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- PDB-8q1l: NMR structure of arthrofactin A in micellar DPC solution -

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Basic information

Entry
Database: PDB / ID: 8q1l
TitleNMR structure of arthrofactin A in micellar DPC solution
Componentsarthrofactin A
KeywordsSURFACTANT PROTEIN / Non-ribosomal polypeptide / Cyclic lipodepsipeptide / Antimicrobial peptide / Biosurfactant
Function / homologypolypeptide(D) / polypeptide(D) (> 10)
Function and homology information
Biological speciesPseudomonas sp. MIS38 (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsKovacs, B. / Geudens, N. / Martins, J.C.
Funding support Belgium, 4items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)EOS project G0G3118N (EOS ID 30650620) Belgium
Gatsby Charitable Foundation
Ghent University Special Research Fund (BOF)BOF.DOC.2016.0009.01 (01D07416) Belgium
Ghent University Special Research Fund (BOF)BOF19-GOA-028 (01G02819) Belgium
CitationJournal: To be published
Title: NMR structure of the cyclic lipodepsipeptide arthrofactin A in micellar DPC solution
Authors: Martins, J.C. / Kovacs, B. / Geudens, N.
History
DepositionJul 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: arthrofactin A


Theoretical massNumber of molelcules
Total (without water)1,3731
Polymers1,3731
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, NMR structure calculation ensemble (1-10) + representative structure from MD simulation (11).
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Polypeptide(D) arthrofactin A


Mass: 1372.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 1) The polypeptide chain of arthrofactin A consists of 11 amino acids. 2) The N-terminal amino acid (D-Leu) is acylated with an (R)-3-hydroxy-decanoic acid (IG8) moeity which is indicated as ...Details: 1) The polypeptide chain of arthrofactin A consists of 11 amino acids. 2) The N-terminal amino acid (D-Leu) is acylated with an (R)-3-hydroxy-decanoic acid (IG8) moeity which is indicated as the first residue. 3) The side-chain of the D-Thr4 residue is of allo-configuration (2TL). 4) The depsi (ester) bond is established between the ASP12 carboxyl and allo-2TL side-chain OH group.
Source: (natural) Pseudomonas sp. MIS38 (bacteria) / Strain: MIS38
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 NOESY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-1H COSY
141isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution
Contents: 1.3 mM NA arthrofactin A, 142.8 mM [U-2H] DPC, 90% H2O/10% D2O
Details: Arthrofactin A was dissolved in the micellar solution of uniformly deuterated dodecylphosphocholine (DPC-d38). Solvent: 10 mM Na2HPO4/NaH2PO4 buffer at pH 7.4.
Label: 1H / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.3 mMarthrofactin ANA1
142.8 mMDPC[U-2H]1
Sample conditionsIonic strength: 26 (buffer only) mM / Label: conditions_1 / pH: 7.4 / Pressure: 1 atm / Temperature: 310 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 700 MHz / Details: Prodigy Cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
AmberToolsCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmandata analysis
TopSpin3.xBruker Biospinprocessing
TopSpin3.xBruker Biospincollection
CcpNmr AnalysisVuister et al.peak picking
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CcpNmr AnalysisVuister et al.chemical shift assignment
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: The lowest energy NMR structure issued from CNS was refined in an unrestrained AMBER molecular dynamics simulation (agains the ff14SB force field). Here, we modelled the interaction of a ...Details: The lowest energy NMR structure issued from CNS was refined in an unrestrained AMBER molecular dynamics simulation (agains the ff14SB force field). Here, we modelled the interaction of a single peptide molecule with an explicit dodecylphosphocholine (DPC) micelle. The representative peptide conformation of the trajectory (=refined structure, #1) was selected using cluster analysis. Solvent model: TIP3P. Occasional too-close contacts present in the NMR structure ensemble (structures #2-#11) are fully removed during the AMBER moleculary dynamics refinement (structure #1). Side-chain outlier values for the 2TL4 residue are the results of the depsi bond.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 11

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