› 7uk8

X-ray diffraction
1.85Å resolution

Apo form of YgiC from Escherichia coli K-12

Released:
DOI: 10.2210/pdb7uk8/pdb
PDB entry 7uk8 coloured by chain, front view.
PDB entry 7uk8 coloured by chain, side view.
PDB entry 7uk8 coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Escherichia coli YgiC and YjfC Possess Peptide─Spermidine Ligase Activity.
Pederick JL, Klose J, Jovcevski B, Pukala TL, Bruning JB
Biochemistry (2023)
PMID: 36745518

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-142375 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Putative acid--amine ligase YgiC Chain: A
Molecule details ›
Chain: A
Length: 394 amino acids
Theoretical weight: 46.09 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0ADT5 (Residues: 1-386; Coverage: 100%)
Gene names: JW3006, b3038, ygiC
Sequence domains: Glutathionylspermidine synthase preATP-grasp

Ligands and Environments

3 bound ligands:
Ligand NI 1 x NI
Ligand SO4 7 x SO4
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX1
Spacegroup: P3121
Unit cell:
a: 88.22Å b: 88.22Å c: 141.598Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.187 0.186 0.211
Expression system: Escherichia coli BL21(DE3)

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