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- PDB-1y5c: The structure of a lactoferricinB derivative bound to micelles (L... -

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Basic information

Entry
Database: PDB / ID: 1y5c
TitleThe structure of a lactoferricinB derivative bound to micelles (LfcinB4-14)
ComponentsLactotransferrin
KeywordsTRANSPORT PROTEIN / Micelle-bound
Function / homologyLactoferrin
Function and homology information
MethodSOLUTION NMR
AuthorsNguyen, L.T. / Schibli, D.J. / Vogel, H.J.
CitationJournal: J.Pept.Sci. / Year: 2005
Title: Structural studies and model membrane interactions of two peptides derived from bovine lactoferricin
Authors: Nguyen, L.T. / Schibli, D.J. / Vogel, H.J.
History
DepositionDec 2, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: 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
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
Revision 1.4May 22, 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: Lactotransferrin


Theoretical massNumber of molelcules
Total (without water)1,5501
Polymers1,5501
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 / 100structures with the lowest energy
Representative

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Components

#1: Protein/peptide Lactotransferrin / Lactoferrin / Lactoferricin B / Lfcin B


Mass: 1549.910 Da / Num. of mol.: 1 / Fragment: residues 4-14 / Source method: obtained synthetically
Details: This sequence is derived from residues 4-14 of lactoferricinB (Bovine).
References: UniProt: Q0PGA5*PLUS

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Experimental details

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Experiment

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

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Sample preparation

DetailsContents: 3mM LfcinB4-14 with 180mM SDS, 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
Sample conditionspH: 4.4 / Pressure: ambient / Temperature: 310 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameClassification
NMRPipeprocessing
XwinNMRcollection
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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