-1 mutant V8R -

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Basic information

Entry
Database: PDB / ID: 5m9u
TitleSpatial structure of antimicrobial peptide arenicin-1 mutant V8R
ComponentsArenicin-1
KeywordsANTIMICROBIAL PROTEIN / STRUCTURE FROM CYANA 3.97
Function / homologyBRICHOS domain / BRICHOS domain / BRICHOS domain profile. / defense response to fungus / killing of cells of another organism / defense response to bacterium / Arenicin-1
Function and homology information
Biological speciesArenicola marina (lugworm)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMyshkin, M.Y. / Shenkarev, Z.O. / Panteleev, P.V. / Ovchinnikova, T.V.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Dimerization of the antimicrobial peptide arenicin plays a key role in the cytotoxicity but not in the antibacterial activity.
Authors: Panteleev, P.V. / Myshkin, M.Y. / Shenkarev, Z.O. / Ovchinnikova, T.V.
History
DepositionNov 2, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arenicin-1


Theoretical massNumber of molelcules
Total (without water)2,8241
Polymers2,8241
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2490 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Arenicin-1


Mass: 2824.409 Da / Num. of mol.: 1 / Mutation: V8R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arenicola marina (lugworm) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5SC60
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic12D 1H-1H TOCSY
151isotropic12D 1H-1H NOESY
161isotropic13D 1H-15N NOESY
171isotropic13D HNHA
181isotropic13D HNHB

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Sample preparation

DetailsType: solution / Contents: 1.8 mM [U-99% 15N] arenicin-1 V8R, 95% H2O/5% D2O / Label: 15N_sample / Solvent system: 95% H2O/5% D2O
SampleConc.: 1.8 mM / Component: arenicin-1 V8R / Isotopic labeling: [U-99% 15N]
Sample conditionsIonic strength: 0 Not defined / Label: conditions_1 / pH: 4.5 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker AvanceI / Manufacturer: Bruker / Model: AvanceI / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
CYANA3.97Guntert, Mumenthaler and Wuthrichrefinement
TopSpinBruker Biospincollection
CARAKeller and Wuthrichchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospinprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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