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- PDB-1p7e: GB3 solution structure obtained by refinement of X-ray structure ... -

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Basic information

Entry
Database: PDB / ID: 1p7e
TitleGB3 solution structure obtained by refinement of X-ray structure with dipolar couplings
ComponentsImmunoglobulin G binding protein G
KeywordsIMMUNE SYSTEM
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
AuthorsUlmer, T.S. / Ramirez, B.E. / Delaglio, F. / Bax, A.
Citation
Journal: J.Am.Chem.Soc. / Year: 2003
Title: Evaluation of backbone proton positions and dynamics in a small protein by liquid crystal NMR spectroscopy.
Authors: Ulmer, T.S. / Ramirez, B.E. / Delaglio, F. / Bax, A.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: THE THIRD IGG-BINDING DOMAIN FROM STREPTOCOCCAL PROTEIN G. AN ANALYSIS BY X-RAY CRYSTALLOGRAPHY OF THE STRUCTURE ALONE AND IN A COMPLEX WITH FAB.
Authors: Derrick, J.P. / Wigley, D.B.
History
DepositionMay 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)6,2151
Polymers6,2151
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 20Best agreement with dipolar constraints
RepresentativeModel #1fewest violations

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Components

#1: Antibody Immunoglobulin G binding protein G / IgG binding protein G / GB3


Mass: 6214.848 Da / Num. of mol.: 1 / Fragment: THIRD IGG-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. 'group G' (bacteria) / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: P19909

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D IPAP [15N,1H]-HSQC
1213D CT(H)CA(CO)NH
13113C-coupled 3D HNCO
141quantitative J-correlation 3D TROSY-HNCO

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Sample preparation

DetailsContents: 25 mM NaH2PO4/Na2HPO4, 0.2 mg/mL NaN3, 1.5 mM GB3 protein and aligning media
Sample conditionsIonic strength: 0.05 / pH: 6.5 / Pressure: ambient / Temperature: 300 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 DMXBrukerDMX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
DYNAMO2.1Delaglio, F.structure solution
DYNAMO2.1Delaglio, F.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: GB3 solution structure obtained by refinement of the X-ray structure of GB3 (1IGD) with C(alpha)-C', C'-N and C(alpha)-H(alpha) dipolar couplings measured in five aligning media (bicelle, ...Details: GB3 solution structure obtained by refinement of the X-ray structure of GB3 (1IGD) with C(alpha)-C', C'-N and C(alpha)-H(alpha) dipolar couplings measured in five aligning media (bicelle, PEG, pf1 phage, negatively and positively charged polyacrylamide gels). HN is placed at the position that yields best agreement with the N-H dipolar couplings. Dipolar couplings originating on residues 10-11, 24-26, 39-41 and the N- and C-terminal residues were excluded, resulting in identity with the X-ray structure for these residues. Less than five N-H couplings could be obtained for residues Q2, E15, E27, N35, N37, and Y45 and for these residues as well as the excluded ones HN is placed on a line that bisects the C'(i-1)-N(i)-C(alpha,i) angle.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: Best agreement with dipolar constraints
Conformers calculated total number: 20 / Conformers submitted total number: 1

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