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- PDB-9bb2: Backbone Modification in the GA Module of Protein PAB: beta3-resi... -

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Basic information

Entry
Database: PDB / ID: 9bb2
TitleBackbone Modification in the GA Module of Protein PAB: beta3-residues at positions 20 and 24
ComponentsPeptostreptococcal albumin-binding protein
KeywordsPROTEIN BINDING / helix bundle / designed variant
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Repeat of unknown function DUF5633 / Family of unknown function (DUF5633) / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain
Similarity search - Domain/homology
Peptostreptococcal albumin-binding protein
Similarity search - Component
Biological speciesFinegoldia magna (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsLin, Y. / Horne, W.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM149220 United States
CitationJournal: Chemistry / Year: 2024
Title: Backbone Modification in a Protein Hydrophobic Core.
Authors: Lin, Y. / Horne, W.S.
History
DepositionApr 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptostreptococcal albumin-binding protein


Theoretical massNumber of molelcules
Total (without water)5,2091
Polymers5,2091
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: not applicable
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: Protein/peptide Peptostreptococcal albumin-binding protein


Mass: 5209.000 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Finegoldia magna (bacteria) / References: UniProt: Q51911
Has ligand of interestY

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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: 1 mM GA Module of Protein PAB: beta3 residues at positions 20 and 24, 0.2 mM DSS, 90% H2O/10% D2O
Label: sample_1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMGA Module of Protein PAB: beta3 residues at positions 20 and 24natural abundance1
0.2 mMDSSnatural abundance1
Sample conditionsIonic strength: 1 mM / Label: conditions_1 / pH: 6 pH* / Pressure: 1 atm / Temperature: 283 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
PokyManthey, Tonelli, Clos II, Rahimi, Markley and Leedata 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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