› 5tfz

X-ray diffraction
2.2Å resolution

Crystal structure of the dimethylsulfoniopropionate (DMSP) lyase DddK complexed with nickel and diacrylate

Released:
DOI: 10.2210/pdb5tfz/pdb
PDB entry 5tfz coloured by chain, front view.
PDB entry 5tfz coloured by chain, side view.
PDB entry 5tfz coloured by chain, top view.
Source organism: Candidatus Pelagibacter ubique HTCC1062
Primary publication:
Structural and Biochemical Insights into Dimethylsulfoniopropionate Cleavage by Cofactor-Bound DddK from the Prolific Marine Bacterium Pelagibacter.
Schnicker NJ, De Silva SM, Todd JD, Dey M
Biochemistry 56 2873-2885 (2017)
PMID: 28511016

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-175509 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Cupin type-2 domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 150 amino acids
Theoretical weight: 16.61 KDa
Source organism: Candidatus Pelagibacter ubique HTCC1062
Expression system: Escherichia coli
UniProt:
  • Canonical: Q4FNM4 (Residues: 1-130; Coverage: 100%)
Gene name: SAR11_0394
Sequence domains: Cupin domain

Ligands and Environments

3 bound ligands:
Ligand NI 2 x NI
Ligand 7BC 2 x 7BC
Ligand PEG 3 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 4.2.2
Spacegroup: P212121
Unit cell:
a: 43.352Å b: 54.667Å c: 118.335Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.175 0.172 0.224
Expression system: Escherichia coli

Quick links

Citations

7 citation in other articles

Aminoacyl sulfonamide assembly in SB-203208 biosynthesis.
Hu et al. (2019)
6 more

3 mentions without citation

Illuminating the catalytic core of ectoine synthase through structural and biochemical analysis.
Czech et al. (2019)
2 more