5VG1

Neutron crystallographic structure of a Jonesia denitrificans lytic polysaccharide monooxygenase


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1021/acs.biochem.7b00019
  • Primary Citation of Related Structures:  

  • 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 equato ...

    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.,Biology and Soft Matter Division, Oak Ridge National Laboratory , 1 Bethel Valley Road, P.O. Box 2008, Oak Ridge, Tennessee 37831, United States.,Advanced Light Source, Lawrence Berkeley Laboratory , 1 Cyclotron Road, Berkeley, California 94720, United States.,Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU) , PO Box 5003, 1430 Ås, Norway.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chitinase
A, B
142Jonesia denitrificans (strain ATCC 14870 / DSM 20603 / CIP 55134)Mutation(s): 0 
EC: 3.2.1.14
Find proteins for C7R4I0 (Jonesia denitrificans (strain ATCC 14870 / DSM 20603 / CIP 55134))
Go to UniProtKB:  C7R4I0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PER
Query on PER

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

Download SDF File 
Download CCD File 
A, B
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.187 
Software Package:
Software NamePurpose
Mantiddata reduction
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-05-31
    Type: Database references