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- PDB-1ss1: STAPHYLOCOCCAL PROTEIN A, B-DOMAIN, Y15W MUTANT, NMR, 25 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1ss1
TitleSTAPHYLOCOCCAL PROTEIN A, B-DOMAIN, Y15W MUTANT, NMR, 25 STRUCTURES
ComponentsImmunoglobulin G binding protein A
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN-BINDING PROTEIN / THREE-HELICAL BUNDLE
Function / homology
Function and homology information


IgG binding / extracellular region
Similarity search - Function
Octapeptide repeat / Octapeptide repeat / Immunoglobulin FC, subunit C / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain ...Octapeptide repeat / Octapeptide repeat / Immunoglobulin FC, subunit C / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK type signal peptide / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Immunoglobulin G-binding protein A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodSOLUTION NMR / standard anneal.inp CNS script
AuthorsSato, S. / Religa, T.L. / Daggett, V. / Fersht, A.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: From The Cover: Testing protein-folding simulations by experiment: B domain of protein A.
Authors: Sato, S. / Religa, T.L. / Daggett, V. / Fersht, A.R.
History
DepositionMar 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Immunoglobulin G binding protein A


Theoretical massNumber of molelcules
Total (without water)6,9461
Polymers6,9461
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)26 / 103back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Antibody Immunoglobulin G binding protein A / IgG binding protein A / Staphylococcal protein A


Mass: 6945.584 Da / Num. of mol.: 1 / Fragment: B DOMAIN / Mutation: Y15W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: SPA / Plasmid: pRSET A / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: P38507

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1313D 15N-separated NOESY

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Sample preparation

DetailsContents: 2mM sample, U-13C, U-15N; 50 mM D-acetate buffer, 100 mM NaCl, pH 5.5; 90% H2O, 10% D2O
Solvent system: 90% H20, 10% D20
Sample conditionsIonic strength: 100 mM NaCl / 50 mM acetate / pH: 5.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2002.044.17.08Delaglio, F. et alprocessing
Sparky3.106Goddard, T. D. et aldata analysis
CNS1.1Brunger, A. T. et alstructure solution
CNS1.1Brunger, A. T. et alrefinement
RefinementMethod: standard anneal.inp CNS script / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with the least restraint violations
Conformers calculated total number: 103 / Conformers submitted total number: 26

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