› 1rlt

X-ray diffraction
2.2Å resolution

Transition State Analogue of ybiV from E. coli K12

Released:
DOI: 10.2210/pdb1rlt/pdb
PDB entry 1rlt coloured by chain, front view.
PDB entry 1rlt coloured by chain, side view.
PDB entry 1rlt coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
YbiV from Escherichia coli K12 is a HAD phosphatase.
Roberts A, Lee SY, McCullagh E, Silversmith RE, Wemmer DE
Proteins 58 790-801 (2005)
PMID: 15657928

Function and Biology Details

Reaction catalysed: 
Sugar phosphate + H(2)O = sugar + phosphate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159998 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Sugar phosphatase YbiV Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 271 amino acids
Theoretical weight: 30.51 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P75792 (Residues: 1-271; Coverage: 100%)
Gene names: JW0806, b0822, supH, ybiV
Sequence domains: haloacid dehalogenase-like hydrolase
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand MG 4 x MG
Ligand ACT 1 x ACT
Ligand AF3 4 x AF3
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P212121
Unit cell:
a: 71.761Å b: 91.166Å c: 183.85Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.242 0.221 0.264
Expression system: Escherichia coli

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Citations

2 review citations

Structure-based function prediction: approaches and applications.
Gherardini et al. (2008)
1 more