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- PDB-5mmu: NMR solution structure of the major apple allergen Mal d 1 -

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Basic information

Entry
Database: PDB / ID: 5mmu
TitleNMR solution structure of the major apple allergen Mal d 1
ComponentsMajor allergen Mal d 1
KeywordsALLERGEN / PR-10 protein apple 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
Similarity search - Function
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 allergen Mal d 1
Similarity search - Component
Biological speciesMalus domestica (apple)
MethodSOLUTION NMR / simulated annealing
AuthorsAhammer, L. / Grutsch, S. / Kamenik, A.S. / Liedl, K.R. / Tollinger, M.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP26849 Austria
Citation
Journal: J. Agric. Food Chem. / Year: 2017
Title: Structure of the Major Apple Allergen Mal d 1.
Authors: Ahammer, L. / Grutsch, S. / Kamenik, A.S. / Liedl, K.R. / Tollinger, M.
#1: Journal: Biomol NMR Assign / Year: 2016
Title: NMR resonance assignments of the major apple allergen Mal d 1
Authors: Ahammer, L. / Grutsch, S. / Tollinger, M.
History
DepositionDec 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_struct_sheet_hbond / struct_sheet_range
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_sheet_hbond.range_1_auth_comp_id ..._pdbx_audit_support.funding_organization / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Revision 1.3May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.4May 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 allergen Mal d 1


Theoretical massNumber of molelcules
Total (without water)17,5441
Polymers17,5441
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8920 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1target function

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Components

#1: Protein Major allergen Mal d 1 / Allergen Mal d I


Mass: 17543.689 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Malus domestica (apple) / Gene: MALD1 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P43211

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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-15C HSQC
132isotropic13D HNCO
142isotropic13D HN(CA)CB
152isotropic13D CBCA(CO)NH
182isotropic23D (H)CCH-TOCSY
172isotropic23D (H)CC(CO)NH-TOCSY
161isotropic23D 1H-15N TOCSY
1101isotropic13D 1H-13N NOESY
192isotropic13D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.8 mM [U-99% 15N] Mal d 1, 10 mM sodium phosphate, 11.2 mM L-ascorbic acid, 91% H2O/9% D2O15N_sample91% H2O/9% D2O
solution20.5 mM [U-13C; U-15N] Mal d 1, 10 mM sodium phosphate, 7 mM L-ascorbic acid, 91% H2O/9% D2O13C_15N_sample91% H2O/9% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMMal d 1[U-99% 15N]1
10 mMsodium phosphatenatural abundance1
11.2 mML-ascorbic acidnatural abundance1
0.5 mMMal d 1[U-13C; U-15N]2
10 mMsodium phosphatenatural abundance2
7 mML-ascorbic acidnatural abundance2
Sample conditionsIonic strength units: Not defined / Label: condition_1 / pH: 6.9 / PH err: 0.1 / Pressure: 960 mbar / Pressure err: 10 / Temperature: 298 K / Temperature err: 0.5

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Agilent Direct DriveAgilentDirect Drive5001
Bruker AVANCE IIBrukerAVANCE II6002Prodigy CryoProbe

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Processing

NMR software
NameVersionDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
Xplor-NIH2.42Schwieters, Kuszewski, Tjandra and Clorestructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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