› 7b59

X-ray diffraction
1.63Å resolution

X-ray crystal structure of Sporosarcina pasteurii urease inhibited by Ag(PEt3)Br determined at 1.63 Angstroms

Released:
DOI: 10.2210/pdb7b59/pdb
PDB entry 7b59 coloured by chain, front view.
PDB entry 7b59 coloured by chain, side view.
PDB entry 7b59 coloured by chain, top view.
Source organism: Sporosarcina pasteurii
Primary publication:
Kinetic and structural analysis of the inactivation of urease by mixed-ligand phosphine halide Ag(I) complexes.
Mazzei L, Cirri D, Cianci M, Messori L, Ciurli S
J Inorg Biochem 218 111375 (2021)
PMID: 33711632

Function and Biology Details

Reaction catalysed: 
Urea + H(2)O = CO(2) + 2 NH(3)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero nonamer (preferred)
PDBe Complex ID:
PDB-CPX-154232 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Urease subunit gamma Chain: AAA
Molecule details ›
Chain: AAA
Length: 100 amino acids
Theoretical weight: 11.13 KDa
Source organism: Sporosarcina pasteurii
UniProt:
  • Canonical: P41022 (Residues: 1-100; Coverage: 100%)
Gene name: ureA
Sequence domains: Urease, gamma subunit
Urease subunit beta Chain: BBB
Molecule details ›
Chain: BBB
Length: 122 amino acids
Theoretical weight: 13.53 KDa
Source organism: Sporosarcina pasteurii
UniProt:
  • Canonical: P41021 (Residues: 5-126; Coverage: 97%)
Gene name: ureB
Sequence domains: Urease beta subunit
Urease subunit alpha Chain: CCC
Molecule details ›
Chain: CCC
Length: 570 amino acids
Theoretical weight: 61.58 KDa
Source organism: Sporosarcina pasteurii
UniProt:
  • Canonical: P41020 (Residues: 1-34, 35-570; Coverage: 100%)
Gene names: NCTC4822_02163, ureC
Sequence domains:

Ligands and Environments

5 bound ligands:
Ligand EDO 14 x EDO
Ligand SO4 18 x SO4
Ligand NI 2 x NI
Ligand O 1 x O
Ligand AG 2 x AG
2 modified residues:
Ligand CXM 1 x CXM
Ligand KCX 1 x KCX

Experiments and Validation Details

Entry percentile scores
X-ray source: PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)
Spacegroup: P6322
Unit cell:
a: 131.41Å b: 131.41Å c: 189.416Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.15 0.149 0.177

Quick links

Citations

2 citation in other articles

Inhibition of Urease by Hydroquinones: A Structural and Kinetic Study.
Mazzei et al. (2022)
1 more