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- PDB-8t0i: Backbone Dialkylation in Peptide Hairpins: (R)-Ethylpropylglycine... -

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Basic information

Entry
Database: PDB / ID: 8t0i
TitleBackbone Dialkylation in Peptide Hairpins: (R)-Ethylpropylglycine variant
ComponentsImmunoglobulin G-binding protein G
KeywordsDE NOVO PROTEIN / hairpin / peptidomimetic / backbone modification
Biological speciesStreptococcus sp. group G (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsHeath, S.L. / Horne, W.S. / Lengyel, G.A.
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: Org.Biomol.Chem. / Year: 2023
Title: Effects of chirality and side chain length in C alpha , alpha-dialkylated residues on beta-hairpin peptide folded structure and stability.
Authors: Heath, S.L. / Horne, W.S. / Lengyel, G.A.
History
DepositionJun 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Immunoglobulin G-binding protein G


Theoretical massNumber of molelcules
Total (without water)1,8831
Polymers1,8831
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: 1883.066 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus sp. group G (bacteria)
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 NOESY
131isotropic12D 1H-1H COSY

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Sample preparation

DetailsType: solution
Contents: 1.4 mM GB1 C-terminal Hairpin Mutant: (R)-Ethylpropylglycine variant, 50 mM sodium phosphate, 0.2 mM DSS, 90% H2O/10% D2O
Label: sample_1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.4 mMGB1 C-terminal Hairpin Mutant: (R)-Ethylpropylglycine variantnatural abundance1
50 mMsodium phosphatenatural abundance1
0.2 mMDSSnatural abundance1
Sample conditionsIonic strength: 250 mM / Label: conditions_1 / pH: 7 pH* / Pressure: 1 atm / Temperature: 298 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
NMRFAM-SPARKYLee W, Tonelli M, Markley JLchemical shift assignment
NMRFAM-SPARKYLee W, Tonelli M, Markley JLpeak picking
ARIALinge, O'Donoghue and Nilgesrefinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 4
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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