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- PDB-8umb: Site-specific Aspartic Acid Dehydration and Isomerization in Stre... -

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Basic information

Entry
Database: PDB / ID: 8umb
TitleSite-specific Aspartic Acid Dehydration and Isomerization in Streptococcal Protein GB1: L-Aspartyl Succinimide 40-41 Variant
ComponentsImmunoglobulin G-binding protein G
KeywordsIMMUNE SYSTEM / immunoglobulin binding domain
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 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsHeath, S.L. / Guseman, A.J. / Gronenborn, A.M. / Horne, W.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)107161 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)149220 United States
CitationJournal: Protein Sci. / Year: 2024
Title: Probing effects of site-specific aspartic acid isomerization on structure and stability of GB1 through chemical protein synthesis.
Authors: Heath, S.L. / Guseman, A.J. / Gronenborn, A.M. / Horne, W.S.
History
DepositionOct 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Antibody Immunoglobulin G-binding protein G


Mass: 6228.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus (bacteria) / References: UniProt: P19909
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H COSY
131isotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: solution
Contents: 0.07 mM B1 Domain of Streptococcal Protein G, L-Aspartyl Succinimide 40-41 Variant, 20 mM sodium phosphate, 0.1 mM DSS, 90% H2O/10% D2O
Label: sample_1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.07 mMB1 Domain of Streptococcal Protein G, L-Aspartyl Succinimide 40-41 Variantnatural abundance1
20 mMsodium phosphatenatural abundance1
0.1 mMDSSnatural abundance1
Sample conditionsIonic strength: 41 mM / Label: conditions_1 / pH: 7 pH* / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
NMRFAM-SPARKYLee, Tonelli, Markleydata analysis
ARIALinge, O'Donoghue and Nilgesrefinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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