› 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 entry 3ekg coloured by chain, front view.
PDB entry 3ekg coloured by chain, side view.
PDB entry 3ekg coloured by chain, top view.
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:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
homo octamer
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-111098 (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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