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- PDB-1mpe: Ensemble of 20 structures of the tetrameric mutant of the B1 doma... -

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Basic information

Entry
Database: PDB / ID: 1mpe
TitleEnsemble of 20 structures of the tetrameric mutant of the B1 domain of streptococcal protein G
ComponentsImmunoglobulin G binding protein G
KeywordsPROTEIN BINDING / strand-exchanged tetramer / channel
Function / homology
Function and homology information


IgG binding / extracellular region
Similarity search - Function
IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Ubiquitin-like (UB roll) - #10 / 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 / GA-like domain / GA-like domain / Ubiquitin-like (UB roll) - #10 / 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
AuthorsFrank, M.K. / Dyda, F. / Dobrodumov, A. / Gronenborn, A.M.
Citation
Journal: Nat.Struct.Biol. / Year: 2002
Title: Core mutations switch monomeric protein GB1 into an intertwined tetramer.
Authors: Kirsten Frank, M. / Dyda, F. / Dobrodumov, A. / 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: FEBS Lett. / Year: 1996
Title: Core Mutants of the Immunoglobulin Binding Domain of Streptococcal Protein G: Stability and Structural Integrity
Authors: Gronenborn, A.M. / Frank, M.K. / Clore, G.M.
History
DepositionSep 12, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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

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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
C: Immunoglobulin G binding protein G
D: Immunoglobulin G binding protein G


Theoretical massNumber of molelcules
Total (without water)25,2124
Polymers25,2124
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 100structures with least restraint violations and phi, psi angles of residue 46 in allowed region of Ramachrandran plot
RepresentativeModel #1minimized average structure

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Components

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


Mass: 6302.931 Da / Num. of mol.: 4 / Fragment: B1 domain, sequence database residues 228-282 / Mutation: T2Q, L5V, A26F, F30V, Y33F, A34F
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
1123D 15N-separated NOESY
122HNHA
1313D 13C-separated NOESY
1434D 13C-separated NOESY
1514D 13C/15N-separated NOESY
1643D 12C-filtered 13C-separated NOESY
NMR detailsText: T1,T2, and heteronuclear NOEs collected. Dipolar couplings (N-H) were collected as well. Dipolar coupling and chemical shifts from residues with heteronuclear NOE below 0.6 were not used.

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Sample preparation

Details
Solution-IDContentsSolvent system
13.5 mM (in monomer) U-15N,13C, 50 mM sodium phosphate buffer, 0.02% sodium azide90% H2O/10% D2O
22.89 mM (in monomer) U-15N, 50 mM sodium phosphate buffer, 0.02% sodium azide90% H2O/10% D2O
33.5 mM (in monomer) U-15N,13C, 50 mM sodium phosphate buffer, 0.02% sodium azide100% D2O
41.4 mM (in monomer) 1:1 mixture unlabelled:U-15N,13C, 50 mM sodium phosphate buffer, 0.02% sodium azide100% D2O
Sample conditionsIonic strength: 50 mM sodium phosphate, 0.02% sodium azide / pH: 5.45 / Pressure: 1 atm / Temperature: 313 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 DMXBrukerDMX6003
Bruker DMXBrukerDMX5004

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.2Frank Delaglioprocessing
PIPP4.3.2Dan Garrettdata analysis
XwinNMR2.6Bruker Corp.collection
X-PLOR4Brungerrefinement
CNS1Brungerstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: NMR constraints (per monomer) 822 NOE-derived distance restraints (534 intramonomer, 288 intermonomer) 42 distance restraints from hydrogen bonds (20 intramonomer, 22 intermonomer) 30 J- ...Details: NMR constraints (per monomer) 822 NOE-derived distance restraints (534 intramonomer, 288 intermonomer) 42 distance restraints from hydrogen bonds (20 intramonomer, 22 intermonomer) 30 J-coupling restraints, 33 Residual dipolar couplings (HN) 66 backbone dihedral angle restraints 31 sidechain dihedral angle restraints
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with least restraint violations and phi, psi angles of residue 46 in allowed region of Ramachrandran plot
Conformers calculated total number: 100 / Conformers submitted total number: 21

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