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- PDB-5twi: Alpha Helix Nucleation by a Simple Cyclic Tetrapeptide -

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Basic information

Entry
Database: PDB / ID: 5twi
TitleAlpha Helix Nucleation by a Simple Cyclic Tetrapeptide
ComponentsCyclic tetrapeptide ALA-ARG-ALA-UN1
KeywordsDE NOVO PROTEIN / alpha turn / helix cap
Biological speciesCheirogaleus major (Greater dwarf lemur)
MethodSOLUTION NMR / simulated annealing
AuthorsHoang, H.N. / Fairlie, D.P.
Funding support Australia, 1items
OrganizationGrant numberCountry
ARC, MHNRCDP1096290, DP130100629, CE140100011 Australia
CitationJournal: To Be Published
Title: Alpha Helix Nucleation by a Simple Cyclic Tetrapeptide
Authors: Hoang, H.N. / Fairlie, D.P.
History
DepositionNov 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Structure summary
Category: entity / pdbx_database_related ...entity / pdbx_database_related / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _entity.pdbx_number_of_molecules / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclic tetrapeptide ALA-ARG-ALA-UN1


Theoretical massNumber of molelcules
Total (without water)4591
Polymers4591
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area390 Å2
ΔGint5 kcal/mol
Surface area540 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)5 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Cyclic tetrapeptide ALA-ARG-ALA-UN1


Mass: 458.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Cheirogaleus major (Greater dwarf lemur)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentSample state: anisotropic / Type: 2D 1H-1H ROESY

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Sample preparation

DetailsType: solid / Contents: 1 mM n helix cap, 93% H2O/7% D2O / Label: ARAhE / Solvent system: 93% H2O/7% D2O
SampleConc.: 1 mM / Component: helix cap / Isotopic labeling: n
Sample conditionsIonic strength: 100 mM / Label: helix / pH: 6 / Pressure: 1 atm / Temperature: 298 K / Temperature err: 1

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
XplorXplor-NIHrefinement
TopSpinBruker Biospinchemical shift assignment
TopSpinBruker Biospinpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 5

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