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- PDB-2a2b: Curvacin A -

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Basic information

Entry
Database: PDB / ID: 2a2b
TitleCurvacin A
ComponentsBacteriocin curvacin A
KeywordsANTIBIOTIC / alfa helix / beta-sheet like strukture
Function / homology
Function and homology information


killing of cells of another organism / defense response to bacterium / extracellular region
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #130 / Bacteriocin-type signal sequence / Bacteriocin class IIa domain superfamily / Bacteriocin, class IIa / Bacteriocin, class IIa, conserved site / Class II bacteriocin / Bacteriocin class IIa family signature. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bacteriocin curvacin-A
Similarity search - Component
Biological speciesLactobacillus curvatus (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsHaugen, H.S. / Kristiansen, P.E.
CitationJournal: Biochemistry / Year: 2005
Title: Three-dimensional structure in lipid micelles of the pediocin-like antimicrobial peptide curvacin A
Authors: Haugen, H.S. / Fimland, G. / Nissen-Meyer, J. / Kristiansen, P.E.
History
DepositionJun 22, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriocin curvacin A


Theoretical massNumber of molelcules
Total (without water)4,3131
Polymers4,3131
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 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Bacteriocin curvacin A / Curvacin A


Mass: 4312.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Lactobacillus curvatus (bacteria) / Strain: LTH1174 / References: UniProt: P0A311

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Experimental details

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Experiment

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

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Sample preparation

DetailsContents: 2.1mM Curvacin A, 350mM DPC, 89.9% H2O, 10% D2O, 0.1% TFA
Solvent system: 89.9% H2O, 10% D2O; 0.1% TFA
Sample conditionspH: 2.8 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglioprocessing
CYANA1.1Guntert, P.structure solution
Sparky3.11Goddarddata analysis
CYANA1.1Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: The structures are based on a total of 607 restraints, 567 are NOE-derived distance constraints, 28 dihedral angle constraints, 12 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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