› 6pc3

X-ray diffraction
2.1Å resolution

Crystal structure of Helicobacter pylori PPX/GppA in complex with GSP

Released:
DOI: 10.2210/pdb6pc3/pdb
PDB entry 6pc3 coloured by chain, front view.
PDB entry 6pc3 coloured by chain, side view.
PDB entry 6pc3 coloured by chain, top view.
Source organism: Helicobacter pylori G27
Primary publication:
Structure and activity of PPX/GppA homologs from Escherichia coli and Helicobacter pylori.
Song H, Dharmasena MN, Wang C, Shaw GX, Cherry S, Tropea JE, Jin DJ, Ji X
FEBS J 287 1865-1885 (2020)
PMID: 31679177

Function and Biology Details

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-110301 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Guanosine pentaphosphate phosphohydrolase Chains: A, B
Molecule details ›
Chains: A, B
Length: 495 amino acids
Theoretical weight: 55.66 KDa
Source organism: Helicobacter pylori G27
Expression system: Escherichia coli
UniProt:
  • Canonical: B5ZA44 (Residues: 2-484; Coverage: 100%)
Gene name: HPG27_257
Sequence domains:

Ligands and Environments

7 bound ligands:
Ligand GSP 2 x GSP
Ligand PO4 2 x PO4
Ligand MG 4 x MG
Ligand K 2 x K
Ligand CL 3 x CL
Ligand EDO 1 x EDO
Ligand TS6 2 x TS6
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: C2
Unit cell:
a: 114.312Å b: 90.856Å c: 105.238Å
α: 90° β: 106.74° γ: 90°
R-values:
R R work R free
0.18 0.179 0.225
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Model systems for studying polyphosphate biology: a focus on microorganisms.
Denoncourt et al. (2021)
1 more

1 mention without citation

Structure and activity of PPX/GppA homologs from Escherichia coli and Helicobacter pylori.
Song et al. (2020)