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- PDB-9eps: NMR structure of MDN-0066 in micellar DPC solution -

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Basic information

Entry
Database: PDB / ID: 9eps
TitleNMR structure of MDN-0066 in micellar DPC solution
ComponentsMDN-0066
KeywordsSURFACTANT PROTEIN / Non-ribosomal polypeptide / Cyclic lipodepsipeptide / Antimicrobial peptide / Biosurfactant
Function / homology: / polypeptide(D)
Function and homology information
Biological speciesPseudomonas azadiae (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsKovacs, B. / Geudens, N. / Martins, J.C.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)EOS project G0G3118N (EOS ID 30650620) Belgium
CitationJournal: To be published
Title: NMR structure of MDN-0066 in micellar DPC solution
Authors: Kovacs, B. / Geudens, N. / Martins, J.C.
History
DepositionMar 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MDN-0066
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,0892
Polymers9011
Non-polymers1881
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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) MDN-0066


Mass: 901.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 1) The polypeptide chain of MDN-0066 consists of 8amino acids. 2) The N-terminal amino acid (DLE) is acylated with an (R)-3-hydroxy-decanoic acid (IG8) moeity which is indicated as the first ...Details: 1) The polypeptide chain of MDN-0066 consists of 8amino acids. 2) The N-terminal amino acid (DLE) is acylated with an (R)-3-hydroxy-decanoic acid (IG8) moeity which is indicated as the first residue. 3) The depsi (ester) bond is established between the ILE9 carboxyl and 2TL4 side-chain OH group.
Source: (natural) Pseudomonas azadiae (bacteria) / Strain: SWRI103
#2: Chemical ChemComp-IG8 / (3~{R})-3-oxidanyldecanoic acid


Mass: 188.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O3
Has ligand of interestN
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
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-1H COSY
141isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution
Contents: 1.5 mM MDN-0066, 104.3 mM [U-2H] DPC, 90% H2O/10% D2O
Details: MDN-0066 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
1.5 mMMDN-0066natural abundance1
104.3 mMDPC[U-2H]1
Sample conditionsIonic strength: 26 (buffer only) mM / Label: conditions_1 / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVACE II / Manufacturer: Bruker / Model: AVACE 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 using unrestrained AMBER molecular dynamics simulations (against the ff14SB force field). Here, we modelled the interaction of a ...Details: The lowest energy NMR structure issued from CNS was refined using unrestrained AMBER molecular dynamics simulations (against 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) 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)
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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