› 4i1d

X-ray diffraction
2.2Å resolution

The crystal structure of an ABC transporter substrate-binding protein from Bradyrhizobium japonicum USDA 110

Released:
DOI: 10.2210/pdb4i1d/pdb
PDB entry 4i1d coloured by chain, front view.
PDB entry 4i1d coloured by chain, side view.
PDB entry 4i1d coloured by chain, top view.
Source organism: Bradyrhizobium diazoefficiens USDA 110
Primary publication:
Structural and functional characterization of solute binding proteins for aromatic compounds derived from lignin: p-coumaric acid and related aromatic acids.
Tan K, Chang C, Cuff M, Osipiuk J, Landorf E, Mack JC, Zerbs S, Joachimiak A, Collart FR
Proteins 81 1709-26 (2013)
PMID: 23606130

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-183543 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
ABC transporter substrate-binding protein Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 324 amino acids
Theoretical weight: 35.74 KDa
Source organism: Bradyrhizobium diazoefficiens USDA 110
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q89F76 (Residues: 44-364; Coverage: 88%)
Gene name: bll6825
Sequence domains: Bacterial extracellular solute-binding protein
Structure domains: Periplasmic binding protein-like II

Ligands and Environments

4 bound ligands:
Ligand SO4 34 x SO4
Ligand GOL 15 x GOL
Ligand ACT 19 x ACT
Ligand MLT 4 x MLT
1 modified residue:
Ligand MSE 24 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P3221
Unit cell:
a: 136.641Å b: 136.641Å c: 185.634Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.174 0.172 0.209
Expression system: Escherichia coli BL21(DE3)

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Citations

1 review citation

Bacterial catabolism of lignin-derived aromatics: New findings in a recent decade: Update on bacterial lignin catabolism.
Kamimura et al. (2017)
10 other articles