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- PDB-7lvg: Jug r 2 Leader Sequence Residues 69-111 -

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Basic information

Entry
Database: PDB / ID: 7lvg
TitleJug r 2 Leader Sequence Residues 69-111
ComponentsVicilin Jug r 2.0101
KeywordsALLERGEN / Seed storage
Function / homology
Function and homology information


nutrient reservoir activity / copper ion binding
Similarity search - Function
Vicilin, N-terminal / Vicilin N terminal region / Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
Vicilin Jug r 2.0101
Similarity search - Component
Biological speciesJuglans regia (English walnut)
MethodSOLUTION NMR / simulated annealing
AuthorsMueller, G.A. / Foo, A.C.Y. / DeRose, E.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Z01-ES102906 United States
CitationJournal: J.Agric.Food Chem. / Year: 2022
Title: Structure, Immunogenicity, and IgE Cross-Reactivity among Walnut and Peanut Vicilin-Buried Peptides.
Authors: Foo, A.C.Y. / Nesbit, J.B. / Gipson, S.A.Y. / Cheng, H. / Bushel, P. / DeRose, E.F. / Schein, C.H. / Teuber, S.S. / Hurlburt, B.K. / Maleki, S.J. / Mueller, G.A.
History
DepositionFeb 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Vicilin Jug r 2.0101


Theoretical massNumber of molelcules
Total (without water)5,8191
Polymers5,8191
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Size-exclusion chromatography elution volume corresponds to molecule with MW<10,000 Da, assay for oligomerization, NMR-determined correlation time of 3.240 ns consistent with a sub-10,000 Da molecular weight complex.
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Vicilin Jug r 2.0101 / 7S globulin / 7S seed storage protein / Allergen Jug r 2 / Vicilin Jug r 2 / Vicilin-like Jug r 2


Mass: 5819.420 Da / Num. of mol.: 1 / Fragment: N-terminal leader sequence, residues 69-111
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Juglans regia (English walnut) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9SEW4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D NOESY
121isotropic23D NOESY
131isotropic12D 1H-13C HSQC aliphatic
141isotropic12D 1H-13C HSQC aromatic
151isotropic12D 1H-15N HSQC
181isotropic13D HNCO
191isotropic13D HN(CA)CB
171isotropic13D CBCA(CO)NH
161isotropic13D C(CO)NH
1101isotropic13D H(CCO)NH

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Sample preparation

DetailsType: solution
Contents: 50 uM Sodium trimethylsilylpropanesulfonate (DSS), 90% H2O/10% D2O
Details: 90% PBS pH 7.4, 10% D20, 50 uM DSS Reference Standard
Label: 13C_15N_JR22 / Solvent system: 90% H2O/10% D2O
SampleConc.: 50 uM / Component: Sodium trimethylsilylpropanesulfonate (DSS) / Isotopic labeling: natural abundance
Sample conditionsDetails: 146 mM NaCl (8g/L) 2.68 mM KCl (0.2g/L) 4.2 mM Na2HPO4.7H20 (1.15g/L) 1.47 mM KH2PO4 (0.2g/L)
Ionic strength: 150 mM / Label: PBS / pH: 7.4 / Pressure: 1 atm / Temperature: 298.15 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
TALOSCornilescu, Delaglio and Baxstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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