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- PDB-6i9f: Solution structure of As-p18 reveals that nematode fatty acid bin... -

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Basic information

Entry
Database: PDB / ID: 6i9f
TitleSolution structure of As-p18 reveals that nematode fatty acid binding proteins exhibit unusual structural features
ComponentsFatty acid-binding protein homolog
KeywordsLIPID BINDING PROTEIN / FABP / Complex
Function / homology
Function and homology information


Fatty acid-binding protein homologue 1/2/3/4 / Cytosolic fatty-acid binding proteins signature. / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
OLEIC ACID / Fatty acid-binding protein homolog
Similarity search - Component
Biological speciesAscaris suum (pig roundworm)
MethodSOLUTION NMR / simulated annealing
AuthorsIbanez Shimabukuro, M. / Rey Burusco, M.F. / Kennedy, M.W. / Corsico, B. / Smith, B.O.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust083625 United Kingdom
Citation
Journal: Biosci.Rep. / Year: 2019
Title: As-p18, an extracellular fatty acid binding protein of nematodes, exhibits unusual structural features.
Authors: Ibanez-Shimabukuro, M. / Rey-Burusco, M.F. / Gabrielsen, M. / Franchini, G.R. / Riboldi-Tunnicliffe, A. / Roe, A.J. / Griffiths, K. / Cooper, A. / Corsico, B. / Kennedy, M.W. / Smith, B.O.
#1: Journal: Biomol.Nmr Assign. / Year: 2014
Title: Resonance assignment of As-p18, a fatty acid binding protein secreted by developing larvae of the parasitic nematode Ascaris suum.
Authors: Ibanez-Shimabukuro, M. / Rey-Burusco, M.F. / Cooper, A. / Kennedy, M.W. / Corsico, B. / Smith, B.O.
History
DepositionNov 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.2Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fatty acid-binding protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6292
Polymers18,3471
Non-polymers2821
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, Stoichiometry from fluorescent ligand displacement titration, Stoichiometry from NMR chemical shift perturbation titration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area770 Å2
ΔGint3 kcal/mol
Surface area8860 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Fatty acid-binding protein homolog / AS-P18


Mass: 18346.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Signal peptide omitted. His-tagged / Source: (gene. exp.) Ascaris suum (pig roundworm) / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P55776
#2: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2 / Feature type: SUBJECT OF INVESTIGATION

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
212isotropic13D 1H-13C NOESY
323isotropic1niceF2filtNOE
333isotropic1F1filtCdec
344isotropic13D 1H-13C NOESY
353isotropic1D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.5 mM [U-99% 13C; U-99% 15N] rAs-p18, 95% H2O/5% D2OpH 7.4 298KNC_noHPLC_Asp1895% H2O/5% D2O
solution20.4 mM [U-99% 13C; U-99% 15N] rAs-p18, 95% H2O/5% D2OpH 7.2 298KNC005Asp1895% H2O/5% D2O
solution30.5 mM [U-99% 13C; U-99% 15N] rAs-p18, 2 mM sodium oleate, 95% H2O/5% D2OpH 7.4 298KAsp1895% H2O/5% D2O
solution40.5 mM [U-99% 13C; U-99% 15N] rAs-p18, 2 mM sodium oleate, 95% H2O/5% D2OpH 7.4 298KAsp18+FullLabeledOLA95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMrAs-p18[U-99% 13C; U-99% 15N]1
0.4 mMrAs-p18[U-99% 13C; U-99% 15N]2
0.5 mMrAs-p18[U-99% 13C; U-99% 15N]3
2 mMsodium oleatenatural abundance3
0.5 mMrAs-p18[U-99% 13C; U-99% 15N]4
2 mMsodium oleatenatural abundance4
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
160 mMCondSet67.4 Not defined1 atm298 K
220 mMAsp18NC0057.2 Not defined1 atm298 K
320 mMAsp18_17.4 Not defined1 atm298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3.1Linge, O'Donoghue and Nilgesstructure calculation
CcpNmr Analysis2.4CCPNdata analysis
AzaraBoucherprocessing
DANGLE1.1Broadhurstdata analysis
TopSpinBruker Biospincollection
CcpNmr Entry Completion Interface2.1CCPN & PDBEdata analysis
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
Refinement
MethodSoftware ordinal
simulated annealing7
simulated annealing1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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