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- PDB-2xv9: The solution structure of ABA-1A saturated with oleic acid -

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Basic information

Entry
Database: PDB / ID: 2xv9
TitleThe solution structure of ABA-1A saturated with oleic acid
ComponentsABA-1A1 REPEAT UNIT
KeywordsLIPID BINDING PROTEIN / FATTY ACID BINDING / RETINOL BINDING / ALLERGEN
Function / homologyNematode polyprotein allergen ABA-1 / Polyprotein allergen, nematode / DVA-1 superfamily / Nematode polyprotein allergen ABA-1 / Death Domain, Fas / retinol binding / Orthogonal Bundle / Mainly Alpha / Polyprotein ABA-1
Function and homology information
Biological speciesASCARIS SUUM (pig roundworm)
MethodSOLUTION NMR / DEFAULT
AuthorsSmith, B.O. / Kennedy, M.W. / Cooper, A. / Meenan, N.A.G. / Bromek, K.
Citation
Journal: PLoS Negl Trop Dis / Year: 2011
Title: Solution structure of a repeated unit of the ABA-1 nematode polyprotein allergen of Ascaris reveals a novel fold and two discrete lipid-binding sites.
Authors: Meenan, N.A. / Ball, G. / Bromek, K. / Uhrin, D. / Cooper, A. / Kennedy, M.W. / Smith, B.O.
#1: Journal: J.Biomol.NMR / Year: 2005
Title: Resonance Assignment of Aba-1A, from Ascaris Suum Nematode Polyprotein Allergen.
Authors: Meenan, N.A.G. / Cooper, A. / Kennedy, M.W. / Smith, B.O.
History
DepositionOct 25, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.2Jan 15, 2020Group: Data collection / Other
Category: pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr ..._pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABA-1A1 REPEAT UNIT


Theoretical massNumber of molelcules
Total (without water)15,1921
Polymers15,1921
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)20 / 20EXPERIMENTALLY DERIVED RESTRAINT ENERGY
RepresentativeModel #11

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Components

#1: Protein ABA-1A1 REPEAT UNIT


Mass: 15192.242 Da / Num. of mol.: 1 / Fragment: RESIDUES 534-662
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ASCARIS SUUM (pig roundworm) / Plasmid: PGEX LAMBDA1T / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q06811
Sequence detailsINCLUDES CLONING ARTEFACTS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N NOESY-HSQC
12113C HSQC
13115N HSQC
1413D 13C NOESY-HSQC
151(H)CCH-TOCSY
161C(CO)NH
171HN(CA)CB
181(H)CC(CO)NH
NMR detailsText: STRUCTURES CREATED BY ARIA2, FROM DATA RECORDED USING 15N AND 15N,13C LABELLED ABA-1A.

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Sample preparation

DetailsContents: 90% H2O/10% D2O
Sample conditionsIonic strength: 100.0 / pH: 7.0 / Pressure: 1.0 atm / Temperature: 308.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3/CNSNILGES M, BRUNGER ATrefinement
DANGLE1.1structure solution
CcpNmr Analysis2.1structure solution
CNS1.21structure solution
ARIA2.3structure solution
ANSIGstructure solution
PALES1structure solution
RefinementMethod: DEFAULT / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: EXPERIMENTALLY DERIVED RESTRAINT ENERGY
Conformers calculated total number: 20 / Conformers submitted total number: 20

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