› 6grh

X-ray diffraction
1.85Å resolution

E. coli Microcin synthetase McbBCD complex with truncated pro-MccB17 bound

Released:
DOI: 10.2210/pdb6grh/pdb
PDB entry 6grh coloured by chain, front view.
PDB entry 6grh coloured by chain, side view.
PDB entry 6grh coloured by chain, top view.
Source organism: Escherichia coli str. K-12 substr. MG1655
Primary publication:
Architecture of Microcin B17 Synthetase: An Octameric Protein Complex Converting a Ribosomally Synthesized Peptide into a DNA Gyrase Poison.
Ghilarov D, Stevenson CEM, Travin DY, Piskunova J, Serebryakova M, Maxwell A, Lawson DM, Severinov K
Mol Cell 73 749-762.e5 (2019)
PMID: 30661981

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
PDBe Complex ID:
PDB-CPX-138794 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Bacteriocin microcin B17 Chain: A
Molecule details ›
Chain: A
Length: 52 amino acids
Theoretical weight: 5.14 KDa
Source organism: Escherichia coli str. K-12 substr. MG1655
Expression system: Escherichia coli BW25113
UniProt:
  • Canonical: P05834 (Residues: 1-46; Coverage: 67%)
Gene name: mcbA
Microcin B17-processing protein McbB Chains: 1, 2
Molecule details ›
Chains: 1, 2
Length: 295 amino acids
Theoretical weight: 34.03 KDa
Source organism: Escherichia coli str. K-12 substr. MG1655
Expression system: Escherichia coli BW25113
UniProt:
  • Canonical: P23184 (Residues: 1-295; Coverage: 100%)
Gene name: mcbB
Microcin B17-processing protein McbC Chain: C
Molecule details ›
Chain: C
Length: 272 amino acids
Theoretical weight: 30.79 KDa
Source organism: Escherichia coli str. K-12 substr. MG1655
Expression system: Escherichia coli BW25113
UniProt:
  • Canonical: P23185 (Residues: 1-272; Coverage: 100%)
Gene name: mcbC
Sequence domains: Nitroreductase family
Microcin B17-processing protein McbD Chain: D
Molecule details ›
Chain: D
Length: 396 amino acids
Theoretical weight: 44.96 KDa
Source organism: Escherichia coli str. K-12 substr. MG1655
Expression system: Escherichia coli BW25113
UniProt:
  • Canonical: P23186 (Residues: 1-396; Coverage: 100%)
Gene name: mcbD
Sequence domains: YcaO cyclodehydratase, ATP-ad Mg2+-binding

Ligands and Environments

6 bound ligands:
Ligand ZN 2 x ZN
Ligand SO4 1 x SO4
Ligand CL 2 x CL
Ligand EDO 7 x EDO
Ligand FMN 1 x FMN
Ligand GOL 1 x GOL
1 modified residue:
Ligand OTZ 1 x OTZ

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: C2
Unit cell:
a: 180.74Å b: 83.76Å c: 87.12Å
α: 90° β: 91.33° γ: 90°
R-values:
R R work R free
0.174 0.172 0.207
Expression system: Escherichia coli BW25113

Quick links

Citations

6 review citations

New developments in RiPP discovery, enzymology and engineering.
Montalbán-López et al. (2021)
5 more

3 mentions without citation

Architecture of Microcin B17 Synthetase: An Octameric Protein Complex Converting a Ribosomally Synthesized Peptide into a DNA Gyrase Poison.
Ghilarov et al. (2019)
2 more