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- PDB-5wrx: VG13P structure in LPS -

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Basic information

Entry
Database: PDB / ID: 5wrx
TitleVG13P structure in LPS
Componentsanalogue peptide VG13P
KeywordsDE NOVO PROTEIN / ANTIMICROBIAL PROTEIN / antimicrobial peptide / endotoxin neutralisation / turn and loop-like structure
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodSOLUTION NMR / simulated annealing
AuthorsDatta, A. / Bhunia, A.
CitationJournal: Biochemistry / Year: 2017
Title: Structural and Dynamic Insights into a Glycine-Mediated Short Analogue of a Designed Peptide in Lipopolysaccharide Micelles: Correlation Between Compact Structure and Anti-Endotoxin Activity.
Authors: Datta, A. / Jaiswal, N. / Ilyas, H. / Debnath, S. / Biswas, K. / Kumar, D. / Bhunia, A.
History
DepositionDec 4, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
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 / _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: analogue peptide VG13P


Theoretical massNumber of molelcules
Total (without water)1,4501
Polymers1,4501
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1450 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 analogue peptide VG13P


Mass: 1449.745 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 homonuclear TOCSY
121isotropic12D trNOESY

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Sample preparation

DetailsType: solution
Contents: 1 mM Peptide VG13P, 0.1 mM TSP, 0.02 mM LPS, 55.5 M Water, 56.5 M D2O, 90% H2O/10% D2O
Label: VG13P in LPS micelle / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPeptide VG13Pnatural abundance1
0.1 mMTSPnatural abundance1
0.02 mMLPSnatural abundance1
55.5 MWaternatural abundance1
56.5 MD2Onatural abundance1
Sample conditionsIonic strength: 0 Not defined / Label: condition_1 / pH: 4.5 / PH err: 0.1 / Pressure: 1 atm / Temperature: 298 K / Temperature err: 0.05

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
TopSpin3.1Bruker Biospinprocessing
Sparky3.114Goddardchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Violated NOE distance constraints were corrected at each refinement step
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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