3T6X

Crystal Structure of Steccherinum ochraceum Laccase obtained by multi-crystals composite data collection technique (20% dose)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Reaction intermediates and redox state changes in a blue laccase from Steccherinum ochraceum observed by crystallographic high/low X-ray dose experiments.

Ferraroni, M.Matera, I.Chernykh, A.Kolomytseva, M.Golovleva, L.A.Scozzafava, A.Briganti, F.

(2012) J.Inorg.Biochem. 111: 203-209

  • DOI: 10.1016/j.jinorgbio.2012.01.011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structure of a blue laccase from Steccherinum ochraceum has been solved at 2.0Å of resolution using a classic data acquisition from a single crystal. The overall structural features are typical of this class of enzymes, however, distances ...

    The crystal structure of a blue laccase from Steccherinum ochraceum has been solved at 2.0Å of resolution using a classic data acquisition from a single crystal. The overall structural features are typical of this class of enzymes, however, distances inside the trinuclear copper cluster are indicative of a reduction of the metal centers induced by free electrons produced during the X-ray data collection. UV-visible spectra collected during the X-ray exposure support the progressive reduction of the metal centers. In order to better detect the reduction progression steps in the trinuclear copper site, a multicrystal data collection strategy based on a systematic spread of the X-ray dose over many crystals has been employed. This approach is based on collecting multicrystal data sets, then combining the slices of the individual data sets experiencing the same radiation dose to obtain composite complete data sets at progressively higher doses. Applying this technique, we have been able to capture sequential frames of the enzyme during the metal centers and molecular oxygen reduction mechanism obtaining a three-dimensional movie of the X-ray-driven catalytic conversion of the molecular oxygen in the active site of laccase: first, the copper ions reduction, then the molecular oxygen binding and its reductive splitting, thus allowing to reconstruct the entire catalytic cycle for multicopper oxidases.


    Organizational Affiliation

    Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, Sesto Fiorentino, Florence, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Laccase
A, B, C
495Steccherinum ochraceumMutation(s): 0 
EC: 1.10.3.2
Find proteins for I1SB14 (Steccherinum ochraceum)
Go to UniProtKB:  I1SB14
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PER
Query on PER

Download SDF File 
Download CCD File 
A, B, C
PEROXIDE ION
O2
ANAIPYUSIMHBEL-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

Download SDF File 
Download CCD File 
A, B, C
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
CBS
Query on CBS

Download SDF File 
Download CCD File 
A, B, C
DI(N-ACETYL-D-GLUCOSAMINE)
C16 H28 N2 O11
CDOJPCSDOXYJJF-KSKNGZLJSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 73.510α = 90.00
b = 140.040β = 90.00
c = 172.980γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
MAR345dtbdata collection
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-18
    Type: Initial release
  • Version 1.1: 2012-10-03
    Type: Database references