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- PDB-6hz2: SOLUTION NMR STRUCTURE OF MAXIMIN 3 IN 50% TRIFLUOROETHANOL -

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Basic information

Entry
Database: PDB / ID: 6hz2
TitleSOLUTION NMR STRUCTURE OF MAXIMIN 3 IN 50% TRIFLUOROETHANOL
ComponentsMaximins 3/H11 type 2
KeywordsANTIMICROBIAL PROTEIN / maximin 3 antimicrobial peptide alpha helix
Function / homologyBombinin / Bombinin / hemolysis in another organism / defense response to fungus / defense response to bacterium / extracellular region / Maximins 3/H11 type 2
Function and homology information
Biological speciesBombina maxima (large-webbed bell toad)
MethodSOLUTION NMR / simulated annealing
AuthorsBenetti, S. / Timmons, P.B. / Hewage, C.M.
Citation
Journal: Eur.Biophys.J. / Year: 2019
Title: NMR model structure of the antimicrobial peptide maximin 3.
Authors: Benetti, S. / Timmons, P.B. / Hewage, C.M.
#1: Journal: Peptides / Year: 2002
Title: Antimicrobial peptides from skin secretions of Chinese red belly toad Bombina maxima.
Authors: Lai, R. / Zheng, Y.T. / Shen, J.H. / Liu, G.J. / Liu, H. / Lee, W.H. / Tang, S.Z. / Zhang, Y.
#2: Journal: J. Proteome Res. / Year: 2011
Title: There are abundant antimicrobial peptides in brains of two kinds of Bombina toads.
Authors: Liu, R. / Liu, H. / Ma, Y. / Wu, J. / Yang, H. / Ye, H. / Lai, R.
History
DepositionOct 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Jun 23, 2021Group: Data collection / Category: pdbx_nmr_spectrometer
Item: _pdbx_nmr_spectrometer.field_strength / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maximins 3/H11 type 2


Theoretical massNumber of molelcules
Total (without water)2,7031
Polymers2,7031
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NA
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2470 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1medoid

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Components

#1: Protein/peptide Maximins 3/H11 type 2


Mass: 2703.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bombina maxima (large-webbed bell toad) / References: UniProt: Q58T64

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic11D
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-1H NOESY
141isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution / Contents: 0.19 mM Maximin 3, trifluoroethanol/water / Details: 50% TFE/water / Label: maximin3_tfe / Solvent system: trifluoroethanol/water
SampleConc.: 0.19 mM / Component: Maximin 3 / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0 Not defined / Label: conditions_1 / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospinprocessing
NMRFAM-SPARKYNATIONAL MAGNETIC RESONANCE FACILITY AT MADISONpeak picking
NMRFAM-SPARKYNATIONAL MAGNETIC RESONANCE FACILITY AT MADISONchemical shift assignment
CYANA2Guntert, Mumenthaler and Wuthrichstructure calculation
NAMDNIH CENTER FOR MACROMOLECULAR MODELING & BIOINFORMATICS - UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGNrefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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