+Open data
-Basic information
Entry | Database: PDB / ID: 8q1l | |||||||||||||||
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Title | NMR structure of arthrofactin A in micellar DPC solution | |||||||||||||||
Components | arthrofactin A | |||||||||||||||
Keywords | SURFACTANT PROTEIN / Non-ribosomal polypeptide / Cyclic lipodepsipeptide / Antimicrobial peptide / Biosurfactant | |||||||||||||||
Function / homology | polypeptide(D) / polypeptide(D) (> 10) Function and homology information | |||||||||||||||
Biological species | Pseudomonas sp. MIS38 (bacteria) | |||||||||||||||
Method | SOLUTION NMR / molecular dynamics | |||||||||||||||
Authors | Kovacs, B. / Geudens, N. / Martins, J.C. | |||||||||||||||
Funding support | Belgium, 4items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8q1l.cif.gz | 45 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8q1l.ent.gz | 31 KB | Display | PDB format |
PDBx/mmJSON format | 8q1l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/8q1l ftp://data.pdbj.org/pub/pdb/validation_reports/q1/8q1l | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Polypeptide(D) | 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 |
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Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: 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 | ||||||||||||
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Sample |
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Sample conditions | Ionic strength: 26 (buffer only) mM / Label: conditions_1 / pH: 7.4 / Pressure: 1 atm / Temperature: 310 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 700 MHz / Details: Prodigy Cryoprobe |
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-Processing
NMR software |
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Refinement | Method: 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 representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 11 |