7WNP

Crystallographic structure of copper amine oxidase from Arthrobacter glibiformis at pD 7.4 determined by both X-ray and neutron diffraction data at 1.72 angstrom resolution.

Summary for 7WNP

• Entry DOI: 10.2210/pdb7wnp/pdb
• Descriptor: Phenylethylamine oxidase, COPPER (II) ION, SODIUM ION, ... (4 entities in total)
• Functional Keywords: topaquinone, tpq, oxidoreductase
• Biological source: Arthrobacter globiformis
• Total number of polymer chains: 1
• Total formula weight: 69080.37

Authors

Murakawa, T.,Okajima, T. (deposition date: 2022-01-19, release date: 2022-04-20, Last modification date: 2022-05-25)

Primary citation

Murakawa, T.,Kurihara, K.,Adachi, M.,Kusaka, K.,Tanizawa, K.,Okajima, T.
Re-evaluation of protein neutron crystallography with and without X-ray/neutron joint refinement.
Iucrj, 9:342-348, 2022

PubMed Abstract: Protein neutron crystallography is a powerful technique to determine the positions of H atoms, providing crucial biochemical information such as the protonation states of catalytic groups and the geometry of hydrogen bonds. Recently, the crystal structure of a bacterial copper amine oxidase was determined by joint refinement using X-ray and neutron diffraction data sets at resolutions of 1.14 and 1.72 Å, respectively [Murakawa (2020 ▸). , , 10818-10824]. While joint refinement is effective for the determination of the accurate positions of heavy atoms on the basis of the electron density, the structural information on light atoms (hydrogen and deuterium) derived from the neutron diffraction data might be affected by the X-ray data. To unravel the information included in the neutron diffraction data, the structure determination was conducted again using only the neutron diffraction data at 1.72 Å resolution and the results were compared with those obtained in the previous study. Most H and D atoms were identified at essentially the same positions in both the neutron-only and the X-ray/neutron joint refinements. Nevertheless, neutron-only refinement was found to be less effective than joint refinement in providing very accurate heavy-atom coordinates that lead to significant improvement of the neutron scattering length density map, especially for the active-site cofactor. Consequently, it was confirmed that X-ray/neutron joint refinement is crucial for determination of the real chemical structure of the catalytic site of the enzyme.

PubMed: 35546796
DOI: 10.1107/S2052252522003657

Experimental method

NEUTRON DIFFRACTION (1.72 Å)
X-RAY DIFFRACTION (1.72 Å)