› 3shd

X-ray diffraction
2.5Å resolution

Crystal structure of Nudix hydrolase Orf153, ymfB, from Escherichia coli K-1

Released:
DOI: 10.2210/pdb3shd/pdb
PDB entry 3shd coloured by chain, front view.
PDB entry 3shd coloured by chain, side view.
PDB entry 3shd coloured by chain, top view.
Source organism: Escherichia coli APEC O1
Entry authors: Hong MK, Kim JK, Kang LW

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-106549 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Phosphatase NudJ 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 APEC O1
Expression system: Escherichia coli
UniProt:
  • Canonical: A1AA28 (Residues: 1-153; Coverage: 100%)
Gene names: APECO1_216, Ecok1_10240, nudJ
Sequence domains: NUDIX domain
Structure domains: Nucleoside Triphosphate Pyrophosphohydrolase

Ligands and Environments

2 bound ligands:
Ligand MN 24 x MN
Ligand SO4 36 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 4A
Spacegroup: P41
Unit cell:
a: 111.126Å b: 111.126Å c: 247.306Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.23 0.226 0.291
Expression system: Escherichia coli

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