› 4y9d

X-ray diffraction
2.01Å resolution

Crystal structure of LigD in complex with NADH from Sphingobium sp. strain SYK-6

Released:
DOI: 10.2210/pdb4y9d/pdb
PDB 4y9d coloured by chain and viewed from the front.
PDB 4y9d coloured by chain and viewed from the side.
PDB 4y9d coloured by chain and viewed from the top.
Source organism: Sphingobium sp. SYK-6
Primary publication:
Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin ��-aryl Ether Cleavage Pathway from Sphingobium sp SYK-6.
Pereira JH, Heins RA, Gall DL, McAndrew RP, Deng K, Holland KC, Donohue TJ, Noguera DR, Simmons BA, Sale KL, Ralph J, Adams PD
J. Biol. Chem. (2016)
PMID: 26940872

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
C alpha-dehydrogenase Chain: A
Molecule details ›
Chain: A
Length: 305 amino acids
Theoretical weight: 32.38 KDa
Source organism: Sphingobium sp. SYK-6
Expression system: Escherichia coli
UniProt:
  • Canonical: G2IN91 (Residues: 1-305; Coverage: 100%)
Gene names: SLG_08640, ligD
Sequence domains: short chain dehydrogenase
Structure domains: NAD(P)-binding Rossmann-like Domain

Ligands and Environments

1 bound ligand:
Ligand NAI 1 x NAI
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.2
Spacegroup: P3121
Unit cell:
a: 61.762Å b: 61.762Å c: 134.713Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.215 0.211 0.248
Expression system: Escherichia coli

Quick links

Citations

6 review citations

Deconstruction of Lignin: From Enzymes to Microorganisms.
Silva et al. (2021)
5 more

1 mention without citation

Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6.
Pereira et al. (2016)