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- PDB-6b34: NMR ensemble of Tyrocidine A analogue AC3.27 -

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Basic information

Entry
Database: PDB / ID: 6b34
TitleNMR ensemble of Tyrocidine A analogue AC3.27
ComponentsTyrocidine A analogue D-PHE-BE2-PHE-D-PHE-ASN-GLN-TYR-VAL-ORN-LEU
KeywordsANTIMICROBIAL PROTEIN / Tyrocidine A Antimicrobial peptide AMP Cyclic peptide 2-aminobenzoic acid 2-Abz Anthranilic acid
Function / homologyTyrocidine A analogue (DPN)(BE2)F(DPN)NQYV(ORN)L
Function and homology information
Biological speciesBrevibacillus brevis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsCameron, A.J. / Ewdards, P.J.B. / Harjes, E. / Sarojini, V.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Tyrocidine A Analogues Bearing the Planar d-Phe-2-Abz Turn Motif: How Conformation Impacts Bioactivity.
Authors: Cameron, A.J. / Edwards, P.J.B. / Harjes, E. / Sarojini, V.
History
DepositionSep 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Aug 12, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_molecule_features ...atom_site / pdbx_molecule_features / pdbx_nmr_spectrometer / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 2.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Tyrocidine A analogue D-PHE-BE2-PHE-D-PHE-ASN-GLN-TYR-VAL-ORN-LEU


Theoretical massNumber of molelcules
Total (without water)1,3101
Polymers1,3101
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area230 Å2
ΔGint1 kcal/mol
Surface area1360 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)9 / 10structures with acceptable covalent geometry
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Tyrocidine A analogue D-PHE-BE2-PHE-D-PHE-ASN-GLN-TYR-VAL-ORN-LEU


Type: Cyclic peptide / Class: Antibiotic / Mass: 1310.497 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthetic analogue of tyrocidine A. Sequence is altered at 2 positions relative to natural product.
Source: (synth.) Brevibacillus brevis (bacteria)
References: Tyrocidine A analogue (DPN)(BE2)F(DPN)NQYV(ORN)L
Compound detailsTyrocidine kills bacteria by interacting with their cytoplasmic membrane and causing leakage of ...Tyrocidine kills bacteria by interacting with their cytoplasmic membrane and causing leakage of their intracellular content. It also affects intracellular membranes such as those of mitochondria

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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 DQF-COSY
131isotropic12D 1H-15N HSQC
141isotropic12D 1H-1H TOCSY

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Sample preparation

DetailsType: solution
Contents: 0.7 mM None D-PHE-2-ABZ-PHE-D-PHE-ASN-GLN-TYR-VAL-ORN-LEU, 50% H20 / 50% MeCN
Label: AC3.27 / Solvent system: 50% H20 / 50% MeCN
SampleConc.: 0.7 mM / Component: D-PHE-2-ABZ-PHE-D-PHE-ASN-GLN-TYR-VAL-ORN-LEU / Isotopic labeling: None
Sample conditionsIonic strength units: M / Label: conditions_1 / pH: 6 / PH err: 2 / 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
NameVersionDeveloperClassification
YASARAKRIEGERrefinement
YASARAstructure solution
ANALYSIS2.4.2structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 10 / Conformers submitted total number: 9

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