› 4kdp

X-ray diffraction
3.6Å resolution

TcaR-ssDNA complex crystal structure reveals the novel ssDNA binding mechanism of the MarR family proteins

Released:
DOI: 10.2210/pdb4kdp/pdb
PDB entry 4kdp coloured by chain, front view.
PDB entry 4kdp coloured by chain, side view.
PDB entry 4kdp coloured by chain, top view.
Source organism: Staphylococcus epidermidis ATCC 12228
Primary publication:
TcaR-ssDNA complex crystal structure reveals new DNA binding mechanism of the MarR family proteins.
Chang YM, Ho CH, Chen CK, Maestre-Reyna M, Chang-Chien MW, Wang AH
Nucleic Acids Res 42 5314-21 (2014)
PMID: 24531929

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero trimer (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-101576 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
HTH marR-type domain-containing protein Chains: A, B, C, D, E, F, G
Molecule details ›
Chains: A, B, C, D, E, F, G
Length: 151 amino acids
Theoretical weight: 17.38 KDa
Source organism: Staphylococcus epidermidis ATCC 12228
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A0H2VJZ8 (Residues: 1-151; Coverage: 100%)
Gene name: SE_1937
Sequence domains: MarR family
Structure domains: Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
DNA (5'-D(*CP*GP*CP*AP*GP*CP*GP*CP*GP*CP*AP*GP*CP*CP*CP*TP*A)-3') Chains: H, J
Molecule details ›
Chains: H, J
Length: 17 nucleotides
Theoretical weight: 5.16 KDa
Source organism: Staphylococcus epidermidis ATCC 12228
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand EDO 6 x EDO
Ligand TRS 5 x TRS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P3221
Unit cell:
a: 91.899Å b: 91.899Å c: 261.534Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.274 0.274 0.285
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 review citations

MarR family transcription factors: dynamic variations on a common scaffold.
Deochand et al. (2017)
1 more

2 mentions without citation

How Aromatic Compounds Block DNA Binding of HcaR Catabolite Regulator.
Kim et al. (2016)
1 more