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- PDB-8bss: Solution Structure of thanatin-like derivative 5 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 8bss
TitleSolution Structure of thanatin-like derivative 5 in complex with E. coli LptA mutant Q62L
Components
  • Lipopolysaccharide export system protein LptA
  • Thanatin-like derivative
KeywordsANTIBIOTIC
Function / homology
Function and homology information


transporter complex / glycolipid transfer activity / lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / defense response to fungus / lipopolysaccharide binding / cell outer membrane / outer membrane-bounded periplasmic space / killing of cells of another organism / periplasmic space ...transporter complex / glycolipid transfer activity / lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / defense response to fungus / lipopolysaccharide binding / cell outer membrane / outer membrane-bounded periplasmic space / killing of cells of another organism / periplasmic space / defense response to bacterium / innate immune response / extracellular region / identical protein binding
Similarity search - Function
Lipopolysaccharide export system protein LptA / Organic solvent tolerance-like, N-terminal / LptA/(LptD N-terminal domain) LPS transport protein
Similarity search - Domain/homology
Lipopolysaccharide export system protein LptA / Thanatin
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Podisus maculiventris (spined soldier bug)
MethodSOLUTION NMR / molecular dynamics
AuthorsOi, K.K. / Jurt, S. / Moehle, K. / Zerbe, O.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
Innosuisse33285.1 IP-LSEuropean Union
CitationJournal: Sci Adv / Year: 2023
Title: Peptidomimetic antibiotics disrupt the lipopolysaccharide transport bridge of drug-resistant Enterobacteriaceae.
Authors: Schuster, M. / Brabet, E. / Oi, K.K. / Desjonqueres, N. / Moehle, K. / Le Poupon, K. / Hell, S. / Gable, S. / Rithie, V. / Dillinger, S. / Zbinden, P. / Luther, A. / Li, C. / Stiegeler, S. / ...Authors: Schuster, M. / Brabet, E. / Oi, K.K. / Desjonqueres, N. / Moehle, K. / Le Poupon, K. / Hell, S. / Gable, S. / Rithie, V. / Dillinger, S. / Zbinden, P. / Luther, A. / Li, C. / Stiegeler, S. / D'Arco, C. / Locher, H. / Remus, T. / DiMaio, S. / Motta, P. / Wach, A. / Jung, F. / Upert, G. / Obrecht, D. / Benghezal, M. / Zerbe, O.
History
DepositionNov 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 2.0Jun 14, 2023Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_entity_src_syn / pdbx_struct_mod_residue / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _pdbx_entity_src_syn.organism_common_name ..._entity.pdbx_description / _pdbx_entity_src_syn.organism_common_name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
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 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipopolysaccharide export system protein LptA
B: Thanatin-like derivative


Theoretical massNumber of molelcules
Total (without water)16,4412
Polymers16,4412
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1660 Å2
ΔGint-4 kcal/mol
Surface area8770 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1target function

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Components

#1: Protein Lipopolysaccharide export system protein LptA


Mass: 14521.276 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: lptA, yhbN, b3200, JW3167 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): K-12 / References: UniProt: P0ADV1
#2: Protein/peptide Thanatin-like derivative


Mass: 1919.318 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: HYP = hydroxyproline; LE1 = penicillamine; DAB = diaminobutyric acid; 4FO = D-DAB
Source: (synth.) Podisus maculiventris (spined soldier bug) / References: UniProt: P55788
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-15N HSQC
121isotropic22D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HNCO
151isotropic13D HN(COCA)CB
161isotropic13D HN(CA)CB
171isotropic13D 1H-15N NOESY
181isotropic13D 1H-13C NOESY aliphatic
191isotropic13D 1H-13C NOESY aromatic
1101isotropic13D HBHA(CO)NH
1111isotropic13D (H)CCH-TOCSY
1121isotropic22D (HB)CB(CGCD)HD
1131isotropic22D (HB)CB(CGCDCE)HE

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Sample preparation

DetailsType: solution
Contents: 300 uM [U-13C; U-15N] E. coli Lipopolysaccharide export system protein LptA mutant Q62L, 500 uM Thanatin-like derivative 5, 50 mM sodium phosphate, 150 mM sodium chloride, 90% H2O/10% D2O
Details: 13C, 15N-labelled Q62L mutant LptAm(28-145) / Label: Q62L_LptAm_15N13C / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uME. coli Lipopolysaccharide export system protein LptA mutant Q62L[U-13C; U-15N]1
500 uMThanatin-like derivative 5none1
50 mMsodium phosphatenone1
150 mMsodium chloridenone1
Sample conditionsIonic strength: 150 mM / Ionic strength err: 10 / Label: conditions_1 / pH: 7.0 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.2

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE NEOBrukerAVANCE NEO7001
Bruker AVANCE NEOBrukerAVANCE NEO6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98Guntert, Mumenthaler and Wuthrichstructure calculation
MOE2020.09Chemical Computing Group ULC, 1010 Sherbook St. West, Suite #910, Montreal, QC, Canada, H3A 2R7, 2022refinement
CYANA3.98Guntert, Mumenthaler and Wuthrichchemical shift assignment
CcpNmr Analysis2.5.2CCPNpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 2
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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