5D6U
X-ray crystal structure of ribonuclease A determined for the real space D/H contrast method
Summary for 5D6U
| Entry DOI | 10.2210/pdb5d6u/pdb |
| Related | 1KF5 |
| Descriptor | Ribonuclease pancreatic, ISOPROPYL ALCOHOL (3 entities in total) |
| Functional Keywords | ribonuclease a, d/h contrast, hydrolase |
| Biological source | Bos taurus (Bovine) |
| Total number of polymer chains | 1 |
| Total formula weight | 13768.42 |
| Authors | Chatake, T.,Fujiwara, S. (deposition date: 2015-08-13, release date: 2016-04-06, Last modification date: 2024-10-23) |
| Primary citation | Chatake, T.,Fujiwara, S. A technique for determining the deuterium/hydrogen contrast map in neutron macromolecular crystallography Acta Crystallogr D Struct Biol, 72:71-82, 2016 Cited by PubMed Abstract: A difference in the neutron scattering length between hydrogen and deuterium leads to a high density contrast in neutron Fourier maps. In this study, a technique for determining the deuterium/hydrogen (D/H) contrast map in neutron macromolecular crystallography is developed and evaluated using ribonuclease A. The contrast map between the D2O-solvent and H2O-solvent crystals is calculated in real space, rather than in reciprocal space as performed in previous neutron D/H contrast crystallography. The present technique can thus utilize all of the amplitudes of the neutron structure factors for both D2O-solvent and H2O-solvent crystals. The neutron D/H contrast maps clearly demonstrate the powerful detectability of H/D exchange in proteins. In fact, alternative protonation states and alternative conformations of hydroxyl groups are observed at medium resolution (1.8 Å). Moreover, water molecules can be categorized into three types according to their tendency towards rotational disorder. These results directly indicate improvement in the neutron crystal structure analysis. This technique is suitable for incorporation into the standard structure-determination process used in neutron protein crystallography; consequently, more precise and efficient determination of the D-atom positions is possible using a combination of this D/H contrast technique and standard neutron structure-determination protocols. PubMed: 26894536DOI: 10.1107/S2059798315021269 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.52 Å) |
Structure validation
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