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- PDB-2jon: Solution structure of the C-terminal domain Ole e 9 -

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Basic information

Entry
Database: PDB / ID: 2jon
TitleSolution structure of the C-terminal domain Ole e 9
ComponentsBeta-1,3-glucanase
KeywordsALLERGEN / olive pollen
Function / homology
Function and homology information


(1->3)-beta-D-glucan catabolic process / glucan endo-1,3-beta-D-glucosidase / glucan endo-1,3-beta-D-glucosidase activity / protein homodimerization activity / extracellular region
Similarity search - Function
Glycoside hydrolase family 17, plant / X8 domain / X8 domain / Possibly involved in carbohydrate binding / Glycoside hydrolase family 17 / Glycosyl hydrolases family 17 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Glucan endo-1,3-beta-D-glucosidase
Similarity search - Component
Biological speciesOlea europaea (common olive)
MethodSOLUTION NMR / molecular dynamics
AuthorsTrevino, M.A. / Palomares, O. / Castrillo, I. / Villalba, M. / Rodriguez, R. / Rico, M. / Santoro, J. / Bruix, M.
CitationJournal: Protein Sci. / Year: 2008
Title: Solution structure of the C-terminal domain of Ole e 9, a major allergen of olive pollen
Authors: Trevino, M.A. / Palomares, O. / Castrillo, I. / Villalba, M. / Rodriguez, R. / Rico, M. / Santoro, J. / Bruix, M.
History
DepositionMar 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 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
Revision 1.3Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999 SEQUENCE AT THE TIME OF PROCESSING, THE SEQUENCE OF THIS PROTEIN IS NOT AVAILABLE AT THE UNP ... SEQUENCE AT THE TIME OF PROCESSING, THE SEQUENCE OF THIS PROTEIN IS NOT AVAILABLE AT THE UNP SEQUENCE DATABASE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-1,3-glucanase


Theoretical massNumber of molelcules
Total (without water)10,5961
Polymers10,5961
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Beta-1,3-glucanase


Mass: 10595.590 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Olea europaea (common olive) / Gene: OLE9 / Production host: Pichia pastoris (fungus) / Strain (production host): KM71 / References: UniProt: Q94G86
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1422D 1H-1H COSY
1522D 1H-1H TOCSY
1622D 1H-1H NOESY
2712D 1H-1H COSY
2812D 1H-1H TOCSY
2912D 1H-1H NOESY
21022D 1H-1H COSY
21122D 1H-1H TOCSY
21222D 1H-1H NOESY
11332D 1H-15N HSQC
11442D 1H-13C HSQC
11543D CBCA(CO)NH
11643D HN(CO)CA
11743D (H)CCH-TOCSY
11843D 1H-13C NOESY
11933D HNHA
12033D 1H-15N NOESY
12143D CBCANH
12243D HNCA
12343D HACANH

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM CtD-Ole e 9, 90% H2O/10% D2O90% H2O/10% D2O
20.7 mM CtD-Ole e 9, 100% D2O100% D2O
30.7 mM [U-15N] CtD-Ole e 9, 90% H2O/10% D2O90% H2O/10% D2O
40.7 mM [U-13C; U-15N] CtD-Ole e 9, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMCtD-Ole e 91
0.7 mMCtD-Ole e 92
0.7 mMCtD-Ole e 9[U-15N]3
0.7 mMCtD-Ole e 9[U-13C; U-15N]4
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
106ambient 298 K
206ambient 283 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRBruker Biospincollection
XwinNMRBruker Biospinprocessing
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddardchemical shift calculation
SparkyGoddarddata analysis
SparkyGoddardpeak picking
MARSJungchemical shift assignment
MARSJungdata analysis
CYANAGuntert, Mumenthaler and Wuthrichdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
MOLMOLKoradi, Billeter and Wuthrichstructures drawing
MOLMOLKoradi, Billeter and Wuthrichstructure analysis
Procheck4.3.3Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, and Mossstructure analysis
CANDIDHerrmann, Guntert and Wuthrichnoe assigment
PREDITOR(PREDITOR) Berjanskii, Neal and Wishartdihedral angle prediction
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsProtein chi angle constraints total count: 0 / Protein phi angle constraints total count: 273 / Protein psi angle constraints total count: 61
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 14.57 ° / Maximum upper distance constraint violation: 0.35 Å

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