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- PDB-1kv4: Solution structure of antibacterial peptide (Moricin) -

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Basic information

Entry
Database: PDB / ID: 1kv4
TitleSolution structure of antibacterial peptide (Moricin)
Componentsmoricin
KeywordsANTIBIOTIC / HELIX / Insect immunity
Function / homology
Function and homology information


defense response to bacterium / innate immune response / extracellular region
Similarity search - Function
Moricin domain / Moricin family / Moricin domain superfamily / Moricin / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBombyx mori (domestic silkworm)
MethodSOLUTION NMR / simulated annealing
AuthorsHemmi, H. / Ishibashi, J. / Hara, S. / Yamakawa, M.
CitationJournal: FEBS Lett. / Year: 2002
Title: Solution structure of moricin, an antibacterial peptide, isolated from the silkworm Bombyx mori.
Authors: Hemmi, H. / Ishibashi, J. / Hara, S. / Yamakawa, M.
History
DepositionJan 25, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 22, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 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: moricin


Theoretical massNumber of molelcules
Total (without water)4,4881
Polymers4,4881
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #6lowest energy

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Components

#1: Protein/peptide moricin


Mass: 4488.476 Da / Num. of mol.: 1 / Mutation: H42A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Plasmid: pXa1 / Production host: Escherichia coli (E. coli) / References: UniProt: P82818

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQF-COSY
131E-COSY
142TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM moricin; 100% CD3OH100% CD3OH
21.5mM moricin; 100% CD3OD100% CD3OD
Sample conditionspH: 2.4 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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 AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
Sparky3.105Goddard and Knellerdata analysis
X-PLOR3.51Brungerstructure solution
X-PLOR3.51Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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