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- PDB-1x22: Solution structure of a novel moricin analogue, an antibacterial ... -

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Basic information

Entry
Database: PDB / ID: 1x22
TitleSolution structure of a novel moricin analogue, an antibacterial peptide from a lepidopteran insect, Spodoptera litura
Componentsmoricin
KeywordsANTIBIOTIC / insect immunity / antibacterial peptide / moricin / purification / gene expression / solution structure
Function / homology
Function and homology information


defense response to bacterium / 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 speciesSpodoptera litura (butterflies/moths)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsOizumi, Y. / Hemmi, H. / Minami, M. / Asaoka, A. / Yamakawa, M.
CitationJournal: Biochim.Biophys.Acta / Year: 2005
Title: Isolation, gene expression and solution structure of a novel moricin analogue, antibacterial peptide from a lepidopteran insect, Spodoptera litura
Authors: Oizumi, Y. / Hemmi, H. / Minami, M. / Asaoka, A. / Yamakawa, M.
History
DepositionApr 18, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2013Group: Database references / Source and taxonomy
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
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

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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)4,5021
Polymers4,5021
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 / 200structures with the lowest energy
RepresentativeModel #5lowest energy

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Components

#1: Protein/peptide moricin / Sl moricin


Mass: 4502.461 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in a lepidopteran insect
Source: (synth.) Spodoptera litura (butterflies/moths) / References: UniProt: Q7YZB4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
131DQF-COSY
1422D TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM Sl moricin; CD3OH; 99.5%DCD3OH(99.5%D)
21.5mM Sl moricin; CD3OD; 99.8%DCD3OD(99.8%D)
Sample conditionspH: 2.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukerprocessing
Sparky3.105Goddard and Knellerdata analysis
X-PLOR3.851Brungerstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: distance geometry, 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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