› 3ekg

X-ray diffraction
1.6Å resolution

CRYSTAL STRUCTURE OF L-RHAMNONATE DEHYDRATASE FROM AZOTOBACTER VINELANDII complexed with Mg and L-TARTRATE

Released:
DOI: 10.2210/pdb3ekg/pdb
PDB 3ekg coloured by chain and viewed from the front.
PDB 3ekg coloured by chain and viewed from the side.
PDB 3ekg coloured by chain and viewed from the top.
Source organism: Azotobacter vinelandii DJ
Entry authors: Fedorov AA, Fedorov EV, Sauder JM, Burley SK, Gerlt JA, Almo SC, New York SGX Research Center for Structural Genomics (NYSGXRC)

Function and Biology Details

Reaction catalysed: 
L-rhamnonate = 2-dehydro-3-deoxy-L-rhamnonate + H(2)O
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
homo octamer
homo dimer (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
L-rhamnonate dehydratase Chains: A, B
Molecule details ›
Chains: A, B
Length: 404 amino acids
Theoretical weight: 46.17 KDa
Source organism: Azotobacter vinelandii DJ
Expression system: Escherichia coli
UniProt:
  • Canonical: C1DMY1 (Residues: 2-394; Coverage: 100%)
Gene names: Avin_09220, rhmD
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand TLA 2 x TLA
Ligand MG 2 x MG
1 modified residue:
Ligand MSE 32 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X4A
Spacegroup: I4
Unit cell:
a: 119.326Å b: 119.326Å c: 116.696Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.198 0.196 0.214
Expression system: Escherichia coli

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