› 3i6b

X-ray diffraction
2.49Å resolution

Crystal structure of YrbI lacking the last 8 residues, in complex with Kdo and inorganic phosphate

Released:
DOI: 10.2210/pdb3i6b/pdb
PDB entry 3i6b coloured by chain, front view.
PDB entry 3i6b coloured by chain, side view.
PDB entry 3i6b coloured by chain, top view.
Source organism: Escherichia coli B
Primary publication:
The tail of KdsC: conformational changes control the activity of a haloacid dehalogenase superfamily phosphatase.
Biswas T, Yi L, Aggarwal P, Wu J, Rubin JR, Stuckey JA, Woodard RW, Tsodikov OV
J Biol Chem 284 30594-603 (2009)
PMID: 19726684

Function and Biology Details

Reaction catalysed: 
3-deoxy-D-manno-octulosonate 8-phosphate + H(2)O = 3-deoxy-D-manno-octulosonate + phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
homo tetramer (preferred)
homo octamer
Assembly name:
PDBe Complex ID:
PDB-CPX-159216 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 180 amino acids
Theoretical weight: 19.21 KDa
Source organism: Escherichia coli B
Expression system: Escherichia coli
UniProt:
  • Canonical: P67653 (Residues: 1-180; Coverage: 96%)
Gene names: c3958, kdsC
Sequence domains: haloacid dehalogenase-like hydrolase
Structure domains: HAD superfamily/HAD-like

Ligands and Environments

3 bound ligands:
Ligand MG 4 x MG
Ligand PO4 4 x PO4
Ligand KDO 2 x KDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: C2221
Unit cell:
a: 64.964Å b: 144.104Å c: 145.854Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.202 0.2 0.238
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Conservation of the 2-keto-3-deoxymanno-octulosonic acid (Kdo) biosynthesis pathway between plants and bacteria.
Smyth et al. (2013)
1 more

2 mentions without citation

The tail of KdsC: conformational changes control the activity of a haloacid dehalogenase superfamily phosphatase.
Biswas et al. (2009)
1 more