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- PDB-1zxg: Solution structure of A219 -

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Basic information

Entry
Database: PDB / ID: 1zxg
TitleSolution structure of A219
ComponentsImmunoglobulin G binding protein A
KeywordsImmune System/Protein Binding / IgG-binding / protein A / phage display / Immune System-Protein Binding COMPLEX
Function / homology
Function and homology information


immunoglobulin binding / extracellular region
Similarity search - Function
Immunoglobulin FC, subunit C / Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain ...Immunoglobulin FC, subunit C / 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 / 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 / CNS 1.1.
AuthorsHe, Y. / Yeh, D.C. / Alexander, P. / Bryan, P.N. / Orban, J.
CitationJournal: Biochemistry / Year: 2005
Title: Solution NMR structures of IgG binding domains with artificially evolved high levels of sequence identity but different folds.
Authors: He, Y. / Yeh, D.C. / Alexander, P. / Bryan, P.N. / Orban, J.
History
DepositionJun 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 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 1.4May 22, 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)6,7331
Polymers6,7331
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50The submitted conformer models are those with the fewest number of constraint violations.
RepresentativeModel #1lowest energy

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Components

#1: Antibody Immunoglobulin G binding protein A


Mass: 6733.484 Da / Num. of mol.: 1 / Mutation: yes
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: pG58-A219 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: Q53759

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
1313D HN(CA)CB, 3DHNCO, 3D CBCA(CO)NH, 3D HBHA(CBCACO)NH, 3D (H)C(CO)NH-TOCSY, H(CCO)NH-TOCSY, 2DTOCSY, 2D-CBHD, 2DCBHE, 2D TOCSY

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Sample preparation

DetailsContents: A219 mutant protein, 2 mM ammonium bicarbonate buffer, pH 7.0, 10% D2O
Solvent system: 2 mM ammonium bicarbonate buffer, 10% D2O.
Sample conditionsIonic strength: 2 mM / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.5Brukercollection
NMRPipeFrank Delaglio, Stephan Grzeiek, Guang Zhu, Geerten W. Vuister, John Pfeifer and Ad Baxprocessing
Sparky3T.D.Goddard and D.G.Kneller,data analysis
CNS1.1A.T.Brunger, P.D.Adams, G.M.Clore, W.L.Delano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warrenstructure solution
CNS1.1A.T.Brunger, P.D.Adams, G.M.Clore, W.L.Delano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warrenrefinement
RefinementMethod: CNS 1.1. / Software ordinal: 1 / Details: simulated annealing.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: The submitted conformer models are those with the fewest number of constraint violations.
Conformers calculated total number: 50 / Conformers submitted total number: 20

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