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- PDB-7qtr: GB1 in mammalian cells, 50 uM -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7qtr
TitleGB1 in mammalian cells, 50 uM
ComponentsImmunoglobulin G-binding protein G
KeywordsIMMUNE SYSTEM / GB1 / B1 domain of streptococcal protein G / in-cell NMR
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 / 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
Similarity search - Domain/homology
Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesStreptococcus sp. 'group G' (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsGerez, J.A. / Prymaczok, N.C. / Kadavath, H. / Gosh, D. / Butikofer, M. / Guntert, P. / Riek, R.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Commun Biol / Year: 2022
Title: Protein structure determination in human cells by in-cell NMR and a reporter system to optimize protein delivery or transexpression.
Authors: Gerez, J.A. / Prymaczok, N.C. / Kadavath, H. / Ghosh, D. / Butikofer, M. / Fleischmann, Y. / Guntert, P. / Riek, R.
History
DepositionJan 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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)6,3601
Polymers6,3601
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 / 100target function
RepresentativeModel #1closest to the average

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Components

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


Mass: 6360.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. 'group G' (bacteria) / Gene: spg / Production host: Escherichia coli (E. coli) / References: UniProt: P06654

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentSample state: isotropic / Type: 3D 15N,13C-combined 1H,1H NOESY

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Sample preparation

DetailsType: solution
Contents: 50 uM [U-13C; U-15N] B1 domain of streptococcal protein G (GB1), 95% H2O/5% D2O
Details: in-cell sample, protein transexpressed in Hek-293 cells
Label: in-cell / Solvent system: 95% H2O/5% D2O
SampleConc.: 50 uM / Component: B1 domain of streptococcal protein G (GB1) / Isotopic labeling: [U-13C; U-15N]
Sample conditionsDetails: in-cell sample, protein transexpressed in Hek-293 cells using electroporation
Ionic strength: 0 Not defined / Label: in-cell sample / pH: 7.4 / Pressure: AMBIENT Pa / Temperature: 283 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.13P. Guntertstructure calculation
OPALp1.4R. Koradirefinement
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.peak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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