4u9i | pdb_00004u9i

High Resolution Structure Of The Ni-R State Of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

spinqualitylabelsall models 4u9i, resolution 1.06Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4u9i is a 2 chain structure with sequence from Desulfovibrio vulgaris str. 'Miyazaki F'. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.06Å Ligands: MG, MPD, NWN, TRS Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function PHNS_NITV9 Catalyzes the reversible oxidoreduction of molecular hydrogen, in conjunction with a specific electron acceptor, cytochrome c3. Publication Abstract from PubMed The enzyme hydrogenase reversibly converts dihydrogen to protons and electrons at a metal catalyst. The location of the abundant hydrogens is of key importance for understanding structure and function of the protein. However, in protein X-ray crystallography the detection of hydrogen atoms is one of the major problems, since they display only weak contributions to diffraction and the quality of the single crystals is often insufficient to obtain sub-angstrom resolution. Here we report the crystal structure of a standard [NiFe] hydrogenase ( approximately 91.3 kDa molecular mass) at 0.89 A resolution. The strictly anoxically isolated hydrogenase has been obtained in a specific spectroscopic state, the active reduced Ni-R (subform Ni-R1) state. The high resolution, proper refinement strategy and careful modelling allow the positioning of a large part of the hydrogen atoms in the structure. This has led to the direct detection of the products of the heterolytic splitting of dihydrogen into a hydride (H-) bridging the Ni and Fe and a proton (H+) attached to the sulphur of a cysteine ligand. The Ni-H- and Fe-H- bond lengths are 1.58 A and 1.78A, respectively. Furthermore, we can assign the Fe-CO and Fe-CN- ligands at the active site, and can obtain the hydrogen-bond networks and the preferred proton transfer pathway in the hydrogenase. Our results demonstrate the precise comprehensive information available from ultra-high-resolution structures of proteins as an alternative to neutron diffraction and other methods such as NMR structural analysis. Hydrogens detected by subatomic resolution protein crystallography in a [NiFe] hydrogenase.,Ogata H, Nishikawa K, Lubitz W Nature. 2015 Jan 26. doi: 10.1038/nature14110. PMID:25624102 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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