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- PDB-6r3c: Solution structure of birch pollen allergen Bet v 1a -

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Basic information

Entry
Database: PDB / ID: 6r3c
TitleSolution structure of birch pollen allergen Bet v 1a
ComponentsMajor pollen allergen Bet v 1-A
KeywordsALLERGEN / Bet v 1 / birch pollen allergen
Function / homology
Function and homology information


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
Pathogenesis-related protein Bet v I family / Pathogenesis-related proteins Bet v I family signature. / 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 pollen allergen Bet v 1-A
Similarity search - Component
Biological speciesBetula pendula (European white birch)
MethodSOLUTION NMR / simulated annealing
AuthorsSchweimer, K.
CitationJournal: Sci Rep / Year: 2019
Title: Identification of a natural ligand of the hazel allergen Cor a 1.
Authors: Jacob, T. / von Loetzen, C.S. / Reuter, A. / Lacher, U. / Schiller, D. / Schobert, R. / Mahler, V. / Vieths, S. / Rosch, P. / Schweimer, K. / Wohrl, B.M.
History
DepositionMar 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major pollen allergen Bet v 1-A


Theoretical massNumber of molelcules
Total (without water)17,4621
Polymers17,4621
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9760 Å2
MethodPISA
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 pollen allergen Bet v 1-A / Allergen Bet v I-A


Mass: 17461.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Betula pendula (European white birch) / Gene: BETVIA, BETVI / Production host: Escherichia coli (E. coli) / References: UniProt: P15494

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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 aromatic
141isotropic13D HNCO
151isotropic13D HNCA
1131isotropic13D CBCA(CO)NH
1121isotropic13D HN(CA)CB
1111isotropic13D HBHA(CO)NH
1101isotropic13D C(CO)NH
191isotropic23D (H)CCH-TOCSY
181isotropic23D CCH-TOCSY
171isotropic13D 1H-15N NOESY
161isotropic13D 1H-13C NOESY aliphatic
1141isotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-13C; U-15N] Betv1a, 0.05 mM sodium chloride, 0.05 mM sodium phosphate, 90% H2O/10% D2O
Label: 13C15N_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMBetv1a[U-13C; U-15N]1
0.05 mMsodium chloridenatural abundance1
0.05 mMsodium phosphatenatural abundance1
Sample conditionsIonic strength: 50 mM / Label: conditions_1 / pH: 8.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIBrukerAVANCE II8001TCI cryoprobe
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
XwinNMRBruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 2
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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