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- PDB-6gd5: The solution structure of the LptA-Thanatin complex -

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Basic information

Entry
Database: PDB / ID: 6gd5
TitleThe solution structure of the LptA-Thanatin complex
Components
  • Lipopolysaccharide export system protein LptA
  • Thanatin
KeywordsANTIBIOTIC / LPS biosynthesis inhibitor complex NMR
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 (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
Lipopolysaccharide export system protein LptA / Thanatin
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Podisus maculiventris (spined soldier bug)
MethodSOLUTION NMR / molecular dynamics
AuthorsMoehle, K. / Zerbe, O.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation205320_146381 Switzerland
Swiss National Science Foundation31003A_160259 Switzerland
CitationJournal: Sci Adv / Year: 2018
Title: Thanatin targets the intermembrane protein complex required for lipopolysaccharide transport inEscherichia coli.
Authors: Vetterli, S.U. / Zerbe, K. / Muller, M. / Urfer, M. / Mondal, M. / Wang, S.Y. / Moehle, K. / Zerbe, O. / Vitale, A. / Pessi, G. / Eberl, L. / Wollscheid, B. / Robinson, J.A.
History
DepositionApr 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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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


Theoretical massNumber of molelcules
Total (without water)15,2112
Polymers15,2112
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1690 Å2
ΔGint-12 kcal/mol
Surface area8310 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Lipopolysaccharide export system protein LptA


Mass: 12769.169 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: the sequence does not contain the signaling sequence (residues 1-27 from UNIPROT entry P0ADV1). The first residue is numbered 28. The expressed construct is 28-159 followed by the linker ...Details: the sequence does not contain the signaling sequence (residues 1-27 from UNIPROT entry P0ADV1). The first residue is numbered 28. The expressed construct is 28-159 followed by the linker SGRVE and a hexa-His tag. Deposited are coordinates for the strucured part containg residues 28-144.
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: lptA, yhbN, b3200, JW3167 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ADV1
#2: Protein/peptide Thanatin


Mass: 2441.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: disulfide bond formed . in the PDB file the first residue of Thanatin is numbered 201.
Source: (gene. exp.) Podisus maculiventris (spined soldier bug)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P55788
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic22D 1H-15N HSQC
124isotropic22D 1H-15N HSQC
132isotropic12D 1H-13C HSQC aliphatic
142isotropic12D 1H-13C HSQC aromatic
154isotropic12D 1H-13C HSQC aliphatic
1194isotropic12D 1H-13C HSQC aromatic
1112isotropic13D HNCO
1102isotropic13D CBCA(CO)NH
192isotropic13D HN(CA)CB
182isotropic13D HBHA(CO)NH
172isotropic13D (H)CCH-TOCSY
162isotropic23D 1H-15N NOESY
1212isotropic23D 1H-13C NOESY aliphatic
1202isotropic23D 1H-13C NOESY aromatic
1262isotropic23D 13C,15N-filtered, 15N edited NOESY
1242isotropic213C,15N filtered, 13C edited (aliph.) NOESY
1352isotropic213C,15N filtered, 13C edited (aro.) NOESY
1234isotropic13D HNCO
1324isotropic13D CBCA(CO)NH
1314isotropic13D HN(CA)CB
1304isotropic13D HBHA(CO)NH
1294isotropic13D (H)CCH-TOCSY
1332isotropic1HBCBCGCDHE
1342isotropic1(HB)CB(CGCDCE)HE
1284isotropic23D 1H-15N NOESY
1274isotropic23D 1H-13C NOESY aliphatic
1254isotropic23D 13C,15N-filtered, 15N edited NOESY
1224isotropic213C,15N filtered, 13C edited (aliph) NOESY
1364isotropic213C,15N filtered, 13C edited (arom.) NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1150 mM sodium chloride, 20 mM CHAPS, 50 mM sodium phosphate, 90% H2O/10% D2O500 uM 15N,13C-labeled LptALptA_Lablelled90% H2O/10% D2O
solution2150 mM sodium chloride, 20 mM CHAPS, 50 mM sodium phosphate, 90% H2O/10% D2O550 uM 13C,15N LptA, 1.2 equiv. unlabled ThanatinLptA_15N13C_Tha_unlab90% H2O/10% D2O
solution3150 mM sodium chloride, 20 mM CHAPS, 50 mM sodium phosphate, 90% H2O/10% D2O500 uM 15N,13C-labled Thanatin15N_Tha90% H2O/10% D2O
solution4150 mM sodium chloride, 20 mM CHAPS, 50 mM sodium phosphate, 90% H2O/10% D2O500 uM 13C,15N-Thanatin plus 1.2 equiv. unlabeled LptA15N13C_Tha_unlab_LptA90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
150 mMsodium chloridenone1
20 mMCHAPSnone1
50 mMsodium phosphatenone1
150 mMsodium chloridenone2
20 mMCHAPSnone2
50 mMsodium phosphatenone2
150 mMsodium chloridenone3
20 mMCHAPSnone3
50 mMsodium phosphatenone3
150 mMsodium chloridenone4
20 mMCHAPSnone4
50 mMsodium phosphatenone4
Sample conditionsDetails: same conditition for all samples / Ionic strength: 1.15 M / Label: Sample_1 / pH: 7.5 / PH err: 0.2 / Pressure: 1 bar / Temperature: 308 K / Temperature err: 0.1

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE NEOBrukerAVANCE NEO6001
Bruker AVANCE NEOBrukerAVANCE NEO7002

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Processing

NMR software
NameVersionDeveloperClassification
CARA1.48Keller and Wuthrichchemical shift assignment
CYANA3.98Guntert, Mumenthaler and Wuthrichstructure calculation
Xplor-NIHSchwieters, Bruengerrefinement
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 3
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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