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- PDB-7qgv: Solid-state NMR structure of Teixobactin-Lipid II. -

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Basic information

Entry
Database: PDB / ID: 7qgv
TitleSolid-state NMR structure of Teixobactin-Lipid II.
Components
  • Lipid II
  • Teixobactin
KeywordsANTIBIOTIC / antimicrobial / beta-sheet / membrane deformation
Function / homologyLipid II / : / PHOSPHONATE / 3-methylbut-2-en-1-ol / polypeptide(D)
Function and homology information
Biological speciesEleftheria terrae (bacteria)
Staphylococcus aureus (bacteria)
MethodSOLID-STATE NMR / distance geometry
AuthorsWeingarth, M.H. / Shukla, R.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO) Netherlands
CitationJournal: Nature / Year: 2022
Title: Teixobactin kills bacteria by a two-pronged attack on the cell envelope.
Authors: Shukla, R. / Lavore, F. / Maity, S. / Derks, M.G.N. / Jones, C.R. / Vermeulen, B.J.A. / Melcrova, A. / Morris, M.A. / Becker, L.M. / Wang, X. / Kumar, R. / Medeiros-Silva, J. / van Beekveld, ...Authors: Shukla, R. / Lavore, F. / Maity, S. / Derks, M.G.N. / Jones, C.R. / Vermeulen, B.J.A. / Melcrova, A. / Morris, M.A. / Becker, L.M. / Wang, X. / Kumar, R. / Medeiros-Silva, J. / van Beekveld, R.A.M. / Bonvin, A.M.J.J. / Lorent, J.H. / Lelli, M. / Nowick, J.S. / MacGillavry, H.D. / Peoples, A.J. / Spoering, A.L. / Ling, L.L. / Hughes, D.E. / Roos, W.H. / Breukink, E. / Lewis, K. / Weingarth, M.
History
DepositionDec 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 17, 2023Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Teixobactin
B: Teixobactin
C: Teixobactin
D: Teixobactin
E: Lipid II
F: Lipid II
G: Lipid II
H: Lipid II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,65932
Polymers7,0008
Non-polymers3,65924
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 25all calculated structures submitted
RepresentativeModel #1medoid

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Components

#1: Protein/peptide
Teixobactin


Type: Peptide-like / Mass: 1260.483 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Eleftheria terrae (bacteria) / References: BIRD: PRD_002384
#2: Polypeptide(D)
Lipid II


Type: Glycopeptide / Class: Glycan component / Mass: 489.542 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus / References: Lipid II
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-alpha-muramic acid


Type: oligosaccharide, Glycopeptide / Class: Glycan component / Mass: 496.463 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
References: Lipid II
DescriptorTypeProgram
DGlcpNAcb1-4MurNAc1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NCC/3=O_3*OC^RCO/4=O/3C][a2122h-1b_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(3+1)][<C3O1>]{}[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Chemical
ChemComp-2PO / PHOSPHONATE


Type: Glycopeptide / Class: Glycan component / Mass: 79.980 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: HO3P / References: Lipid II
#5: Chemical
ChemComp-P1W / 3-methylbut-2-en-1-ol


Type: Glycopeptide / Class: Glycan component / Mass: 86.132 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C5H10O / References: Lipid II
Compound detailsLipid II is a precursor molecule in the synthesis of the cell wall of bacteria
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D NH
121isotropic12D CC
131isotropic22D TOBSY
141isotropic13D HNCA
151isotropic13D HNCO

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Sample preparation

DetailsType: membrane
Contents: 25 mM sodium chloride, 40 mM sodium phosphate, 1.6 mM [U-99% 13C; U-99% 15N] teixobactin, 0.8 mM [U-99% 13C; U-99% 15N] lipid II, 40mM Phosphate 25mM NaCl
Label: 13C15N_txb+LII / Solvent system: 40mM Phosphate 25mM NaCl
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
25 mMsodium chloridenatural abundance1
40 mMsodium phosphatenatural abundance1
1.6 mMteixobactin[U-99% 13C; U-99% 15N]1
0.8 mMlipid II[U-99% 13C; U-99% 15N]1
Sample conditionsIonic strength: 40 mM / Label: standard / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III9501
Bruker AVANCE IIIBrukerAVANCE III7002

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Processing

NMR software
NameVersionDeveloperClassification
HADDOCK2.4Bonvinstructure calculation
TopSpin4.11Bruker Biospinchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
TopSpinBruker Biospinpeak picking
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 25 / Conformers submitted total number: 25

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