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- PDB-2poa: Schistosoma mansoni Sm14 Fatty Acid-Binding Protein: improvement ... -

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Basic information

Entry
Database: PDB / ID: 2poa
TitleSchistosoma mansoni Sm14 Fatty Acid-Binding Protein: improvement of protein stability by substitution of the single Cys62 residue
Components14 kDa fatty acid-binding protein
KeywordsLIPID BINDING PROTEIN / Schistosoma mansoni / fatty acid binding protein / site directed mutagenesis / protein stability / molecular dynamics / vaccine antigen
Function / homology
Function and homology information


lipid binding / cytoplasm
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
14 kDa fatty acid-binding protein
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodSOLUTION NMR / torsion angle dynamics using dyana software, further minimization with discover module of the insight package
AuthorsRamos, C.R.R. / Oyama Jr., S. / Sforca, M.L. / Pertinhez, T.A. / Ho, P.L. / Spisni, A.
CitationJournal: Biochim.Biophys.Acta / Year: 2009
Title: Stability improvement of the fatty acid binding protein Sm14 from S. mansoni by Cys replacement: Structural and functional characterization of a vaccine candidate.
Authors: Ramos, C.R. / Spisni, A. / Oyama, S. / Sforca, M.L. / Ramos, H.R. / Vilar, M.M. / Alves, A.C. / Figueredo, R.C. / Tendler, M. / Zanchin, N.I. / Pertinhez, T.A. / Ho, P.L.
History
DepositionApr 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 15, 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

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Assembly

Deposited unit
A: 14 kDa fatty acid-binding protein


Theoretical massNumber of molelcules
Total (without water)14,8631
Polymers14,8631
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)17 / 40target function
RepresentativeModel #17fewest violations

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Components

#1: Protein 14 kDa fatty acid-binding protein / Sm14-M20 / Sm14


Mass: 14862.772 Da / Num. of mol.: 1 / Mutation: C62V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Plasmid: pAE-Sm14(C62V) / Production host: Escherichia coli (E. coli) / References: UniProt: P29498

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA
121HN(CO)CA
131HN(CA)CB
141CBCA(CO)NH
1523D 13C-separated NOESY
1613D 15N-separated NOESY
NMR detailsText: the structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
1U-15N, 13C; 50 mM phosphate buffer pH 6.3; 0.05% sodium Azide; 95% H2O, 5% D2O.95% H2O/5% D2O
2U-15N, 13C; 100% D2O100% D2O
Sample conditionsIonic strength: 50 mM phosphate buffer / pH: 6.3 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Bruker AVANCEBrukerAVANCE6003

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guntert, Braun and Wuthrichstructure solution
Discoverrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
RefinementMethod: torsion angle dynamics using dyana software, further minimization with discover module of the insight package
Software ordinal: 1
Details: minimization were conducted with 5000 iterations using steepest descents algorithim until the maximum derivative is less than 1.000 kcal/A followed by 50000 iterations using conjugate ...Details: minimization were conducted with 5000 iterations using steepest descents algorithim until the maximum derivative is less than 1.000 kcal/A followed by 50000 iterations using conjugate gradients until the maximum derivative is less than 0.00100cal/A
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 40 / Conformers submitted total number: 17

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