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- PDB-2kk9: Anti-group A streptococcal vaccine epitope: structure, stability ... -

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Basic information

Entry
Database: PDB / ID: 2kk9
TitleAnti-group A streptococcal vaccine epitope: structure, stability and its ability to interact with HLA class II molecules
ComponentsM protein, serotype 5
KeywordsANTIMICROBIAL PROTEIN / S. pyogenes / M5 protein / Synthetic peptide vaccine / Cell wall / Peptidoglycan-anchor / Phagocytosis / Secreted / Virulence / UNKNOWN FUNCTION
Function / homology
Function and homology information


cell wall / : / phagocytosis / extracellular region / membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #460 / M protein repeat / M protein repeat / : / M protein-type anchor domain / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #460 / M protein repeat / M protein repeat / : / M protein-type anchor domain / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
M protein, serotype 5
Similarity search - Component
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsfewest violations
AuthorsGuilherme, L. / Alba, M.P. / Patarroyo, M.E. / Kalil, J.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Anti-Group A Streptococcal Vaccine Epitope: STRUCTURE, STABILITY, AND ITS ABILITY TO INTERACT WITH HLA CLASS II MOLECULES.
Authors: Guilherme, L. / Alba, M.P. / Ferreira, F.M. / Oshiro, S.E. / Higa, F. / Patarroyo, M.E. / Kalil, J.
History
DepositionJun 16, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: M protein, serotype 5


Theoretical massNumber of molelcules
Total (without water)6,3781
Polymers6,3781
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)1 / 50structures with the lowest energy
RepresentativeModel #1

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Components

#1: Protein M protein, serotype 5


Mass: 6378.198 Da / Num. of mol.: 1 / Fragment: UNP residues 300-354 / Source method: obtained synthetically / Details: A 55-mer-long synthetic peptide / References: UniProt: P02977

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: A 55-mer-long synthetic peptide was designed after selecting T and B cell epitopes using a large panel of PMBCs and sera healthy induividuals and rheumatic fever patients based on the ...Details: A 55-mer-long synthetic peptide was designed after selecting T and B cell epitopes using a large panel of PMBCs and sera healthy induividuals and rheumatic fever patients based on the sequuences of the C-terminal portion of S. pyogenes M5 protein as described by Robinson et al Int. Inmunol. 6:1235-1244
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY

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Sample preparation

DetailsContents: 5.4 mg/mL, trifluoroethanol/water 30/70% / Solvent system: trifluoroethanol/water 30/70%
SampleConc.: 5.4 mM / Component: entity-1
Sample conditionspH: 3.7 / Pressure: ambient atm / Temperature: 295 K

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NMR measurement

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

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Processing

NMR softwareName: TOPSPIN / Developer: Bruker Biospin / Classification: processing
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 1

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