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| | ==Neutron crystal structure of ribonuclease A determined by the real space D/H contrast method== | | ==Neutron crystal structure of ribonuclease A determined by the real space D/H contrast method== |
| - | <StructureSection load='4zz4' size='340' side='right' caption='[[4zz4]], [[Resolution|resolution]] 1.80Å' scene=''> | + | <StructureSection load='4zz4' size='340' side='right'caption='[[4zz4]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4zz4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZZ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZZ4 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4zz4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZZ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZZ4 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Neutron Diffraction, [[Resolution|Resolution]] 1.798Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1kf5|1kf5]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pancreatic_ribonuclease Pancreatic ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.5 3.1.27.5] </span></td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4zz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zz4 OCA], [https://pdbe.org/4zz4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zz4 RCSB], [https://www.ebi.ac.uk/pdbsum/4zz4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zz4 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4zz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zz4 OCA], [http://pdbe.org/4zz4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zz4 RCSB], [http://www.ebi.ac.uk/pdbsum/4zz4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4zz4 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RNAS1_BOVIN RNAS1_BOVIN]] Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single stranded and double stranded RNA.<ref>PMID:7479688</ref> | + | [https://www.uniprot.org/uniprot/RNAS1_BOVIN RNAS1_BOVIN] Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single stranded and double stranded RNA.<ref>PMID:7479688</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | ==See Also== | | ==See Also== |
| - | *[[Ribonuclease|Ribonuclease]] | + | *[[Ribonuclease 3D structures|Ribonuclease 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Bos taurus]] | | [[Category: Bos taurus]] |
| - | [[Category: Pancreatic ribonuclease]] | + | [[Category: Large Structures]] |
| - | [[Category: Chatake, T]] | + | [[Category: Chatake T]] |
| - | [[Category: Fujiwara, S]] | + | [[Category: Fujiwara S]] |
| - | [[Category: D/h contrast]]
| + | |
| - | [[Category: Hydrolase]]
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| - | [[Category: Ribonuclease some]]
| + | |
| Structural highlights
Function
RNAS1_BOVIN Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single stranded and double stranded RNA.[1]
Publication Abstract from PubMed
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 A). 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.
A technique for determining the deuterium/hydrogen contrast map in neutron macromolecular crystallography.,Chatake T, Fujiwara S Acta Crystallogr D Struct Biol. 2016 Jan;72(Pt 1):71-82. doi:, 10.1107/S2059798315021269. Epub 2016 Jan 1. PMID:26894536[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ delCardayre SB, Ribo M, Yokel EM, Quirk DJ, Rutter WJ, Raines RT. Engineering ribonuclease A: production, purification and characterization of wild-type enzyme and mutants at Gln11. Protein Eng. 1995 Mar;8(3):261-73. PMID:7479688
- ↑ Chatake T, Fujiwara S. A technique for determining the deuterium/hydrogen contrast map in neutron macromolecular crystallography. Acta Crystallogr D Struct Biol. 2016 Jan;72(Pt 1):71-82. doi:, 10.1107/S2059798315021269. Epub 2016 Jan 1. PMID:26894536 doi:http://dx.doi.org/10.1107/S2059798315021269
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