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- PDB-7tiq: Backbone-modified variant of the B domain of Staphylococcal prote... -

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Basic information

Entry
Database: PDB / ID: 7tiq
TitleBackbone-modified variant of the B domain of Staphylococcal protein A: Aib residues in helix 2
ComponentsImmunoglobulin G binding protein A
KeywordsDE NOVO PROTEIN
Function / homology
Function and homology information


cell envelope / immunoglobulin binding / extracellular region
Similarity search - Function
Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily
Similarity search - Domain/homology
Immunoglobulin G-binding protein A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsSanthouse, J.R. / Leung, J.M.G. / Chong, L.T. / Horne, W.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1807301 United States
CitationJournal: Chem Sci / Year: 2022
Title: Implications of the unfolded state in the folding energetics of heterogeneous-backbone protein mimetics.
Authors: Santhouse, J.R. / Leung, J.M.G. / Chong, L.T. / Horne, W.S.
History
DepositionJan 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release

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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)6,4581
Polymers6,4581
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Antibody Immunoglobulin G binding protein A


Mass: 6458.166 Da / Num. of mol.: 1 / Fragment: B domain, residues 185-242 / Mutation: G29A / Source method: obtained synthetically / Source: (synth.) Staphylococcus aureus (bacteria) / References: UniProt: Q2UW47
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-1H COSY

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Sample preparation

DetailsType: solution
Contents: 0.64 mM B Domain of Staphylococcal protein A: Aib25, Aib27, Aib32, Aib35, 0.2 mM dss, 90% H2O/10% D2O
Label: sample_1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.64 mMB Domain of Staphylococcal protein A: Aib25, Aib27, Aib32, Aib35natural abundance1
0.2 mMdssnatural abundance1
Sample conditionsIonic strength: 10 mM / Label: conditions_1 / pH: 5 pH* / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
NMRFAM-SPARKYLee, Tonelli, Markleydata analysis
ARIALinge, O'Donoghue and Nilgesstructure calculation
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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