› 4pfm

X-ray diffraction
2.33Å resolution

SHEWANELLA BENTHICA DHDPS WITH LYSINE AND PYRUVATE

Released:
DOI: 10.2210/pdb4pfm/pdb
PDB entry 4pfm coloured by chain, front view.
PDB entry 4pfm coloured by chain, side view.
PDB entry 4pfm coloured by chain, top view.
Source organism: Shewanella benthica KT99
Entry authors: Wubben JM, Paxman JJ, Dogovski C, Panjikar S, Perugini MA

Function and Biology Details

Reaction catalysed: 
Pyruvate + L-aspartate-4-semialdehyde = (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate + H(2)O
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-108975 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
4-hydroxy-tetrahydrodipicolinate synthase Chains: A, B
Molecule details ›
Chains: A, B
Length: 295 amino acids
Theoretical weight: 31.15 KDa
Source organism: Shewanella benthica KT99
Expression system: Escherichia coli
UniProt:
  • Canonical: A9DKW4 (Residues: 16-310; Coverage: 95%)
Gene names: KT99_11964, dapA
Sequence domains: Dihydrodipicolinate synthetase family
Structure domains: Aldolase class I

Ligands and Environments

4 bound ligands:
Ligand LYS 3 x LYS
Ligand GOL 2 x GOL
Ligand NA 2 x NA
Ligand FLC 1 x FLC
1 modified residue:
Ligand KPI 2 x KPI

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: P212121
Unit cell:
a: 74.273Å b: 83.929Å c: 143.868Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.165 0.162 0.206
Expression system: Escherichia coli

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