› 4nfw

X-ray diffraction
2.3Å resolution

Structure and atypical hydrolysis mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli

Released:
DOI: 10.2210/pdb4nfw/pdb
PDB entry 4nfw coloured by chain, front view.
PDB entry 4nfw coloured by chain, side view.
PDB entry 4nfw coloured by chain, top view.
Source organism: Escherichia coli str. 'clone D i14'
Primary publication:
Divalent metal ion-based catalytic mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli.
Hong MK, Ribeiro AJ, Kim JK, Ngo HP, Kim J, Lee CH, Ahn YJ, Fernandes PA, Li Q, Ramos MJ, Kang LW
Acta Crystallogr D Biol Crystallogr 70 1297-310 (2014)
PMID: 24816099

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-164881 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Putative Nudix hydrolase ymfB Chains: A, B, C, D, E, F, G, H, I, J, K, L
Molecule details ›
Chains: A, B, C, D, E, F, G, H, I, J, K, L
Length: 153 amino acids
Theoretical weight: 17.45 KDa
Source organism: Escherichia coli str. 'clone D i14'
Expression system: Escherichia coli
Structure domains: Nucleoside Triphosphate Pyrophosphohydrolase

Ligands and Environments

2 bound ligands:
Ligand MN 22 x MN
Ligand SO4 35 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 4A
Spacegroup: P41
Unit cell:
a: 111.387Å b: 111.387Å c: 247.489Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.243 0.24 0.289
Expression system: Escherichia coli

Quick links

Citations

3 citation in other articles

Structural and Enzymatic Characterization of a Nucleoside Diphosphate Sugar Hydrolase from Bdellovibrio bacteriovorus.
de la Peña et al. (2015)
2 more