› 5khd

X-ray diffraction
1.75Å resolution

Structure of 1.75 A BldD C-domain-c-di-GMP complex

Released:
DOI: 10.2210/pdb5khd/pdb
PDB entry 5khd coloured by chain, front view.
PDB entry 5khd coloured by chain, side view.
PDB entry 5khd coloured by chain, top view.
Source organism: Streptomyces venezuelae ATCC 10712
Primary publication:
Tetrameric c-di-GMP mediates effective transcription factor dimerization to control Streptomyces development.
Tschowri N, Schumacher MA, Schlimpert S, Chinnam NB, Findlay KC, Brennan RG, Buttner MJ
Cell 158 1136-1147 (2014)
PMID: 25171413

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-123403 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
HTH cro/C1-type domain-containing protein Chains: A, R
Molecule details ›
Chains: A, R
Length: 91 amino acids
Theoretical weight: 10.16 KDa
Source organism: Streptomyces venezuelae ATCC 10712
Expression system: Escherichia coli
UniProt:
  • Canonical: F2RCL8 (Residues: 80-166; Coverage: 52%)
Gene name: SVEN_1089
Sequence domains: DNA-binding protein BldD-like, C-terminal domain
Structure domains: Arc Repressor Mutant, subunit A

Ligands and Environments

1 bound ligand:
Ligand C2E 4 x C2E
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.3.1
Spacegroup: C2221
Unit cell:
a: 36.16Å b: 95.58Å c: 99.58Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.183 0.183 0.185
Expression system: Escherichia coli

Quick links

Citations

37 review citations

Taxonomy, Physiology, and Natural Products of Actinobacteria.
Barka et al. (2016)
36 more

1 mention without citation

Cyclic di-AMP, a second messenger of primary importance: tertiary structures and binding mechanisms.
He et al. (2020)