› 5c6m

X-ray diffraction
1.76Å resolution

Crystal structure of deoxyribose-phosphate aldolase from Shewanella halifaxensis

Released:
DOI: 10.2210/pdb5c6m/pdb
PDB entry 5c6m coloured by chain, front view.
PDB entry 5c6m coloured by chain, side view.
PDB entry 5c6m coloured by chain, top view.
Source organism: Shewanella halifaxensis
Primary publication:
Trading off stability against activity in extremophilic aldolases.
Dick M, Weiergräber OH, Classen T, Bisterfeld C, Bramski J, Gohlke H, Pietruszka J
Sci Rep 6 17908 (2016)
PMID: 26783049

Function and Biology Details

Reaction catalysed: 
2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-109215 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Deoxyribose-phosphate aldolase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 265 amino acids
Theoretical weight: 28.18 KDa
Source organism: Shewanella halifaxensis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: B0TQ91 (Residues: 1-257; Coverage: 100%)
Gene names: Shal_3136, deoC
Sequence domains: DeoC/LacD family aldolase
Structure domains: Aldolase class I

Ligands and Environments

2 bound ligands:
Ligand NA 2 x NA
Ligand CL 4 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: C2
Unit cell:
a: 154.03Å b: 52.51Å c: 143.21Å
α: 90° β: 122.34° γ: 90°
R-values:
R R work R free
0.17 0.168 0.198
Expression system: Escherichia coli BL21(DE3)

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Citations

4 review citations

Physical and molecular bases of protein thermal stability and cold adaptation.
Pucci et al. (2017)
3 more