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- PDB-2lg6: NMR structure of chicken AvBD2-K31A mutant -

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Basic information

Entry
Database: PDB / ID: 2lg6
TitleNMR structure of chicken AvBD2-K31A mutant
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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_ref_seq_dif.details
Revision 1.2Oct 16, 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)3,8701
Polymers3,8701
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: 3869.548 Da / Num. of mol.: 1 / Mutation: K31A / 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
12.4 mM chicken AvBD2-K31A mutant, 90% H2O/10% D2O90% H2O/10% D2O
22.4 mM chicken AvBD2-K31A mutant, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
2.4 mMchicken AvBD2-K31A mutant-11
2.4 mMchicken AvBD2-K31A mutant-22
Sample conditionsIonic strength: 0 / pH: 4.1 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
ARIA1.1Linge, O'Donoghue and Nilgesstructure solution
ARIA1.1Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1069 / NOE intraresidue total count: 296 / NOE long range total count: 342 / NOE medium range total count: 170 / NOE sequential total count: 261
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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