5VG0

Room temperature X-ray crystallographic structure of a Jonesia denitrificans lytic polysaccharide monooxygenase at 1.1 angstrom resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.128 
  • R-Value Work: 0.114 
  • R-Value Observed: 0.114 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Neutron and Atomic Resolution X-ray Structures of a Lytic Polysaccharide Monooxygenase Reveal Copper-Mediated Dioxygen Binding and Evidence for N-Terminal Deprotonation.

Bacik, J.P.Mekasha, S.Forsberg, Z.Kovalevsky, A.Y.Vaaje-Kolstad, G.Eijsink, V.G.H.Nix, J.C.Coates, L.Cuneo, M.J.Unkefer, C.J.Chen, J.C.

(2017) Biochemistry 56: 2529-2532

  • DOI: https://doi.org/10.1021/acs.biochem.7b00019
  • Primary Citation of Related Structures:  
    5VG0, 5VG1

  • PubMed Abstract: 

    A 1.1 Å resolution, room-temperature X-ray structure and a 2.1 Å resolution neutron structure of a chitin-degrading lytic polysaccharide monooxygenase domain from the bacterium Jonesia denitrificans (JdLPMO10A) show a putative dioxygen species equatorially bound to the active site copper. Both structures show an elongated density for the dioxygen, most consistent with a Cu(II)-bound peroxide. The coordination environment is consistent with Cu(II). In the neutron and X-ray structures, difference maps reveal the N-terminal amino group, involved in copper coordination, is present as a mixed ND 2 and ND - , suggesting a role for the copper ion in shifting the pK a of the amino terminus.


  • Organizational Affiliation

    Protein Crystallography Station, Bioscience Division, Los Alamos National Laboratory , Los Alamos, New Mexico 87545, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chitinase
A, B
142Jonesia denitrificans DSM 20603Mutation(s): 0 
Gene Names: Jden_1381
EC: 3.2.1.14
UniProt
Find proteins for C7R4I0 (Jonesia denitrificans (strain ATCC 14870 / DSM 20603 / BCRC 15368 / CIP 55.134 / JCM 11481 / NBRC 15587 / NCTC 10816 / Prevot 55134))
Explore C7R4I0 
Go to UniProtKB:  C7R4I0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC7R4I0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.128 
  • R-Value Work: 0.114 
  • R-Value Observed: 0.114 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.04α = 90
b = 75.56β = 90
c = 120.36γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-05-31
    Changes: Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description