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- PDB-1ss3: Solution structure of Ole e 6, an allergen from olive tree pollen -

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Basic information

Entry
Database: PDB / ID: 1ss3
TitleSolution structure of Ole e 6, an allergen from olive tree pollen
ComponentsPollen allergen Ole e 6
KeywordsALLERGEN / alpha-helix protein
Function / homologyPollen allergen ole e 6 / Pollen allergen ole e 6 / Pollen allergen ole e 6 superfamily / Pollen allergen Ole e 6 / IgG binding / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Major pollen allergen Ole e 6
Function and homology information
Biological speciesOlea europaea (common olive)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsTrevino, M.A. / Garcia-Mayoral, M.F. / Barral, P. / Villalba, M. / Santoro, J. / Rico, M. / Rodriguez, R. / Bruix, M.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: NMR Solution Structure of Ole e 6, a Major Allergen from Olive Tree Pollen.
Authors: Trevino, M.A. / Garcia-Mayoral, M.F. / Barral, P. / Villalba, M. / Santoro, J. / Rico, M. / Rodriguez, R. / Bruix, M.
History
DepositionMar 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pollen allergen Ole e 6


Theoretical massNumber of molelcules
Total (without water)5,8441
Polymers5,8441
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)25 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Pollen allergen Ole e 6


Mass: 5843.530 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Olea europaea (common olive) / Gene: OLE6 / Plasmid: pPIC9 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 his 4 / References: UniProt: O24172

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
1422D NOESY
1522D TOCSY
1633D 15N-separated NOESY
NMR detailsText: These structures were determined using standard 2D-NOE homonuclear techniques and 3D-NOE heteronuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM ole e 6; 95% H2O, 5% D2O95% H2O/5% D2O
20.6 mM ole e 6; 100% D2O100% D2O
31mM ole e 6 U-15N; 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditionsIonic strength: null / pH: 6.0 / Pressure: ambient / Temperature: 308 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionClassification
XwinNMR3.1collection
XwinNMR3.1processing
ANSIG3.3data analysis
DYANA1.5structure solution
DYANA1.5refinement
Amber7refinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: the structures are based on a total of 1428 unambigous NOEs, which leads to 900 upper limit distances. 486 relevant distance restraints, and 24 angle constraints were used. The best ...Details: the structures are based on a total of 1428 unambigous NOEs, which leads to 900 upper limit distances. 486 relevant distance restraints, and 24 angle constraints were used. The best conformers were energy-minimized with AMBER7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 25

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