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- PDB-2lg5: NMR structure of Chicken AvBD2 defensin -

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Basic information

Entry
Database: PDB / ID: 2lg5
TitleNMR structure of Chicken AvBD2 defensin
ComponentsGallinacin-2
KeywordsANTIMICROBIAL PROTEIN
Function / homology
Function and homology information


CCR6 chemokine receptor binding / chemoattractant activity / secretory granule / cell chemotaxis / defense response / defense response to bacterium / extracellular space
Similarity search - Function
Beta defensin type / Beta defensin
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsMeudal, H. / Landon, C.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Initial insights into structure-activity relationships of avian defensins.
Authors: Derache, C. / Meudal, H. / Aucagne, V. / Mark, K.J. / Cadene, M. / Delmas, A.F. / Lalmanach, A.C. / Landon, C.
History
DepositionJul 21, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gallinacin-2


Theoretical massNumber of molelcules
Total (without water)3,9281
Polymers3,9281
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)10 / 200structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Gallinacin-2 / Gal-2 / Beta-defensin 2


Mass: 3927.650 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Gallus gallus (chicken) / References: UniProt: P46158
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1422D 1H-1H COSY
1522D 1H-1H TOCSY
1622D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.1 mM Chicken AvBD2 defensin, 90% H2O/10% D2O90% H2O/10% D2O
20.1 mM Chicken AvBD2 defensin, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.1 mMChicken AvBD2 defensin-11
0.1 mMChicken AvBD2 defensin-22
Sample conditionsIonic strength: 0 / pH: 4.1 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.1Linge, O'Donoghue and Nilgesstructure solution
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ARIA1.1Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 530 / NOE intraresidue total count: 279 / NOE long range total count: 110 / NOE medium range total count: 29 / NOE sequential total count: 112
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 10

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