7wnp | pdb_00007wnp

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.

spinqualitylabelsall models 7wnp, resolution 1.72Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 7wnp is a 1 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: CU, DOD, NA NonStd Res: ASA, TPQ Activity: Primary-amine oxidase, with EC number 1.4.3.21 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed 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 A, respectively [Murakawa et al. (2020 black triangle right). Proc. Natl Acad. Sci. USA, 117, 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 A 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. Re-evaluation of protein neutron crystallography with and without X-ray/neutron joint refinement.,Murakawa T, Kurihara K, Adachi M, Kusaka K, Tanizawa K, Okajima T IUCrJ. 2022 Apr 8;9(Pt 3):342-348. doi: 10.1107/S2052252522003657. eCollection, 2022 May 1. PMID:35546796 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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