› 1jcl

X-ray diffraction
1.05Å resolution

OBSERVATION OF COVALENT INTERMEDIATES IN AN ENZYME MECHANISM AT ATOMIC RESOLUTION

Released:
DOI: 10.2210/pdb1jcl/pdb
Model geometry
Fit model/data
PDB entry 1jcl coloured by chain, front view.
PDB entry 1jcl coloured by chain, side view.
PDB entry 1jcl coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Observation of covalent intermediates in an enzyme mechanism at atomic resolution.
Heine A, DeSantis G, Luz JG, Mitchell M, Wong CH, Wilson IA
Science 294 369-74 (2001)
PMID: 11598300

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 domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-141373 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Deoxyribose-phosphate aldolase Chains: A, B
Molecule details ›
Chains: A, B
Length: 260 amino acids
Theoretical weight: 27.91 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A6L0 (Residues: 1-259; Coverage: 100%)
Gene names: JW4344, b4381, deoC, dra, thyR
Sequence domains: DeoC/LacD family aldolase
Structure domains: Aldolase class I

Ligands and Environments

1 bound ligand:
Ligand HPD 2 x HPD
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: P21
Unit cell:
a: 48.54Å b: 41.95Å c: 144.98Å
α: 90° β: 98.36° γ: 90°
R-values:
R R work R free
0.143 not available 0.169
Expression system: Escherichia coli

Quick links

Citations

20 review citations

Computational enzyme design.
Kiss et al. (2013)
19 more

20 mentions without citation

Current state of and need for enzyme engineering of 2-deoxy-D-ribose 5-phosphate aldolases and its impact.
Rouvinen et al. (2021)
19 more