› 5krv

X-ray diffraction
2.3Å resolution

1-deoxy-D-xylulose 5-phosphate reductoisomerase from Vibrio vulnificus in complex Arginine

Released:
DOI: 10.2210/pdb5krv/pdb
PDB entry 5krv coloured by chain, front view.
PDB entry 5krv coloured by chain, side view.
PDB entry 5krv coloured by chain, top view.
Source organism: Vibrio vulnificus CMCP6
Primary publication:
Structural characterization of 1-deoxy-D-xylulose 5-phosphate Reductoisomerase from Vibrio vulnificus.
Ussin NK, Bagnell AM, Offermann LR, Abdulsalam R, Perdue ML, Magee P, Chruszcz M
Biochim Biophys Acta Proteins Proteom 1866 1209-1215 (2018)
PMID: 30278288

Function and Biology Details

Reaction catalysed: 
2-C-methyl-D-erythritol 4-phosphate + NADP(+) = 1-deoxy-D-xylulose 5-phosphate + NADPH
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-184042 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
1-deoxy-D-xylulose 5-phosphate reductoisomerase Chains: A, B
Molecule details ›
Chains: A, B
Length: 427 amino acids
Theoretical weight: 46.15 KDa
Source organism: Vibrio vulnificus CMCP6
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8DBF5 (Residues: 1-402; Coverage: 100%)
Gene names: VV1_1866, dxr
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand EDO 11 x EDO
Ligand ARG 1 x ARG
Ligand CL 1 x CL
Ligand SRT 1 x SRT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: C2221
Unit cell:
a: 65.165Å b: 149.129Å c: 245.089Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.187 0.186 0.215
Expression system: Escherichia coli BL21(DE3)

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