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- PDB-7uv4: Pis v 3.0101 vicilin leader sequence residues 56-115 -

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Basic information

Entry
Database: PDB / ID: 7uv4
TitlePis v 3.0101 vicilin leader sequence residues 56-115
ComponentsVicilin Pis v 3.0101
KeywordsALLERGEN / Seed storage
Function / homology: / Cupin / Cupin 1 / Cupin / nutrient reservoir activity / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / Vicilin Pis v 3.0101
Function and homology information
Biological speciesPistacia vera (pistachio)
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: 2023
Title: Structure and IgE Cross-Reactivity among Cashew, Pistachio, Walnut, and Peanut Vicilin-Buried Peptides.
Authors: Foo, A.C.Y. / Nesbit, J.B. / Gipson, S.A.Y. / DeRose, E.F. / Cheng, H. / Hurlburt, B.K. / Kulis, M.D. / Kim, E.H. / Dreskin, S.C. / Mustafa, S. / Maleki, S.J. / Mueller, G.A.
History
DepositionApr 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vicilin Pis v 3.0101


Theoretical massNumber of molelcules
Total (without water)7,3091
Polymers7,3091
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
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 Vicilin Pis v 3.0101 / 7S globulin / 7S seed storage protein / 7S vicilin-like protein Pis v 3 / Vicilin Pis v 3


Mass: 7309.122 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pistacia vera (pistachio) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B4X640
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D 1H-13C NOESY
121isotropic23D 1H-15N NOESY
131isotropic23D C(CO)NH
141isotropic23D H(CCO)NH
151isotropic23D CBCA(CO)NH
161isotropic23D HNCO
181isotropic23D HN(CA)CB
171isotropic22D 1H-13C HSQC aliphatic
191isotropic22D 1H-13C HSQC aromatic

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Sample preparation

DetailsType: solution / Contents: 50 uM DSS, 90% H2O/10% D2O / Details: 90% PBS pH 7.4, 50 uM DSS reference standard / Label: 13C_15N / Solvent system: 90% H2O/10% D2O
SampleConc.: 50 uM / Component: DSS / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 150 mM / Label: PBS / pH: 7.5 / Pressure: 1 atm / Temperature: 298.15 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
NMRViewJohnson, One Moon Scientificpeak picking
TALOSCornilescu, Delaglio and Baxstructure calculation
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 6
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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