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- PDB-2jni: Spatial structure of antimicrobial peptide arenicin-2 in aqueous ... -

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Basic information

Entry
Database: PDB / ID: 2jni
TitleSpatial structure of antimicrobial peptide arenicin-2 in aqueous solution
ComponentsArenicin-2
KeywordsANTIMICROBIAL PROTEIN / antimicrobial / beta-sheet
Function / homologyBRICHOS domain / BRICHOS domain / BRICHOS domain profile. / defense response to fungus / killing of cells of another organism / defense response to bacterium / Arenicin-2
Function and homology information
Biological speciesArenicola marina (lugworm)
MethodSOLUTION NMR / simulated annealing
AuthorsOvchinnikova, T.V. / Shenkarev, Z.O. / Nadezhdin, K.D. / Balandin, S.V. / Zhmak, M.N. / Kudelina, I.A. / Finkina, E.I. / Kokryakov, V.N. / Arseniev, A.S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2007
Title: Recombinant expression, synthesis, purification, and solution structure of arenicin
Authors: Ovchinnikova, T.V. / Shenkarev, Z.O. / Nadezhdin, K.D. / Balandin, S.V. / Zhmak, M.N. / Kudelina, I.A. / Finkina, E.I. / Kokryakov, V.N. / Arseniev, A.S.
History
DepositionJan 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 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 1.3Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arenicin-2


Theoretical massNumber of molelcules
Total (without water)2,7801
Polymers2,7801
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Arenicin-2 /


Mass: 2780.373 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arenicola marina (lugworm) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21 (DE3) / References: UniProt: Q5SC59

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D DQF-COSY
1312D 1H-1H NOESY

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Sample preparation

DetailsContents: 0.6 mM arenicin-2, 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.6 mM / Component: arenicin-2
Sample conditionsIonic strength: 0 / pH: 3.3 / Pressure: ambient / Temperature: 288 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
Bruker DRXBrukerDRX5001
Varian UnityVarianUNITY6002

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Processing

NMR software
NameVersionDeveloperClassification
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.peak picking
TopSpinBruker Biospincollection
TopSpinBruker Biospindata analysis
TopSpinBruker Biospinprocessing
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
VNMRVariancollection
VNMRVariandata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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