› 2oz3

X-ray diffraction
2Å resolution

Crystal structure of L-Rhamnonate dehydratase from Azotobacter vinelandii

Released:
DOI: 10.2210/pdb2oz3/pdb
PDB entry 2oz3 coloured by chain, front view.
PDB entry 2oz3 coloured by chain, side view.
PDB entry 2oz3 coloured by chain, top view.
Source organism: Azotobacter vinelandii DJ
Entry authors: Patskovsky Y, Toro R, Sauder JM, Freeman JC, Bain K, Gheyi T, Wu B, Wasserman SR, Smith D, Gerlt J, Burley SK, 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 (preferred)
homo tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-111100 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
L-rhamnonate dehydratase Chains: A, B, C, D, E, F, G, H
Molecule details ›
Chains: A, B, C, D, E, F, G, H
Length: 404 amino acids
Theoretical weight: 46.17 KDa
Source organism: Azotobacter vinelandii DJ
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: C1DMY1 (Residues: 2-394; Coverage: 100%)
Gene names: Avin_09220, rhmD
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand GOL 31 x GOL
Ligand NA 2 x NA
1 modified residue:
Ligand MSE 128 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: C2
Unit cell:
a: 170.772Å b: 115.397Å c: 164.113Å
α: 90° β: 96.06° γ: 90°
R-values:
R R work R free
0.197 0.196 0.257
Expression system: Escherichia coli BL21(DE3)

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