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- PDB-2kht: NMR Structure of human alpha defensin HNP-1 -

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Basic information

Entry
Database: PDB / ID: 2kht
TitleNMR Structure of human alpha defensin HNP-1
ComponentsNeutrophil defensin 1
KeywordsANTIMICROBIAL PROTEIN / microcrystalline protein / human alpha defensin / Defensin / Secreted / Antibiotic / Antiviral defense / Fungicide / Phosphoprotein
Function / homology
Function and homology information


pore-forming activity / Defensins / disruption of plasma membrane integrity in another organism / killing by host of symbiont cells / T cell chemotaxis / Alpha-defensins / defense response to protozoan / intracellular estrogen receptor signaling pathway / defense response to fungus / innate immune response in mucosa ...pore-forming activity / Defensins / disruption of plasma membrane integrity in another organism / killing by host of symbiont cells / T cell chemotaxis / Alpha-defensins / defense response to protozoan / intracellular estrogen receptor signaling pathway / defense response to fungus / innate immune response in mucosa / Golgi lumen / chemotaxis / azurophil granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / collagen-containing extracellular matrix / defense response to virus / killing of cells of another organism / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / immune response / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Mammalian defensins signature. / Alpha-defensin, C-terminal / Mammalian defensin / Defensin propeptide / Alpha-defensin propeptide / Alpha-defensin / Defensin propeptide / Beta/alpha-defensin, C-terminal / Defensin/corticostatin family
Similarity search - Domain/homology
Neutrophil defensin 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLID-STATE NMR / DGSA-distance geometry simulated annealing, simulated annealing
Model detailsminimized average, model 1
AuthorsZhang, Y. / Li, S. / Doherty, T.F. / Lubkowski, J. / Lu, W. / Li, J. / Barinka, C. / Hong, M.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Resonance assignment and three-dimensional structure determination of a human alpha-defensin, HNP-1, by solid-state NMR.
Authors: Zhang, Y. / Doherty, T. / Li, J. / Lu, W. / Barinka, C. / Lubkowski, J. / Hong, M.
History
DepositionApr 11, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2014Group: Experimental preparation
Revision 1.3Feb 26, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neutrophil defensin 1


Theoretical massNumber of molelcules
Total (without water)3,4521
Polymers3,4521
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)10 / 200structures with the lowest energy
RepresentativeModel #1minimized average

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Components

#1: Protein/peptide Neutrophil defensin 1 / HNP-1 / HP-1 / HP1 / Defensin / alpha 1 / HP 1-56 / Neutrophil defensin 2 / HNP-2 / HP-2 / HP2


Mass: 3452.111 Da / Num. of mol.: 1 / Fragment: Residues 65-94
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DEF1, DEFA1, DEFA2, MRS / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: P59665

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
Details: HNP-1 structure determination through 2D & 3D CC and NC correlation experiments by solid state NMR.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 13C-13C DARR 40 ms, 100 ms & 200 ms
1212D 15N-15N PDSD 3 s
2312D CM5RR 0.8 ms & 1.5 ms
2412D CHHC 200 us & 300 us
1513D 15N-13C-13C NCACX
1613D 15N-13C-13C NCOCX
2712D 15N-13C NCX

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Sample preparation

DetailsContents: Polycrystalline sample grown from 60% w/v PEG400, 30 mM Cacodylate, 60 mM Lithium Sulfate
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.5 1 atm268 K
26.5 1 atm253 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.21Schwieters, Kuszewski, Tjandra and Clorerefinement
Sparky3.113Goddardchemical shift assignment
TopSpin1.3Bruker Biospinprocessing
UCSF-Chimera1.3Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., and Ferrin, T.Erefinement
RefinementMethod: DGSA-distance geometry simulated annealing, simulated annealing
Software ordinal: 1
NMR constraintsProtein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 28 / Protein psi angle constraints total count: 28
NMR representativeSelection criteria: minimized average
NMR ensembleAverage torsion angle constraint violation: 12.41 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0.53 Å / Maximum torsion angle constraint violation: 22.622 ° / Maximum upper distance constraint violation: 2.68 Å / Torsion angle constraint violation method: TALOS
NMR ensemble rmsDistance rms dev: 0.58 Å

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