|
|
| Line 3: |
Line 3: |
| | <StructureSection load='3f6r' size='340' side='right'caption='[[3f6r]], [[Resolution|resolution]] 2.00Å' scene=''> | | <StructureSection load='3f6r' size='340' side='right'caption='[[3f6r]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3f6r]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_desulfuricans"_(beijerinck_1895)_saltet_1900 "bacillus desulfuricans" (beijerinck 1895) saltet 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F6R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3F6R FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3f6r]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_desulfuricans Desulfovibrio desulfuricans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F6R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3F6R FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3f6s|3f6s]]</div></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">flavodoxin ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=876 "Bacillus desulfuricans" (Beijerinck 1895) Saltet 1900])</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=3f6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f6r OCA], [https://pdbe.org/3f6r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3f6r RCSB], [https://www.ebi.ac.uk/pdbsum/3f6r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3f6r ProSAT]</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=3f6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f6r OCA], [https://pdbe.org/3f6r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3f6r RCSB], [https://www.ebi.ac.uk/pdbsum/3f6r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3f6r ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/FLAV_DESDE FLAV_DESDE]] Low-potential electron donor to a number of redox enzymes.
| + | [https://www.uniprot.org/uniprot/FLAV_DESDE FLAV_DESDE] Low-potential electron donor to a number of redox enzymes. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| Line 37: |
Line 36: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Desulfovibrio desulfuricans]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Guelker, M]] | + | [[Category: Guelker M]] |
| - | [[Category: Shamoo, Y]] | + | [[Category: Shamoo Y]] |
| - | [[Category: Electron transport]]
| + | |
| - | [[Category: Flavodoxin-like fold]]
| + | |
| - | [[Category: Flavoprotein]]
| + | |
| - | [[Category: Fmn]]
| + | |
| - | [[Category: Fmn binding]]
| + | |
| - | [[Category: Oxidized]]
| + | |
| - | [[Category: Transport]]
| + | |
| Structural highlights
Function
FLAV_DESDE Low-potential electron donor to a number of redox enzymes.
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The crystal structure of oxidized flavodoxin from Desulfovibrio desulfuricans (ATCC 29577) was determined by molecular replacement in two crystal forms, P3(1)21 and P4(3), at 2.5 and 2.0 A resolution, respectively. Structure determination in space group P3(1)21 was challenging owing to the presence of pseudo-translational symmetry and a high copy number in the asymmetric unit (8). Initial phasing attempts in space group P3(1)21 by molecular replacement using a poor search model (46% identity) and multi-wavelength anomalous dispersion were unsuccessful. It was necessary to solve the structure in a second crystal form, space group P4(3), which was characterized by almost perfect twinning, in order to obtain a suitable search model for molecular replacement. This search model with complementary approaches to molecular replacement utilizing the pseudo-translational symmetry operators determined by analysis of the native Patterson map facilitated the selection and manual placement of molecules to generate an initial solution in the P3(1)21 crystal form. During the early stages of refinement, application of the appropriate twin law, (-h, -k, l), was required to converge to reasonable R-factor values despite the fact that in the final analysis the data were untwinned and the twin law could subsequently be removed. The approaches used in structure determination and refinement may be applicable to other crystal structures characterized by these complicating factors. The refined model shows flexibility of the flavin mononucleotide coordinating loops indicated by the isolation of two loop conformations and provides a starting point for the elucidation of the mechanism used for protein-partner recognition.
Pseudosymmetry, high copy number and twinning complicate the structure determination of Desulfovibrio desulfuricans (ATCC 29577) flavodoxin.,Guelker M, Stagg L, Wittung-Stafshede P, Shamoo Y Acta Crystallogr D Biol Crystallogr. 2009 Jun;65(Pt 6):523-34. Epub 2009, May 15. PMID:19465766[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Guelker M, Stagg L, Wittung-Stafshede P, Shamoo Y. Pseudosymmetry, high copy number and twinning complicate the structure determination of Desulfovibrio desulfuricans (ATCC 29577) flavodoxin. Acta Crystallogr D Biol Crystallogr. 2009 Jun;65(Pt 6):523-34. Epub 2009, May 15. PMID:19465766 doi:10.1107/S0907444909010075
|
