6RGH

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. First structure of the series with 15 KGy dose.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.119 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

The subatomic resolution study of laccase inhibition by chloride and fluoride anions using single-crystal serial crystallography: insights into the enzymatic reaction mechanism.

Polyakov, K.M.Gavryushov, S.Fedorova, T.V.Glazunova, O.A.Popov, A.N.

(2019) Acta Crystallogr D Struct Biol 75: 804-816

  • DOI: 10.1107/S2059798319010684
  • Primary Citation of Related Structures:  
    6RGH, 6RHI, 6RHH, 6RGP, 6RII, 6RIL, 6RIK, 6RHU, 6RI6, 6RI8, 6RHX, 6RHO, 6RI0, 6RI2, 6RHP, 6RI4, 6RHR

  • PubMed Abstract: 
  • Laccases are enzymes that catalyze the oxidation of a wide range of organic and inorganic substrates accompanied by the reduction of molecular oxygen to water. Here, a subatomic resolution X-ray crystallographic study of the mechanism of inhibition of the laccase from the basidiomycete fungus Steccherinum murashkinskyi by chloride and fluoride ions is presented ...

    Laccases are enzymes that catalyze the oxidation of a wide range of organic and inorganic substrates accompanied by the reduction of molecular oxygen to water. Here, a subatomic resolution X-ray crystallographic study of the mechanism of inhibition of the laccase from the basidiomycete fungus Steccherinum murashkinskyi by chloride and fluoride ions is presented. Three series of X-ray diffraction data sets were collected with increasing doses of absorbed X-ray radiation from a native S. murashkinskyi laccase crystal and from crystals of complexes of the laccase with chloride and fluoride ions. The data for the native laccase crystal confirmed the previously deduced enzymatic mechanism of molecular oxygen reduction. The structures of the complexes allowed the localization of chloride and fluoride ions in the channel near the T2 copper ion. These ions replace the oxygen ligand of the T2 copper ion in this channel and can play the role of this ligand in the enzymatic reaction. As follows from analysis of the structures from the increasing dose series, the inhibition of laccases by chloride and fluoride anions can be explained by the fact that the binding of these negatively charged ions at the position of the oxygen ligand of the T2 copper ion impedes the reduction of the T2 copper ion.


    Organizational Affiliation

    ESRF - The European Synchrotron, CS40220, 38043 Grenoble CEDEX 9, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Laccase 2A499Steccherinum murashkinskyiMutation(s): 0 
EC: 1.10.3.2
UniProt
Find proteins for I1VE66 (Steccherinum murashkinskyi)
Explore I1VE66 
Go to UniProtKB:  I1VE66
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.119 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.23α = 90
b = 84.129β = 90
c = 112.356γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Foundation for Basic ResearchRussian Federation16-04-00552

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-09-11
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary