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- PDB-8qhh: NMR solution structure of the green kiwi fruit allergen Act d 8.0101 -

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Basic information

Entry
Database: PDB / ID: 8qhh
TitleNMR solution structure of the green kiwi fruit allergen Act d 8.0101
ComponentsBet v 1 related allergen
KeywordsALLERGEN / PR-10 allergen
Function / homology
Function and homology information


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 / Bet v I type allergen / Bet v I/Major latex protein / Pathogenesis-related protein Bet v 1 family / : / START-like domain superfamily
Similarity search - Domain/homology
Bet v 1 related allergen
Similarity search - Component
Biological speciesActinidia deliciosa (Chinese gooseberry)
MethodSOLUTION NMR / simulated annealing
AuthorsZeindl, R. / Tollinger, M.
Funding support Austria, 2items
OrganizationGrant numberCountry
Austrian Science FundP26849 Austria
Austrian Research Promotion Agency858017 Austria
CitationJournal: Biomol NMR Assign / Year: 2021
Title: NMR resonance assignments of the PR-10 allergens Act c 8 and Act d 8 from golden and green kiwifruit.
Authors: Zeindl, R. / Tollinger, M.
History
DepositionSep 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bet v 1 related allergen


Theoretical massNumber of molelcules
Total (without water)16,8121
Polymers16,8121
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Bet v 1 related allergen


Mass: 16812.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinidia deliciosa (Chinese gooseberry)
Gene: ypr-10 / Production host: Escherichia coli (E. coli) / References: UniProt: D1YSM5

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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
122isotropic12D 1H-13C HSQC
132isotropic12D 1H-13C HSQC aromatic
142isotropic13D HNCO
152isotropic13D HN(CA)CO
162isotropic13D HN(CA)CB
172isotropic13D CBCA(CO)NH
182isotropic13D (H)CCH-TOCSY
191isotropic13D 1H-15N TOCSY
1102isotropic13D (H)CC(CO)NH-TOCSY
1111isotropic13D 1H-15N NOESY
1122isotropic13D 1H-13C NOESY
1132isotropic13D 1H-13C NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-99% 15N] Green kiwi fruit allergen Act d 8.0101, 20 mM sodium phosphate, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution20.5 mM [U-99% 13C; U-99% 15N] Green kiwi fruit allergen Act d 8.0101, 20 mM sodium phosphate, 90% H2O/10% D2O13C_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMGreen kiwi fruit allergen Act d 8.0101[U-99% 15N]1
20 mMsodium phosphatenatural abundance1
0.5 mMGreen kiwi fruit allergen Act d 8.0101[U-99% 13C; U-99% 15N]2
20 mMsodium phosphatenatural abundance2
Sample conditionsIonic strength: 0 Not defined / Label: conditions_1 / pH: 6.9 / Pressure: 1 bar / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Agilent Direct Drive / Manufacturer: Agilent / Model: Direct Drive / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20

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