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- PDB-8onu: Solution structure of thanatin analogue 7 in complex with LptAm(Ab)1.0 -

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Basic information

Entry
Database: PDB / ID: 8onu
TitleSolution structure of thanatin analogue 7 in complex with LptAm(Ab)1.0
Components
  • Lipopolysaccharide export system protein LptA
  • Thanatin-like derivative
KeywordsANTIBIOTIC / STRUCTURE FROM CYANA 3.98.13
Function / homology
Function and homology information


lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / defense response to fungus / lipopolysaccharide binding / killing of cells of another organism / periplasmic space / defense response to bacterium / innate immune response / extracellular region
Similarity search - Function
Lipopolysaccharide (LPS) transport protein A like domain / : / Lipopolysaccharide export system protein LptA / lipopolysaccharide transport protein A fold / Organic solvent tolerance-like, N-terminal / LptA/(LptD N-terminal domain) LPS transport protein / Sandwich / Mainly Beta
Similarity search - Domain/homology
Thanatin / Lipopolysaccharide export system protein LptA
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
Podisus maculiventris (spined soldier bug)
MethodSOLUTION NMR / molecular dynamics
AuthorsOi, K.K. / Moehle, K. / Zerbe, O.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
Innosuisse33285.1 IP-LSEuropean Union
CitationJournal: Molecules / Year: 2023
Title: Early Molecular Insights into Thanatin Analogues Binding to A. baumannii LptA.
Authors: Oi, K.K. / Moehle, K. / Schuster, M. / Zerbe, O.
History
DepositionApr 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Nov 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
Revision 2.1Nov 29, 2023Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name

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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)16,2732
Polymers16,2732
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1720 Å2
ΔGint-1 kcal/mol
Surface area9030 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: 14265.767 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: DH5a
Gene: lptA, A7M90_06575, AB945B12_03460, ABCAM1_1308, ABKPCSM17A_03058, ABR2091_1232, ABUW_2646, ACX61_12145, APD31_17240, AUO97_13655, AYR68_06125, B7L45_12725, B9X95_15845, BAA1790NC_1298, C6N18_ ...Gene: lptA, A7M90_06575, AB945B12_03460, ABCAM1_1308, ABKPCSM17A_03058, ABR2091_1232, ABUW_2646, ACX61_12145, APD31_17240, AUO97_13655, AYR68_06125, B7L45_12725, B9X95_15845, BAA1790NC_1298, C6N18_07050, CBE85_10985, CBL15_11855, CSB70_1068, CTZ19_12250, D8O08_008535, DLI71_18810, DOL94_11450, DVA69_07650, E1A86_07710, E1A87_18595, EA686_18135, EA706_10880, EA720_004080, EA722_14830, EGM95_13940, EKS29_04650, EWO96_18090, F2P40_12435, F4T85_13200, FDN00_13585, FE003_12605, FJU36_12005, FJU42_14040, FR761_07300, G3N53_13510, GNY86_07325, GSE42_07235, H0529_08305, HB367_02715, HBK86_04580, HIN86_12575, IAG11_06185, IMO23_06220, ITE13_09135, NCTC13305_01082, NCTC13421_02501, SAMEA104305318_02787, SAMEA104305340_03609, SAMEA104305385_03383
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: V5VEZ9
#2: Protein/peptide Thanatin-like derivative


Mass: 2007.387 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: VAN = valine capped with guanidine group, 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
111isotropic22D 1H-15N HSQC
121isotropic22D 1H-13C HSQC aliphatic
131isotropic22D 1H-13C HSQC aromatic
141isotropic23D HNCO
151isotropic23D HN(COCA)CB
161isotropic23D 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

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Sample preparation

DetailsType: solution
Contents: 300 uM [U-13C; U-15N] A. baumannii lipopolysaccharide transport protein A (LptA) (33-164), 500 uM Thanatin analogue 7, 50 mM sodium phosphate, 150 mM sodium chloride, 90% H2O/10% D2O
Details: 13C, 15N-labelled LptAm(33-150) / Label: LptAm_15N13C / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMA. baumannii lipopolysaccharide transport protein A (LptA) (33-164)[U-13C; U-15N]1
500 uMThanatin analogue 7none1
50 mMsodium phosphatenone1
150 mMsodium chloridenone1
Sample conditionsIonic strength: 150 mM / Ionic strength err: 10 / Label: conditions_1 / pH: 7 / 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 Sherbooke St West, Suite #910, Montreal, QC, Canada, H3A 2R7, 2022refinement
CARAKeller and Wuthrichchemical shift assignment
CcpNmr Analysis2.5CCPNpeak 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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