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- PDB-8s8n: NMR structure of tanniamide in micellar DPC solution -

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Basic information

Entry
Database: PDB / ID: 8s8n
TitleNMR structure of tanniamide in micellar DPC solution
ComponentsTanniamide
KeywordsSURFACTANT PROTEIN / Non-ribosomal polypeptide / Cyclic lipodepsipeptide / Antimicrobial peptide / Biosurfactant
Function / homology: / polypeptide(D) / polypeptide(D) (> 10)
Function and homology information
Biological speciesPseudomonas ekonensis (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 tanniamide in micellar DPC solution
Authors: Kovacs, B. / Geudens, N. / Martins, J.C.
History
DepositionMar 6, 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: Tanniamide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,6002
Polymers1,3861
Non-polymers2141
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, not applicable
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) Tanniamide


Mass: 1385.603 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 1) The polypeptide chain of tanniamide consists of 12 amino acids. 2) The N-terminal amino acid (DLE) is acylated with an (R)-3-hydroxy-dodecenoic acid (DEA) moeity which is indicated as the ...Details: 1) The polypeptide chain of tanniamide consists of 12 amino acids. 2) The N-terminal amino acid (DLE) is acylated with an (R)-3-hydroxy-dodecenoic acid (DEA) moeity which is indicated as the first residue. (double bond between the 5th and 6th carbon atoms) 3) The side-chains of the 2TL4 and 28J5 residues are of allo-configuration. 4) The depsi bond is established between the GLU13 mainchain carboxyl and the 2TL4 side-chain OH group.
Source: (natural) Pseudomonas ekonensis (bacteria) / Strain: COR58
#2: Chemical ChemComp-A1H5T / (~{Z},3~{R})-3-oxidanyldodec-5-enoic acid


Mass: 214.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H22O3
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 NOESY
121isotropic12D TOCSY
131isotropic12D COSY
141isotropic12D 1H-13 HSQC

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Sample preparation

DetailsType: solution
Contents: 1.82 mM tanniamide, 102.2 mM [U-2H] DPC, 90% H2O/10% D2O
Details: Tanniamide 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
1.82 mMtanniamidenatural abundance1
102.2 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. (CCPN)peak picking
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CcpNmr AnalysisCCPNchemical 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). 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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