› 5chr

X-ray diffraction
1.98Å resolution

Dehaloperoxidase B in complex with substrate p-nitrocatechol

Released:
DOI: 10.2210/pdb5chr/pdb
PDB entry 5chr coloured by chain, front view.
PDB entry 5chr coloured by chain, side view.
PDB entry 5chr coloured by chain, top view.
Source organism: Amphitrite ornata
Primary publication:
Nonmicrobial Nitrophenol Degradation via Peroxygenase Activity of Dehaloperoxidase-Hemoglobin from Amphitrite ornata.
McCombs NL, D'Antonio J, Barrios DA, Carey LM, Ghiladi RA
Biochemistry 55 2465-78 (2016)
PMID: 27070125

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-576144 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Globin domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 137 amino acids
Theoretical weight: 15.41 KDa
Source organism: Amphitrite ornata
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9NAV7 (Residues: 2-138; Coverage: 99%)
Sequence domains: Globin
Structure domains: Globins

Ligands and Environments

5 bound ligands:
Ligand HEM 2 x HEM
Ligand SO4 2 x SO4
Ligand 4NC 2 x 4NC
Ligand OXY 1 x OXY
Ligand GOL 3 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 59.883Å b: 67.192Å c: 67.442Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.17 0.165 0.22
Expression system: Escherichia coli

Quick links

Citations

6 citation in other articles

Active Sites of O2-Evolving Chlorite Dismutases Probed by Halides and Hydroxides and New Iron-Ligand Vibrational Correlations.
Geeraerts et al. (2017)
5 more

1 mention without citation

Metadata Analysis of mcr-1-Bearing Plasmids Inspired by the Sequencing Evidence for Horizontal Transfer of Antibiotic Resistance Genes Between Polluted River and Wild Birds.
Lin et al. (2020)