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- PDB-2nau: Solution structure of KYE28A in lipopolysachharide -

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Basic information

Entry
Database: PDB / ID: 2nau
TitleSolution structure of KYE28A in lipopolysachharide
Componentsentity
KeywordsANTIMICROBIAL PROTEIN / antimicrobial peptide mutant
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / distance geometry
Model detailslowest energy, model1
AuthorsBhunia, A. / Malmsten, M. / Datta, A.
CitationJournal: J. Biol. Chem. / Year: 2016
Title: Role of Aromatic Amino Acids in Lipopolysaccharide and Membrane Interactions of Antimicrobial Peptides for Use in Plant Disease Control.
Authors: Datta, A. / Bhattacharyya, D. / Singh, S. / Ghosh, A. / Schmidtchen, A. / Malmsten, M. / Bhunia, A.
History
DepositionJan 11, 2016Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2May 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: entity


Theoretical massNumber of molelcules
Total (without water)3,2841
Polymers3,2841
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 #1lowest energy

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Components

#1: Protein/peptide entity


Mass: 3283.855 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY

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Sample preparation

DetailsContents: 1mM entity-1, 1mM TSP-2, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMentity-11
1 mMTSP-21
Sample conditionsIonic strength: 0 / pH: 4.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Ascend TM / Manufacturer: Bruker / Model: Ascend TM / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANArefinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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