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- PDB-6anf: Design of a short thermo-stable alpha-helix embedded in a macrocycle -

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Basic information

Entry
Database: PDB / ID: 6anf
TitleDesign of a short thermo-stable alpha-helix embedded in a macrocycle
ComponentsCapped-strapped peptide
KeywordsDE NOVO PROTEIN / De novo / constrained peptide
Function / homology3,3'-dimethyl-1,1'-biphenyl
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsWu, H. / Acharyya, A. / Wu, Y. / Liu, L. / Jo, H. / Gai, F. / DeGrado, W.F.
CitationJournal: Chembiochem / Year: 2018
Title: Design of a Short Thermally Stable alpha-Helix Embedded in a Macrocycle.
Authors: Wu, H. / Acharyya, A. / Wu, Y. / Liu, L. / Jo, H. / Gai, F. / DeGrado, W.F.
History
DepositionAug 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capped-strapped peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,6282
Polymers1,4461
Non-polymers1821
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area120 Å2
ΔGint1 kcal/mol
Surface area1530 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Capped-strapped peptide


Mass: 1445.716 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-B0I / 3,3'-dimethyl-1,1'-biphenyl


Mass: 182.261 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14

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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 NOESY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution
Contents: 0.156 mM Capped-strapped peptide A37, 95% H2O/5% D2O
Label: non-labeled / Solvent system: 95% H2O/5% D2O
SampleConc.: 0.156 mM / Component: Capped-strapped peptide A37 / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 100 mM / Label: con1 / pH: 4.1 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 900 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
CYANAGuntert, Mumenthaler and Wuthrichdata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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