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- PDB-2lwl: Structural Basis for the Interaction of Human β-Defensin 6 a... -

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Basic information

Entry
Database: PDB / ID: 2lwl
TitleStructural Basis for the Interaction of Human β-Defensin 6 and Its Putative Chemokine Receptor CCR2 and Breast Cancer Microvesicles
ComponentsBeta-defensin 106
KeywordsANTIMICROBIAL PROTEIN / breast cancer / dynamic
Function / homology
Function and homology information


microvesicle / CCR2 chemokine receptor binding / Beta defensins / Defensins / antifungal innate immune response / extrinsic component of membrane / lipopolysaccharide binding / heparin binding / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium ...microvesicle / CCR2 chemokine receptor binding / Beta defensins / Defensins / antifungal innate immune response / extrinsic component of membrane / lipopolysaccharide binding / heparin binding / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / innate immune response / nucleus
Similarity search - Function
Beta-defensin / Beta defensin / Antimicrobial Peptide, Beta-defensin 2; Chain A / Antimicrobial Peptide, Beta-defensin 2; Chain A / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
Model detailslowest energy, model1
Authorsde Paula, V.S. / Gomes, N.S.F. / Lima, L.G. / Miyamoto, C.A. / Monteiro, R.Q. / Almeida, F.C.L. / Valente, A.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Structural Basis for the Interaction of Human beta-Defensin 6 and Its Putative Chemokine Receptor CCR2 and Breast Cancer Microvesicles.
Authors: De Paula, V.S. / Gomes, N.S. / Lima, L.G. / Miyamoto, C.A. / Monteiro, R.Q. / Almeida, F.C. / Valente, A.P.
History
DepositionAug 2, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Nov 13, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-defensin 106


Theoretical massNumber of molelcules
Total (without water)5,4441
Polymers5,4441
Non-polymers00
Water0
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 #1lowest energy

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Components

#1: Protein/peptide Beta-defensin 106 / Beta-defensin 6 / BD-6 / DEFB-6 / Defensin / beta 106


Mass: 5444.380 Da / Num. of mol.: 1 / Mutation: C40S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DEFB106A, BD6, DEFB106, DEFB6, DEFB106B / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N104

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-13C NOESY
1213D 1H-15N NOESY

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Sample preparation

DetailsContents: 0.6 mM [U-99% 13C; U-99% 15N] sodium phosphate, 0.2-0.6 mM [U-99% 15N] sodium phosphate, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
0.6 mMsodium phosphate-1[U-99% 13C; U-99% 15N]1
mMsodium phosphate-2[U-99% 15N]0.2-0.61
Sample conditionsIonic strength: 5 / pH: 5.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance8001
Bruker DRXBrukerDRX6002

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Processing

NMR softwareName: ARIA/CNS version / Version: 1.2 / Developer: Nilges, M. / Classification: refinement
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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