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- PDB-2oed: GB3 solution structure obtained by refinement of X-ray structure ... -

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Basic information

Entry
Database: PDB / ID: 2oed
TitleGB3 solution structure obtained by refinement of X-ray structure with dipolar couplings
ComponentsImmunoglobulin G-binding protein G
KeywordsIMMUNE SYSTEM / residual dipolar couplings
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 / 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. / Grishaev, 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. / Wiggley, D.B.
History
DepositionDec 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: 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 1.4Dec 27, 2023Group: 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 / 1all calculated structures submitted
RepresentativeModel #1best agreement with dipolar restraints

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Components

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


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) / Gene: spg / Plasmid: PET-11A / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: P19909, UniProt: Q54181*PLUS

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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, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0.05 / pH: 6.5 / Pressure: ambient / Temperature: 300 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 DMXBrukerDMX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
DYNAMO2.1Delagliorefinement
DYNAMO2.1Delagliostructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: GB3 solution structure is obtained by refinement of the x-ray structure of gb3 (1igd) with c(alpha)-c', c'-n, c(alpha)-h(alpha) and N-H dipolar couplings measured in five aligning media ...Details: GB3 solution structure is obtained by refinement of the x-ray structure of gb3 (1igd) with c(alpha)-c', c'-n, c(alpha)-h(alpha) and N-H dipolar couplings measured in five aligning media (bicelle, peg, pf1 phage, negatively and positively charged polyacrylamide gels). Dipolar couplings originating on residues 10-11, 24-26, 39-41 and the n- and c-terminal residues were excluded, resulting in near-identity with the x-ray structure for these residues. This deposition corresponds to the refined-II structure of the primary citation that was refined against all 4 types of dipolar couplings in 5 media. The related depositions 1P7E and 1P7F correspond to the refined-III and refined-IV structures, respectively. The deposited structure was calculated with DYNAMO 2.1 following a short low-temperature molecular dynamics simulated annealing run starting from the regularized coordinates of the X-ray structure 1IGD using atomic coordinate restraints to the overlapping 3-residue segments of 1IGD. The force constants for the HN-N-C-Ca impropers were softened 10-fold relative to their standard settings. See the primary citation and the corresponding supporting information file for a detailed description of the refinement procedure. The deposited restraints file includes, in addition to the dipolar couplings and backbone H-bond distance restraints (XPLOR/CNS format), an Xplor-NIH script designed to mimic the deposited structure, and the force field parameter files. A set of overlapping 3-residue NCS restraint terms is used in this script in place of the Dynamo atomic coordinate restraints.
NMR representativeSelection criteria: best agreement with dipolar restraints
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 1 / Conformers submitted total number: 1

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