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- PDB-7lxk: Ara h 1 leader sequence, Ara h 1.0101 (25-83) A25G -

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Basic information

Entry
Database: PDB / ID: 7lxk
TitleAra h 1 leader sequence, Ara h 1.0101 (25-83) A25G
ComponentsAllergen Ara h 1, clone P41B
KeywordsALLERGEN / Peanut Allergen
Function / homologyCupin / Cupin 1 / Cupin / IgE binding / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / Allergen Ara h 1, clone P41B
Function and homology information
Biological speciesArachis hypogaea (peanut)
MethodSOLUTION NMR / simulated annealing
AuthorsMueller, G. / London, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Z01-ES102885-01 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
DepositionMar 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Allergen Ara h 1, clone P41B


Theoretical massNumber of molelcules
Total (without water)6,7331
Polymers6,7331
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5800 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 Allergen Ara h 1, clone P41B / Allergen Ara h I


Mass: 6733.499 Da / Num. of mol.: 1 / Fragment: Leader sequence, residues 25-83 / Mutation: A25G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arachis hypogaea (peanut) / Production host: Escherichia coli (E. coli) / References: UniProt: P43238

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Experimental details

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Experiment

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

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-13C; U-15N] A1pro, 137 mM sodium chloride, 10 mM sodium phosphate, 2.7 mM potassium chloride, 0.2 uM DSS, 95% H2O/5% D2O
Label: 13C15N / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMA1pro[U-13C; U-15N]1
137 mMsodium chloridenatural abundance1
10 mMsodium phosphatenatural abundance1
2.7 mMpotassium chloridenatural abundance1
0.2 uMDSSnatural abundance1
Sample conditionsIonic strength: 0.15 M / Label: structure determination / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Agilent DD2AgilentDD26001
Agilent DD2AgilentDD28002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRViewJohnson, One Moon Scientificpeak picking
RefinementMethod: simulated annealing / 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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