› 4omy

X-ray diffraction
3.06Å resolution

Crystal Structure of SeMet NolR from Sinorhizobium fredii in complex with oligo AT DNA

Released:
DOI: 10.2210/pdb4omy/pdb
PDB entry 4omy coloured by chain, front view.
PDB entry 4omy coloured by chain, side view.
PDB entry 4omy coloured by chain, top view.
Source organism: Sinorhizobium fredii
Primary publication:
Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR.
Lee SG, Krishnan HB, Jez JM
Proc Natl Acad Sci U S A 111 6509-14 (2014)
PMID: 24733893

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117924 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
HTH arsR-type domain-containing protein Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 118 amino acids
Theoretical weight: 12.98 KDa
Source organism: Sinorhizobium fredii
Expression system: Escherichia coli
UniProt:
  • Canonical: Q83TD2 (Residues: 1-118; Coverage: 100%)
Gene name: nolR
Sequence domains: Bacterial regulatory protein, arsR family
Structure domains: Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
DNA (5 -D(*TP*AP*TP*TP*AP*GP*AP*GP*AP*AP*CP*CP*CP*TP*GP*AP*AP*GP*TP*TP*AP*A)-3 ) Chains: E, G
Molecule details ›
Chains: E, G
Length: 22 nucleotides
Theoretical weight: 6.78 KDa
Source organism: Sinorhizobium fredii
Expression system: Not provided
DNA (5 -D(*TP*AP*AP*TP*CP*TP*CP*TP*TP*GP*GP*GP*AP*CP*TP*TP*CP*AP*AP*TP*TP*A)-3 ) Chains: F, H
Molecule details ›
Chains: F, H
Length: 22 nucleotides
Theoretical weight: 6.72 KDa
Source organism: Sinorhizobium fredii
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand MSE 20 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P31
Unit cell:
a: 131.019Å b: 131.019Å c: 67.688Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.134 0.132 0.178
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

4 review citations

Metal homeostasis in bacteria: the role of ArsR-SmtB family of transcriptional repressors in combating varying metal concentrations in the environment.
Saha et al. (2017)
3 more

3 mentions without citation

Protein metalation in biology.
Foster et al. (2022)
2 more