› 7ne4

X-ray diffraction
2.72Å resolution

E125A mutant of oligopeptidase B from S. proteomaculans with modified hinge region

Released:
DOI: 10.2210/pdb7ne4/pdb
PDB entry 7ne4 coloured by chain, front view.
PDB entry 7ne4 coloured by chain, side view.
PDB entry 7ne4 coloured by chain, top view.
Source organism: Serratia proteamaculans
Primary publication:
First Crystal Structure of Bacterial Oligopeptidase B in an Intermediate State: The Roles of the Hinge Region Modification and Spermine.
Petrenko DE, Timofeev VI, Britikov VV, Britikova EV, Kleymenov SY, Vlaskina AV, Kuranova IP, Mikhailova AG, Rakitina TV
Biology (Basel) 10 (2021)
PMID: 34681120

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-109948 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Prolyl oligopeptidase family serine peptidase Chain: A
Molecule details ›
Chain: A
Length: 676 amino acids
Theoretical weight: 78.26 KDa
Source organism: Serratia proteamaculans
Expression system: Escherichia coli
UniProt:
  • Canonical: B3VI58 (Residues: 2-677; Coverage: 100%)
Gene names: JKX24_00380, opdB
Sequence domains:

Ligands and Environments

1 bound ligand:
Ligand SPM 3 x SPM
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: KURCHATOV SNC BEAMLINE K4.4
Spacegroup: P212121
Unit cell:
a: 68.84Å b: 98.56Å c: 108.26Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.253 0.25 0.306
Expression system: Escherichia coli

Quick links

Citations

1 review citation

COVID-19 and Diarylamidines: The Parasitic Connection.
Hulme J. (2023)
1 other article

1 mention without citation

First Crystal Structure of Bacterial Oligopeptidase B in an Intermediate State: The Roles of the Hinge Region Modification and Spermine.
Petrenko et al. (2021)