› 6ojd

X-ray diffraction
1.99Å resolution

A high-resolution crystal structure of covalent complex of NocB thioesterase domain with fluorophosphonate nocardicin G analog

Released:
DOI: 10.2210/pdb6ojd/pdb
PDB entry 6ojd coloured by chain, front view.
PDB entry 6ojd coloured by chain, side view.
PDB entry 6ojd coloured by chain, top view.
Source organism: Nocardia uniformis subsp. tsuyamanensis
Primary publication:
Structure of a bound peptide phosphonate reveals the mechanism of nocardicin bifunctional thioesterase epimerase-hydrolase half-reactions.
Patel KD, d'Andrea FB, Gaudelli NM, Buller AR, Townsend CA, Gulick AM
Nat Commun 10 3868 (2019)
PMID: 31455765

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-177257 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Carrier domain-containing protein Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 257 amino acids
Theoretical weight: 27.74 KDa
Source organism: Nocardia uniformis subsp. tsuyamanensis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5J1Q6 (Residues: 1690-1925; Coverage: 12%)
Gene name: nocB
Sequence domains: Thioesterase domain

Ligands and Environments

3 bound ligands:
Ligand GOL 12 x GOL
Ligand MUY 4 x MUY
Ligand CA 4 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P212121
Unit cell:
a: 73.68Å b: 78.56Å c: 146.89Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.189 0.188 0.225
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Biosynthesis of depsipeptides, or Depsi: The peptides with varied generations.
Alonzo et al. (2020)
1 more

2 mentions without citation

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