› 6ecf

X-ray diffraction
2.5Å resolution

Vlm2 thioesterase domain with genetically encoded 2,3-diaminopropionic acid bound with a dodecadepsipeptide, space group P1

Released:
DOI: 10.2210/pdb6ecf/pdb
PDB entry 6ecf coloured by chain, front view.
PDB entry 6ecf coloured by chain, side view.
PDB entry 6ecf coloured by chain, top view.
Source organisms:
Primary publication:
Trapping biosynthetic acyl-enzyme intermediates with encoded 2,3-diaminopropionic acid.
Huguenin-Dezot N, Alonzo DA, Heberlig GW, Mahesh M, Nguyen DP, Dornan MH, Boddy CN, Schmeing TM, Chin JW
Nature 565 112-117 (2019)
PMID: 30542153

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-166659 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Carrier domain-containing protein Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 303 amino acids
Theoretical weight: 33.1 KDa
Source organism: Streptomyces tsusimaensis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q1PSF3 (Residues: 2368-2655; Coverage: 11%)
Gene name: vlm2
Sequence domains: Thioesterase domain
dodecadepsipeptide Chains: G, H, I, J, K, L
Molecule details ›
Chains: G, H, I, J, K, L
Length: 12 amino acids
Theoretical weight: 1.13 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
3 modified residues:
Ligand DPP 6 x DPP
Ligand VAD 18 x VAD
Ligand DVA 18 x DVA

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: P1
Unit cell:
a: 76.996Å b: 77.129Å c: 90.329Å
α: 91.768° β: 114.886° γ: 117.938°
R-values:
R R work R free
0.2 0.197 0.249
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

6 review citations

Reprogramming the genetic code.
de la Torre et al. (2021)
5 more

3 mentions without citation

Structural advances toward understanding the catalytic activity and conformational dynamics of modular nonribosomal peptide synthetases.
Patel et al. (2023)
2 more