› 5y6f

X-ray diffraction
2.3Å resolution

Crystal structure of YcgR in complex with c-di-GMP from Escherichia coli

Released:
DOI: 10.2210/pdb5y6f/pdb
PDB entry 5y6f coloured by chain, front view.
PDB entry 5y6f coloured by chain, side view.
PDB entry 5y6f coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Structural insights into the mechanism of c-di-GMP-bound YcgR regulating flagellar motility in Escherichia coli.
Hou YJ, Yang WS, Hong Y, Zhang Y, Wang DC, Li DF
J Biol Chem 295 808-821 (2020)
PMID: 31836667

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-160030 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Flagellar brake protein YcgR Chain: A
Molecule details ›
Chain: A
Length: 257 amino acids
Theoretical weight: 29.42 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P76010 (Residues: 1-244; Coverage: 100%)
Gene names: JW1183, b1194, ycgR
Sequence domains:

Ligands and Environments

2 bound ligands:
Ligand SO4 1 x SO4
Ligand C2E 2 x C2E
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: R3
Unit cell:
a: 93.98Å b: 93.98Å c: 109.64Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.186 0.183 0.233
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

Ways to control harmful biofilms: prevention, inhibition, and eradication.
Yin et al. (2021)
3 more

4 mentions without citation

The World of Cyclic Dinucleotides in Bacterial Behavior.
Aline Dias da et al. (2020)
3 more