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- PDB-1zxh: G311 mutant protein -

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Basic information

Entry
Database: PDB / ID: 1zxh
TitleG311 mutant protein
ComponentsImmunoglobulin G binding protein G
KeywordsImmune system/protein binding / IgG-binding / protein G / phage display / Immune system-protein binding COMPLEX
Function / homology
Function and homology information


IgG binding / extracellular region
Similarity search - Function
IgG-binding B / B domain / M protein-type anchor domain / Ubiquitin-like (UB roll) - #10 / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. ...IgG-binding B / B domain / M protein-type anchor domain / Ubiquitin-like (UB roll) - #10 / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesStreptococcus sp. (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 G


Theoretical massNumber of molelcules
Total (without water)6,3031
Polymers6,3031
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 G / IgG binding protein G


Mass: 6302.960 Da / Num. of mol.: 1 / Mutation: yes
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. (bacteria) / Gene: spg / Plasmid: pG58-G311 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P19909

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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, 3D HNCO, 3DCBCACONH, 3D HBHA(CBCACO)NH, 3D (H)C(CO)NH-TOCSY, H(CCO)NH-TOCSY, 2D TOCSY, 2D-CBHD, 2DCBHE, 2D TOCSY

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Sample preparation

DetailsContents: G311 mutant protein, 0.1 M KPi, pH7.0, ~0.6 M GuHCl.
Solvent system: 0.1 M KPi, pH7.0, ~0.6 M GuHCl.
Sample conditionsIonic strength: 0.1M / pH: 7 / Pressure: ambient / Temperature: 275 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
XwinNMR2.5Bruker Co.collection
NMRPipeFrank Delaglio Stephan Grzeiek, Guang Zhu, Geerten W. Vuister, John Pfeifer, and Ad Baxprocessing
Sparky3T. D. Goddard and D. G. Knellerdata 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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