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- PDB-2n9a: 3D Structure of Decoralin-NH2 by Solution NMR -

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Basic information

Entry
Database: PDB / ID: 2n9a
Title3D Structure of Decoralin-NH2 by Solution NMR
ComponentsDecoralin
KeywordsANTIMICROBIAL PROTEIN / antimicrobial peptides / leishmanicidal activity / membrane targeting peptides
Function / homology
Function and homology information


cytolysis / other organism cell membrane / positive regulation of mast cell degranulation / mast cell degranulation / defense response to protozoan / defense response to fungus / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / extracellular region / membrane
Similarity search - Function
Biological speciesOreumenes decoratus (insect)
MethodSOLUTION NMR / simulated annealing
Model detailslowest target function, model1
AuthorsFadel, V. / Cabrera, M.P.S.
CitationJournal: Chem Biol Drug Des / Year: 2017
Title: MD simulations and multivariate studies for modeling the antileishmanial activity of peptides.
Authors: Guerra, M.E.R. / Fadel, V. / Maltarollo, V.G. / Baldissera, G. / Honorio, K.M. / Ruggiero, J.R. / Dos Santos Cabrera, M.P.
History
DepositionNov 12, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.3Jun 14, 2023Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Decoralin


Theoretical massNumber of molelcules
Total (without water)1,2571
Polymers1,2571
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 / 40target function
RepresentativeModel #1lowest target function

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Components

#1: Protein/peptide Decoralin


Mass: 1256.603 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Oreumenes decoratus (insect) / References: UniProt: P85870

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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

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Sample preparation

DetailsContents: 2.65 mM Decoralin-NH2, trifluoroethanol/water / Solvent system: trifluoroethanol/water
SampleConc.: 2.65 mM / Component: Decoralin-NH2-1
Sample conditionspH: 5.0 / Pressure: ambient / Temperature: 298 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
UNIO_102.0.2Herrmannstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
GROMACSvan der Spoel, van Buuren, Apol, Meulenhoff, Tieleman, Sijbers, Hess, Feenstra, Lindahl, van Drunen, Berendsenrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 126 / NOE intraresidue total count: 57 / NOE medium range total count: 30 / NOE sequential total count: 39
NMR representativeSelection criteria: lowest target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 40 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0 Å
NMR ensemble rmsDistance rms dev: 0.012 Å

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