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- PDB-1q10: Ensemble of 40 Structures of the Dimeric Mutant of the B1 Domain ... -

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Basic information

Entry
Database: PDB / ID: 1q10
TitleEnsemble of 40 Structures of the Dimeric Mutant of the B1 Domain of Streptococcal Protein G
ComponentsImmunoglobulin G binding protein G
KeywordsPROTEIN BINDING / GB1 / core mutants / domain-swapping / oligomerization
Function / homology
Function and homology information


IgG binding / extracellular region
Similarity search - Function
IgG-binding B / B domain / Ubiquitin-like (UB roll) - #10 / M protein-type anchor domain / 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 / Ubiquitin-like (UB roll) - #10 / M protein-type anchor domain / 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. 'group G' (bacteria)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsByeon, I.J. / Louis, J.M. / Gronenborn, A.M.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: A Protein Contortionist: Core Mutations of GB1 that Induce Dimerization and Domain Swapping
Authors: Byeon, I.J. / Louis, J.M. / Gronenborn, A.M.
#1: Journal: Science / Year: 1991
Title: A Novel, Highly Stable Fold of the Immunoglobulin Binding Domain of Streptococcal Protein G
Authors: Gronenborn, A.M. / Filpula, D.R. / Essig, N.Z. / Achari, A. / Whitlow, M. / Wingfield, P.T. / Clore, G.M.
#2: Journal: Nat.Struct.Biol. / Year: 2002
Title: Core Mutations Switch Monomeric Protein GB1 Into an Intertwined Tetramer
Authors: Frank, M.K. / Dyda, F. / Dobrodumov, A. / Gronenborn, A.M.
History
DepositionJul 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2003Provider: 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: 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
B: Immunoglobulin G binding protein G


Theoretical massNumber of molelcules
Total (without water)12,4542
Polymers12,4542
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 100structures with the lowest energy,target function
RepresentativeModel #1minimized average structure

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Components

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


Mass: 6226.835 Da / Num. of mol.: 2 / Fragment: B1 Domain / Mutation: T228Q,L231V,F256V,Y259F,A260F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. 'group G' (bacteria) / Gene: SPG / Plasmid: pET11A / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: P06654

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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
1323D 13C-separated/12C-filtered NOESY
1433D 13C-separated/12C-filtered NOESY
1542D NOESY
1652D NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.7mM (in monomer) U-15N,13C, 50mM phosphate buffer, 0.02% NaN3, 92.5% H2O, 7.5% D2O92.5% H2O, 7.5% D2O
20.85mM (in monomer) U-15N,13C, 0.85mM (in monomer) unlabeled, 50mM phosphate buffer (pH 5.5), 0.02 % NaN3, 92.5% H2O, 7.5% D2O92.5% H2O, 7.5% D2O
30.85mM (in monomer) U-15N,13C, 0.85mM (in monomer) unlabeled, 50mM phosphate buffer, 0.02% NaN3, 100% D2O100% D2O
41.7mM (in monomer) unlabeled, 50mM phosphate buffer, 0.02% NaN3, 92.5% H2O, 7.5% D2O92.5% H2O, 7.5% D2O
51.7mM (in monomer) unlabeled, 50mM phosphate buffer, 0.02% NaN3, 100% D2O100% D2O
Sample conditionsIonic strength: 50mM sodium phosphate buffer / pH: 5.5 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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 DRXBrukerDRX8001
Bruker DMXBrukerDMX7502
Bruker DRXBrukerDRX6003
Bruker DMXBrukerDMX6004
Bruker DMXBrukerDMX5005

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6 and 3.1Brukercollection
NMRPipe2.2Delaglioprocessing
PIPP4.3.2Garrettdata analysis
CNS1.1Brungerstructure solution
CNS1.1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 1311 constraints per monomeric subunit: 1035 NOE-derived distance constraints, 72 hydrogen bond distance constraints, 148 dihedral angle constraints, ...Details: The structures are based on a total of 1311 constraints per monomeric subunit: 1035 NOE-derived distance constraints, 72 hydrogen bond distance constraints, 148 dihedral angle constraints, and 56 residual N-H dipolar coupling constraints.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy,target function
Conformers calculated total number: 100 / Conformers submitted total number: 40

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