› 5yiw

X-ray diffraction
1.55Å resolution

Caulobacter crescentus GcrA DNA-binding domain (DBD) in complex with methylated dsDNA (crystal form 2)

Released:
DOI: 10.2210/pdb5yiw/pdb
PDB entry 5yiw coloured by chain, front view.
PDB entry 5yiw coloured by chain, side view.
PDB entry 5yiw coloured by chain, top view.
Source organisms:
Primary publication:
Structural insights into the unique mechanism of transcription activation by Caulobacter crescentus GcrA.
Wu X, Haakonsen DL, Sanderlin AG, Liu YJ, Shen L, Zhuang N, Laub MT, Zhang Y
OpenAccess logo Nucleic Acids Res 46 3245-3256 (2018)
PMID: 29514271

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero trimer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-493902 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Cell cycle regulatory protein GcrA Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 49 amino acids
Theoretical weight: 5.32 KDa
Source organism: Caulobacter vibrioides NA1000
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A0H3C9J4 (Residues: 1-45; Coverage: 26%)
Gene names: CCNA_02328, gcrA
DNA (5'-D(*CP*CP*CP*TP*GP*(6MA)P*TP*TP*CP*GP*C)-3') Chain: D
Molecule details ›
Chain: D
Length: 11 nucleotides
Theoretical weight: 3.3 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*GP*CP*GP*(6MA)P*AP*TP*CP*AP*GP*G)-3') Chain: E
Molecule details ›
Chain: E
Length: 11 nucleotides
Theoretical weight: 3.4 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand BU3 1 x BU3
1 modified residue:
Ligand 6MA 2 x 6MA

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: C2221
Unit cell:
a: 49.81Å b: 63.658Å c: 126.73Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.205 0.204 0.234
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

3 review citations

Diverse and unified mechanisms of transcription initiation in bacteria.
Chen et al. (2021)
2 more

1 mention without citation

Structural insights into the unique mechanism of transcription activation by Caulobacter crescentus GcrA.
Wu et al. (2018)