› 7ywz

X-ray diffraction
1.75Å resolution

Modified oligopeptidase B from S. proteomaculans in intermediate conformation with 4 spermine molecules at 1.75 A resolution

Released:
DOI: 10.2210/pdb7ywz/pdb
PDB entry 7ywz coloured by chain, front view.
PDB entry 7ywz coloured by chain, side view.
PDB entry 7ywz coloured by chain, top view.
Source organism: Serratia proteamaculans
Entry authors: Petrenko DE, Boyko KM, Nikolaeva AY, Vlaskina AV, Mikhailova AG, Timofeev VI, Rakitina TV

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:
Oligopeptidase B Chain: A
Molecule details ›
Chain: A
Length: 677 amino acids
Theoretical weight: 78.46 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

2 bound ligands:
Ligand SPM 4 x SPM
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P212121
Unit cell:
a: 72.89Å b: 100.44Å c: 108.55Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.174 0.172 0.202
Expression system: Escherichia coli

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