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- PDB-7l7a: Solution Structure of NuxVA -

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Basic information

Entry
Database: PDB / ID: 7l7a
TitleSolution Structure of NuxVA
ComponentsNuxVA
KeywordsTOXIN / conotoxin / malaria / bioplex assay / proteogenomics / Erythrocyte Membrane Protein 1
Biological speciesConus nux (invertebrata)
MethodSOLUTION NMR / simulated annealing
AuthorsMari, F. / Dovell, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI137721 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI092120 United States
CitationJournal: J Proteomics / Year: 2020
Title: Conus venom fractions inhibit the adhesion of Plasmodium falciparum erythrocyte membrane protein 1 domains to the host vascular receptors.
Authors: Padilla, A. / Dovell, S. / Chesnokov, O. / Hoggard, M. / Oleinikov, A.V. / Mari, F.
History
DepositionDec 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jun 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: NuxVA


Theoretical massNumber of molelcules
Total (without water)1,4811
Polymers1,4811
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)32 / 100structures with acceptable covalent geometry
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide NuxVA


Mass: 1480.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Conus nux (invertebrata)

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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 NOESY
121isotropic12D 1H-1H TOCSY
131isotropic11D 1H exchange

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Sample preparation

DetailsType: solution
Contents: 1.275 mM nuxVA, 10 % [U-99% 2H] D2O, 0.025 mM TSP, 90 % H2O, 90% H2O/10% D2O
Label: 1H_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.275 mMnuxVAnatural abundance1
10 %D2O[U-99% 2H]1
0.025 mMTSPnatural abundance1
90 %H2Onatural abundance1
Sample conditionsIonic strength: low-medium Not defined / Label: conditions_1 / pH: 3.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMRVarianprocessing
X-PLOR NIH2.21Schwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
NMRFAM-SPARKYGoddardchemical shift assignment
SparkyGoddardpeak picking
AQUARullmann, Doreleijers and Kapteindata analysis
PROCHECK / PROCHECK-NMRLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntondata analysis
RefinementMethod: simulated annealing / Software ordinal: 5 / Details: torsion angle dynamics
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 100 / Conformers submitted total number: 32

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