› 5zxm

X-ray diffraction
1.94Å resolution

Crystal Structure of GyraseB N-terminal at 1.93A Resolution

Released:
DOI: 10.2210/pdb5zxm/pdb
PDB entry 5zxm coloured by chain, front view.
PDB entry 5zxm coloured by chain, side view.
PDB entry 5zxm coloured by chain, top view.
Source organism: Salmonella enterica subsp. enterica
Primary publication:
Structural insights into the transient closed conformation and pH dependent ATPase activity of S.Typhi GyraseB N- terminal domain.
Gupta D, Tiwari P, Haque MA, Sachdeva E, Hassan MI, Ethayathulla AS, Kaur P
Arch Biochem Biophys 701 108786 (2021)
PMID: 33548211

Function and Biology Details

Reaction catalysed: 
ATP-dependent breakage, passage and rejoining of double-stranded DNA
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-104967 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA gyrase subunit B Chains: A, B
Molecule details ›
Chains: A, B
Length: 400 amino acids
Theoretical weight: 44.24 KDa
Source organism: Salmonella enterica subsp. enterica
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A3R0U328 (Residues: 1-394; Coverage: 49%)
Gene names: AGQ90_12210, F2V25_18670, gyrB
Sequence domains:
Structure domains:

Ligands and Environments

5 bound ligands:
Ligand ADP 2 x ADP
Ligand SO4 2 x SO4
Ligand PEG 3 x PEG
Ligand MG 1 x MG
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE MASSIF-1
Unit cell:
a: 79.42Å b: 86.53Å c: 135.99Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.182 0.182 0.226
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 citations in other articles

Pharmacophore-Based Virtual Screening and Molecular Dynamics Simulation for Identification of a Novel DNA Gyrase B Inhibitor with Benzoxazine Acetamide Scaffold.
Elseginy et al. (2022)