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- PDB-2jwd: protein A -

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Basic information

Entry
Database: PDB / ID: 2jwd
Titleprotein A
ComponentsImmunoglobulin G-binding protein A
KeywordsIMMUNE SYSTEM / protein a / poly glutamine / Cell wall / IgG-binding protein / Peptidoglycan-anchor / Secreted
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 / torsion angle dynamics
Model detailsImmunoglobulin G binding protein A with N-terminal 5Q expansion
AuthorsRobertson, A. / Horne, J. / Scanlon, M.J. / Bottomley, S.P.
CitationJournal: To be Published
Title: Polyglutamine length-dependent midfolding is confined to the Poly-Q region
Authors: Robertson, A. / Horne, J. / Thomas, B. / Ellisdon, A.M. / Scanlon, M.J. / Bottomley, S.P.
History
DepositionOct 9, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)6,7721
Polymers6,7721
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)29 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

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


Mass: 6772.414 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 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P38507

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Immunoglobulin G binding protein A with N-terminal 5Q expansion
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-1H NOESY
1313D HN(CA)CB
1413D HNCO
1513D HN(CO)CA
1613D H(CCO)NH
1713D 1H-15N NOESY

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Sample preparation

DetailsContents: 20mM sodium acetate, 100mM sodium chloride, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
20 mMsodium acetate1
100 mMsodium chloride1
10 %D2O1
90 %H2O1
Sample conditionsIonic strength: 100 / pH: 5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian Unity / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichchemical shift assignment
X-PLOR NIH2.11Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.11Schwieters, Kuszewski, Tjandra and Clorerefinement
Sparky3.112Goddarddata analysis
Sparky3.112Goddardpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: Long, slow-cooling annealing protocol with final Powell minimisation step. Ramachandran potential included in Xplor-nih.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 29

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