› 2nyg

X-ray diffraction
2.6Å resolution

Crystal structure of YokD protein from Bacillus subtilis

Released:
DOI: 10.2210/pdb2nyg/pdb
PDB entry 2nyg coloured by chain, front view.
PDB entry 2nyg coloured by chain, side view.
PDB entry 2nyg coloured by chain, top view.
Source organism: Bacillus subtilis
Entry authors: Madegowda M, Eswaramoorthy S, Burley SK, Swaminathan S, New York SGX Research Center for Structural Genomics (NYSGXRC)

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128398 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
SPbeta prophage-derived aminoglycoside N(3')-acetyltransferase-like protein YokD Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 273 amino acids
Theoretical weight: 31.02 KDa
Source organism: Bacillus subtilis
Expression system: Escherichia coli
UniProt:
  • Canonical: O32003 (Residues: 2-272; Coverage: 100%)
Gene names: BSU21630, yokD
Sequence domains: Aminoglycoside 3-N-acetyltransferase

Ligands and Environments

1 bound ligand:
Ligand COA 5 x COA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X12C
Spacegroup: P212121
Unit cell:
a: 73.02Å b: 132.39Å c: 185.8Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.257 0.257 0.296
Expression system: Escherichia coli

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