› 6erd

X-ray diffraction
2Å resolution

Crystal structure of a putative acetyltransferase from Bacillus cereus species.

Released:
DOI: 10.2210/pdb6erd/pdb
PDB entry 6erd coloured by chain, front view.
PDB entry 6erd coloured by chain, side view.
PDB entry 6erd coloured by chain, top view.
Source organism: Bacillus cereus ATCC 14579
Primary publication:
Functional and structural characterisation of RimL from Bacillus cereus, a new Nα-acetyltransferase of ribosomal proteins that was wrongly assigned as an aminoglycosyltransferase.
Leonardo Silvestre H, Asensio JL, Blundell TL, Bastida A, Bolanos-Garcia VM
Int J Biol Macromol 263 130348 (2024)
PMID: 38395274

Function and Biology Details

Reaction catalysed: 
Acetyl-CoA + kanamycin-B = CoA + N(6')-acetylkanamycin-B
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-182493 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
N-acetyltransferase domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 211 amino acids
Theoretical weight: 24.58 KDa
Source organism: Bacillus cereus ATCC 14579
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q81D84 (Residues: 2-169; Coverage: 99%)
Gene name: BC_2494
Sequence domains: Acetyltransferase (GNAT) domain
N-acetyltransferase domain-containing protein Chains: C, D
Molecule details ›
Chains: C, D
Length: 211 amino acids
Theoretical weight: 24.5 KDa
Source organism: Bacillus cereus ATCC 14579
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q81D84 (Residues: 2-169; Coverage: 99%)
Gene name: BC_2494
Sequence domains: Acetyltransferase (GNAT) domain

Ligands and Environments

2 bound ligands:
Ligand GOL 8 x GOL
Ligand CL 3 x CL
2 modified residues:
Ligand MSE 36 x MSE
Ligand CME 2 x CME

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P21
Unit cell:
a: 68.52Å b: 84.17Å c: 72.08Å
α: 90° β: 98.49° γ: 90°
R-values:
R R work R free
0.166 0.164 0.201
Expression system: Escherichia coli BL21

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