› 6rgp

X-ray diffraction
0.97Å resolution

Single crystal serial study of the X-ray induced enzymatic reduction of molecular oxygen to water for laccase from Steccherinum murashkinskyi at sub-atomic resolution. Second structure of the series with 165 KGy dose.

Released:
DOI: 10.2210/pdb6rgp/pdb
PDB entry 6rgp coloured by chain, front view.
PDB entry 6rgp coloured by chain, side view.
PDB entry 6rgp coloured by chain, top view.
Source organism: Steccherinum murashkinskyi
Primary publication:
The subatomic resolution study of laccase inhibition by chloride and fluoride anions using single-crystal serial crystallography: insights into the enzymatic reaction mechanism.
Polyakov KM, Gavryushov S, Fedorova TV, Glazunova OA, Popov AN
Acta Crystallogr D Struct Biol 75 804-816 (2019)
PMID: 31478903

Function and Biology Details

Reaction catalysed: 
4 benzenediol + O(2) = 4 benzosemiquinone + 2 H(2)O
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-125040 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Laccase 2 Chain: A
Molecule details ›
Chain: A
Length: 499 amino acids
Theoretical weight: 53.38 KDa
Source organism: Steccherinum murashkinskyi
UniProt:
  • Canonical: I1VE66 (Residues: 20-518; Coverage: 95%)
Sequence domains:
Structure domains: Cupredoxins - blue copper proteins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
2 bound ligands:
Ligand CU 4 x CU
Ligand OXY 1 x OXY
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P212121
Unit cell:
a: 56.233Å b: 84.115Å c: 112.336Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.109 0.108 0.123

Quick links

Citations

1 review citation

Fungal Laccases: The Forefront of Enzymes for Sustainability.
Loi et al. (2021)
6 other articles

2 mentions without citation

Quantum Mechanical Study of Oxygen Ligands Protonation for the Stable States of the Laccase Active Site.
Gavryushov et al. (2023)
1 more