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- PDB-7bx2: The solution NMR structure of VV14 peptide in the presence of Deu... -

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Basic information

Entry
Database: PDB / ID: 7bx2
TitleThe solution NMR structure of VV14 peptide in the presence of Deuterated SDS micelle.
ComponentsVAL-LYS-TRP-VAL-LYS-LYS-VAL-VAL-LYS-TRP-VAL-LYS-LYS-VAL
KeywordsANTIMICROBIAL PROTEIN / STRUCTURE FROM CYANA 2.1 / Antimicrobial peptide / SDS micelle / alpha helix.
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / distance geometry
AuthorsBhunia, A. / Mohid, S.A. / Chowdhury, N.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)EMR/2017/003457 India
CitationJournal: Chemmedchem / Year: 2021
Title: Effect of Secondary Structure and Side Chain Length of Hydrophobic Amino Acid Residues on the Antimicrobial Activity and Toxicity of 14-Residue-Long de novo AMPs.
Authors: Pandit, G. / Chowdhury, N. / Abdul Mohid, S. / Bidkar, A.P. / Bhunia, A. / Chatterjee, S.
History
DepositionApr 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 3, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VAL-LYS-TRP-VAL-LYS-LYS-VAL-VAL-LYS-TRP-VAL-LYS-LYS-VAL


Theoretical massNumber of molelcules
Total (without water)1,7601
Polymers1,7601
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1820 Å2
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 VAL-LYS-TRP-VAL-LYS-LYS-VAL-VAL-LYS-TRP-VAL-LYS-LYS-VAL


Mass: 1760.298 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-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
141isotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: solution
Contents: 1 mM 1H VAL-LYS-TRP-VAL-LYS-LYS-VAL-VAL-LYS-TRP-VAL-LYS-LYS-VAL, 90% H2O/10% D2O
Label: 1mM_VV14_peptide / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM
Component: VAL-LYS-TRP-VAL-LYS-LYS-VAL-VAL-LYS-TRP-VAL-LYS-LYS-VAL
Isotopic labeling: 1H
Sample conditionsDetails: 1mM VV14 peptide in 10mM Sodium phosphate buffer. / Ionic strength: 0 Not defined / Ionic strength err: 0 / Label: Conditions_1 / pH: 4.5 / PH err: 0.05 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.2

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III7001
Bruker AVANCE IIIBrukerAVANCE III5002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.5Bruker Biospincollection
TopSpin3.5Bruker Biospinprocessing
Sparky3.114Goddardchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: distance geometry / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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