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- PDB-2lpx: Solution Structure of Strawberry Allergen Fra a 1e -

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Basic information

Entry
Database: PDB / ID: 2lpx
TitleSolution Structure of Strawberry Allergen Fra a 1e
ComponentsMajor strawberry allergen Fra a 1-E
KeywordsUNKNOWN FUNCTION / Bet v 1 homologous protein
Function / homology
Function and homology information


flavonoid binding / flavonoid biosynthetic process / response to biotic stimulus / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity / nucleus / cytoplasm
Similarity search - Function
Bet v I type allergen / Bet v I/Major latex protein / Pathogenesis-related protein Bet v 1 family / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Major strawberry allergen Fra a 1-E
Similarity search - Component
Biological speciesFragaria x ananassa (strawberry)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsSeutter von Loetzen, C. / Hartl-Spiegelhauer, O. / Schweimer, K. / Schwab, W. / Roesch, P.
CitationJournal: Biosci.Rep. / Year: 2012
Title: Solution structure of the strawberry allergen Fra a 1.
Authors: Seutter von Loetzen, C. / Schweimer, K. / Schwab, W. / Rosch, P. / Hartl-Spiegelhauer, O.
History
DepositionFeb 20, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref / struct_ref_seq_dif
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 / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details
Revision 1.3May 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: Major strawberry allergen Fra a 1-E


Theoretical massNumber of molelcules
Total (without water)19,0121
Polymers19,0121
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 120structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Major strawberry allergen Fra a 1-E


Mass: 19012.428 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fragaria x ananassa (strawberry) / Gene: FRAA1E.2, FRAA1E.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q256S2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D CBCA(CO)NH
1813D HBHA(CO)NH
1913D C(CO)NH
11013D (H)CCH-TOCSY
11113D CCH-TOCSY
11213D 1H-15N NOESY
11313D 1H-13C NOESY aliphatic
11413D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 700 uM [U-99% 13C; U-99% 15N] protein, 150 mM sodium chloride, 20 mM HEPES, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
700 uMentity-1[U-99% 13C; U-99% 15N]1
150 mMsodium chloride-21
20 mMHEPES-31
Sample conditionspH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.6Bruker Biospincollection
NMRViewJohnson, One Moon Scientificdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 120 / Conformers submitted total number: 20

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