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- PDB-5jxv: Solid-state MAS NMR structure of immunoglobulin beta 1 binding do... -

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Basic information

Entry
Database: PDB / ID: 5jxv
TitleSolid-state MAS NMR structure of immunoglobulin beta 1 binding domain of protein G (GB1)
ComponentsImmunoglobulin G-binding protein G
KeywordsIMMUNE SYSTEM / Globular / alpha beta
Function / homologyUbiquitin-like (UB roll) - #10 / Ubiquitin-like (UB roll) / Roll / Alpha Beta / :
Function and homology information
Biological speciesStreptococcus dysgalactiae subsp. equisimilis (bacteria)
MethodSOLID-STATE NMR / torsion angle dynamics
AuthorsAndreas, L.B. / Jaudzems, K. / Stanek, J. / Lalli, D. / Bertarello, A. / Le Marchand, T. / Cala-De Paepe, D. / Kotelovica, S. / Akopjana, I. / Knott, B. ...Andreas, L.B. / Jaudzems, K. / Stanek, J. / Lalli, D. / Bertarello, A. / Le Marchand, T. / Cala-De Paepe, D. / Kotelovica, S. / Akopjana, I. / Knott, B. / Wegner, S. / Engelke, F. / Lesage, A. / Emsley, L. / Tars, K. / Herrmann, T. / Pintacuda, G.
Funding support France, Germany, 6items
OrganizationGrant numberCountry
Centre national de la recherche scientifiqueIR-RMN FR3050 France
European Union's FP72012-ITN no 317127 France
European Research Council648974 France
European Union's FP7624918 France
European Union's Horison 2020661175 France
European Molecular Biology OrganizationGA-2013-609409 Germany
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structure of fully protonated proteins by proton-detected magic-angle spinning NMR.
Authors: Andreas, L.B. / Jaudzems, K. / Stanek, J. / Lalli, D. / Bertarello, A. / Le Marchand, T. / Cala-De Paepe, D. / Kotelovica, S. / Akopjana, I. / Knott, B. / Wegner, S. / Engelke, F. / Lesage, ...Authors: Andreas, L.B. / Jaudzems, K. / Stanek, J. / Lalli, D. / Bertarello, A. / Le Marchand, T. / Cala-De Paepe, D. / Kotelovica, S. / Akopjana, I. / Knott, B. / Wegner, S. / Engelke, F. / Lesage, A. / Emsley, L. / Tars, K. / Herrmann, T. / Pintacuda, G.
History
DepositionMay 13, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Aug 31, 2016Group: Database references
Revision 1.3Feb 7, 2018Group: Experimental preparation / Category: pdbx_nmr_exptl_sample_conditions
Item: _pdbx_nmr_exptl_sample_conditions.temperature / _pdbx_nmr_exptl_sample_conditions.temperature_units
Revision 1.4Feb 28, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Aug 21, 2019Group: Data collection / Category: pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.6Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)6,2291
Polymers6,2291
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4100 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80target function
RepresentativeModel #1target function

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Components

#1: Antibody Immunoglobulin G-binding protein G


Mass: 6228.809 Da / Num. of mol.: 1 / Mutation: T2Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus dysgalactiae subsp. equisimilis (bacteria)
Gene: WH79_02070 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F5P4G8

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic1(H)NCAH
1111isotropic1(H)N(CO)CAH
1121isotropic1(H)COCAH
1131isotropic1(H)CO(N)CAH
121isotropic1(H)CANH
131isotropic1(H)(CO)CA(CO)NH
141isotropic1(H)(CA)CB(CA)NH
151isotropic1(H)N(CA)(CO)NH
161isotropic1(H)N(CO)(CA)NH
171isotropic1(H)CCH-TOCSY
181isotropic1(H)NHH-RFDR
191isotropic1(H)CHH-RFDR
1101isotropic1H(H)CH-RFDR-aromatic13C

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Sample preparation

DetailsType: solid
Contents: 12.5 mM sodium phosphate, 45 % methyl-2,4-pentane diol, 22.5 % isopropyl alcohol, 800 mg/mL [U-99% 13C; U-99% 15N] B1 domain of Immunoglobulin G-Binding protein G, H20/MPD/IPA
Details: microcrystalline / Label: A / Solvent system: H20/MPD/IPA
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
12.5 mMsodium phosphatenatural abundance1
45 %methyl-2,4-pentane diolnatural abundance1
22.5 %isopropyl alcoholnatural abundance1
800 mg/mLB1 domain of Immunoglobulin G-Binding protein G[U-99% 13C; U-99% 15N]1
Sample conditionsIonic strength: 12.5 mM / Ionic strength err: 5 / Label: A / pH: 5.6 / PH err: 0.1 / Pressure: variable atm / Temperature: 283 K / Temperature err: 5

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 1000 MHz / Details: MAS 111 kHz

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Processing

NMR software
NameVersionDeveloperClassification
CANDID2.6.0Herrmann, Guntert and Wuthrichstructure calculation
CARAKeller and Wuthrichchemical shift assignment
SparkyGoddardchemical shift assignment
TopSpinBruker Biospincollection
TALOSCornilescu, Delaglio and Baxstructure calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 80 / Conformers submitted total number: 20

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