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- PDB-5wye: Structure of gold nano particle-tagged VG16KRKP in Salmonella typ... -

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Basic information

Entry
Database: PDB / ID: 5wye
TitleStructure of gold nano particle-tagged VG16KRKP in Salmonella typhi LPS
ComponentsAu-VG16KRKP
KeywordsANTIMICROBIAL PROTEIN / ANTIMICROBIAL PEPTIDE / GOLD NANOPARTICLE TAGGED / TURN AND LOOP TYPE STRUCTURE / AMPHIPATHIC STRUCTURE
Biological speciesDengue virus
MethodSOLUTION NMR / distance geometry
AuthorsIlyas, H. / Bhunia, A.
Funding support India, 1items
OrganizationGrant numberCountry
Bose InstituteInstitutional Plan Project II India
CitationJournal: Nanoscale / Year: 2017
Title: Multivalent gold nanoparticle-peptide conjugates for targeting intracellular bacterial infections
Authors: Chowdhury, R. / Ilyas, H. / Ghosh, A. / Ali, H. / Ghorai, A. / Midya, A. / Jana, N.R. / Das, S. / Bhunia, A.
History
DepositionJan 12, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: citation / database_2 ...citation / database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2May 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: Au-VG16KRKP


Theoretical massNumber of molelcules
Total (without water)1,7651
Polymers1,7651
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1730 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Au-VG16KRKP


Mass: 1765.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence was chemically synthesized / Source: (synth.) Dengue virus

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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
121isotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: solution
Contents: 0.5 mM None Au-VG16KRKP, 15 uM None LPS from S. typhosa, 55.5 M None H2O, 50 M None D2O, 1 mM None TSP, 90% H2O/10% D2O
Label: Au-VG16KRKP_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMAu-VG16KRKPNone1
15 uMLPS from S. typhosaNone1
55.5 MH2ONone1
50 MD2ONone1
1 mMTSPNone1
Sample conditionsDetails: The sample was prepared at 298.15 K and the pH was adjusted to 6.5. No heating effect occurred.
Ionic strength: 0.00 M / Ionic strength err: 0 / Label: Au-VG16KRKP_conditions / pH: 6.5 / PH err: 0 / Pressure: 1 atm / Pressure err: 0 / Temperature: 298.15 K / Temperature err: 0

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz / Details: with cryoprobe

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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