› 3ndr

X-ray diffraction
2.88Å resolution

Crystal structure of tetrameric pyridoxal 4-dehydrogenase from Mesorhizobium loti

Released:
DOI: 10.2210/pdb3ndr/pdb
PDB entry 3ndr coloured by chain, front view.
PDB entry 3ndr coloured by chain, side view.
PDB entry 3ndr coloured by chain, top view.
Source organism: Mesorhizobium loti
Entry author: Chu HN

Function and Biology Details

Reaction catalysed: 
Pyridoxal + NAD(+) = 4-pyridoxolactone + NADH
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-189125 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyridoxal 4-dehydrogenase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 247 amino acids
Theoretical weight: 25.66 KDa
Source organism: Mesorhizobium loti
Expression system: Escherichia coli
UniProt:
  • Canonical: Q988B7 (Residues: 2-248; Coverage: 100%)
Gene names: mlr6807, pldh-t
Sequence domains: Enoyl-(Acyl carrier protein) reductase
Structure domains: NAD(P)-binding Rossmann-like Domain

Ligands and Environments


Cofactor: Ligand NAD 4 x NAD
No bound ligands
1 modified residue:
Ligand MSE 20 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL38B1
Spacegroup: P21
Unit cell:
a: 86.203Å b: 51.109Å c: 91.732Å
α: 90° β: 89.36° γ: 90°
R-values:
R R work R free
0.188 0.185 0.248
Expression system: Escherichia coli

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