› 3o6z

X-ray diffraction
2.05Å resolution

Structure of the D152A E.coli GDP-mannose hydrolase (yffh) in complex with Mg++

Released:
DOI: 10.2210/pdb3o6z/pdb
PDB entry 3o6z coloured by chain, front view.
PDB entry 3o6z coloured by chain, side view.
PDB entry 3o6z coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Structural studies of the Nudix GDP-mannose hydrolase from E. coli reveals a new motif for mannose recognition.
Boto AN, Xu W, Jakoncic J, Pannuri A, Romeo T, Bessman MJ, Gabelli SB, Amzel LM
Proteins 79 2455-66 (2011)
PMID: 21638333

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153360 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
GDP-mannose pyrophosphatase Chains: A, B
Molecule details ›
Chains: A, B
Length: 191 amino acids
Theoretical weight: 21.73 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P37128 (Residues: 1-191; Coverage: 100%)
Gene names: JW2451, b2467, nudK, yffH
Sequence domains: NUDIX domain
Structure domains: Nucleoside Triphosphate Pyrophosphohydrolase

Ligands and Environments

4 bound ligands:
Ligand MG 3 x MG
Ligand CL 2 x CL
Ligand PEG 2 x PEG
Ligand TRS 1 x TRS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E+ DW
Spacegroup: P212121
Unit cell:
a: 58.916Å b: 69.333Å c: 99.612Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.238 0.235 0.303
Expression system: Escherichia coli

Quick links

Citations

11 citation in other articles

The evolution of function within the Nudix homology clan.
Srouji et al. (2017)
10 more

1 mention without citation

Structural studies of the Nudix GDP-mannose hydrolase from E. coli reveals a new motif for mannose recognition.
Boto et al. (2011)