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- PDB-1kj6: Solution Structure of Human beta-Defensin 3 -

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Basic information

Entry
Database: PDB / ID: 1kj6
TitleSolution Structure of Human beta-Defensin 3
ComponentsBeta-defensin 3
KeywordsANTIBIOTIC / defensin / antimicrobial protein / human beta-defensin 3 / beta-defensin / HBD3
Function / homology
Function and homology information


CCR6 chemokine receptor binding / Beta defensins / Defensins / killing by host of symbiont cells / chemoattractant activity / cell chemotaxis / Golgi lumen / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...CCR6 chemokine receptor binding / Beta defensins / Defensins / killing by host of symbiont cells / chemoattractant activity / cell chemotaxis / Golgi lumen / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / extracellular space / extracellular region
Similarity search - Function
Antimicrobial Peptide, Beta-defensin 2; Chain A / Antimicrobial Peptide, Beta-defensin 2; Chain A / Beta defensin type / Beta defensin / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Distance geometry, Simulated Annealing, Molecular Dynamics
AuthorsSchibli, D.J. / Hunter, H.N. / Aseyev, V. / Starner, T.D. / Wiencek, J.M. / McCray Jr., P.B. / Tack, B.F. / Vogel, H.J.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: The solution structures of the human beta-defensins lead to a better understanding of the potent bactericidal activity of HBD3 against Staphylococcus aureus.
Authors: Schibli, D.J. / Hunter, H.N. / Aseyev, V. / Starner, T.D. / Wiencek, J.M. / McCray Jr., P.B. / Tack, B.F. / Vogel, H.J.
History
DepositionDec 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-defensin 3


Theoretical massNumber of molelcules
Total (without water)5,1741
Polymers5,1741
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
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Beta-defensin 3 / BD-3 / hBD-3


Mass: 5174.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P81534
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1312D COSY
1422D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.36 mM HBD390% H2O/10% D2O
20.36 mM HBD3100% D2O
Sample conditionspH: 4 / Pressure: ambient / Temperature: 298 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 AVANCEBrukerAVANCE5001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe1.8Delaglio, G., Grzejiek, S., Vuister, G., Zhu, G., Pfeifer, J., Bax, A.processing
NMRView4.1.3Johnson, B.A., Blevins, R.A.data analysis
CNS1A.T.Brunger, P.D.Adams, G.M.Clore, W.L.Delano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warrenrefinement
ARIA1J.Linge, S.O'Donoghue, M.Nilgesrefinement
RefinementMethod: Distance geometry, Simulated Annealing, Molecular Dynamics
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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