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| | ==Neutron structure of Perdeuterated Rubredoxin refined against 1.75 resolution data collected on the new IMAGINE instrument at HFIR, ORNL== | | ==Neutron structure of Perdeuterated Rubredoxin refined against 1.75 resolution data collected on the new IMAGINE instrument at HFIR, ORNL== |
| - | <StructureSection load='4k9f' size='340' side='right' caption='[[4k9f]], [[Resolution|resolution]] 1.75Å' scene=''> | + | <StructureSection load='4k9f' size='340' side='right'caption='[[4k9f]], [[Resolution|resolution]] 1.75Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4k9f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrfu Pyrfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K9F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4K9F FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4k9f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus_DSM_3638 Pyrococcus furiosus DSM 3638]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K9F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4K9F 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=FE:FE+(III)+ION'>FE</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]] 1.75Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3kyx|3kyx]], [[3rzt|3rzt]], [[1vcx|1vcx]], [[4ar3|4ar3]], [[3ryg|3ryg]], [[3ss2|3ss2]]</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=FE:FE+(III)+ION'>FE</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PF1282, rub ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</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=4k9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k9f OCA], [https://pdbe.org/4k9f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4k9f RCSB], [https://www.ebi.ac.uk/pdbsum/4k9f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4k9f 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=4k9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k9f OCA], [http://pdbe.org/4k9f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4k9f RCSB], [http://www.ebi.ac.uk/pdbsum/4k9f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4k9f ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RUBR_PYRFU RUBR_PYRFU]] Rubredoxin is a small nonheme, iron protein lacking acid-labile sulfide. Its single Fe, chelated to 4 Cys, functions as an electron acceptor and may also stabilize the conformation of the molecule. | + | [https://www.uniprot.org/uniprot/RUBR_PYRFU RUBR_PYRFU] Rubredoxin is a small nonheme, iron protein lacking acid-labile sulfide. Its single Fe, chelated to 4 Cys, functions as an electron acceptor and may also stabilize the conformation of the molecule. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 4k9f" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 4k9f" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Rubredoxin 3D structures|Rubredoxin 3D structures]] |
| | + | *[[Rubredoxin PDB structures|Rubredoxin PDB structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Pyrfu]] | + | [[Category: Large Structures]] |
| - | [[Category: Meilleur, F]] | + | [[Category: Pyrococcus furiosus DSM 3638]] |
| - | [[Category: Munshi, P]] | + | [[Category: Meilleur F]] |
| - | [[Category: Myles, D]] | + | [[Category: Munshi P]] |
| - | [[Category: Electron transport]] | + | [[Category: Myles D]] |
| - | [[Category: Iron]]
| + | |
| - | [[Category: Metal-binding]]
| + | |
| - | [[Category: Transport]]
| + | |
| Structural highlights
Function
RUBR_PYRFU Rubredoxin is a small nonheme, iron protein lacking acid-labile sulfide. Its single Fe, chelated to 4 Cys, functions as an electron acceptor and may also stabilize the conformation of the molecule.
Publication Abstract from PubMed
The first high-resolution neutron protein structure of perdeuterated rubredoxin from Pyrococcus furiosus (PfRd) determined using the new IMAGINE macromolecular neutron crystallography instrument at the Oak Ridge National Laboratory is reported. Neutron diffraction data extending to 1.65 A resolution were collected from a relatively small 0.7 mm(3) PfRd crystal using 2.5 d (60 h) of beam time. The refined structure contains 371 out of 391, or 95%, of the D atoms of the protein and 58 solvent molecules. The IMAGINE instrument is designed to provide neutron data at or near atomic resolution (1.5 A) from crystals with volume <1.0 mm(3) and with unit-cell edges <100 A. Beamline features include novel elliptical focusing mirrors that deliver neutrons into a 2.0 x 3.2 mm focal spot at the sample position with full-width vertical and horizontal divergences of 0.5 and 0.6 degrees , respectively. Variable short- and long-wavelength cutoff optics provide automated exchange between multiple-wavelength configurations (lambdamin = 2.0, 2.8, 3.3 A to lambdamax = 3.0, 4.0, 4.5, approximately 20 A). These optics produce a more than 20-fold increase in the flux density at the sample and should help to enable more routine collection of high-resolution data from submillimetre-cubed crystals. Notably, the crystal used to collect these PfRd data was 5-10 times smaller than those previously reported.
The IMAGINE instrument: first neutron protein structure and new capabilities for neutron macromolecular crystallography.,Meilleur F, Munshi P, Robertson L, Stoica AD, Crow L, Kovalevsky A, Koritsanszky T, Chakoumakos BC, Blessing R, Myles DA Acta Crystallogr D Biol Crystallogr. 2013 Oct;69(Pt 10):2157-60. doi:, 10.1107/S0907444913019604. Epub 2013 Sep 20. PMID:24100333[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Meilleur F, Munshi P, Robertson L, Stoica AD, Crow L, Kovalevsky A, Koritsanszky T, Chakoumakos BC, Blessing R, Myles DA. The IMAGINE instrument: first neutron protein structure and new capabilities for neutron macromolecular crystallography. Acta Crystallogr D Biol Crystallogr. 2013 Oct;69(Pt 10):2157-60. doi:, 10.1107/S0907444913019604. Epub 2013 Sep 20. PMID:24100333 doi:http://dx.doi.org/10.1107/S0907444913019604
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