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2rdv

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[[Image:2rdv.gif|left|200px]]<br />
 
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<applet load="2rdv" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2rdv, resolution 1.9&Aring;" />
 
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'''RUBREDOXIN FROM DESULFOVIBRIO VULGARIS MIYAZAKI F, MONOCLINIC CRYSTAL FORM'''<br />
 
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==Overview==
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==RUBREDOXIN FROM DESULFOVIBRIO VULGARIS MIYAZAKI F, MONOCLINIC CRYSTAL FORM==
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The structures of two crystal forms (form I, P3221, a = b = 43.7, c = 50.7, A; form II, P21, a = 27.3, b = 44.9, c = 51.2 A and beta = 90. 6 degrees ), of the rubredoxin from Desulfovibrio vulgaris Miyazaki F have been solved, by the molecular-replacement method. Form I has been refined at a, resolution of 2.0 A to an R value of 20.8% and includes 32 water, molecules. Form II includes 86 water molecules and has been refined at 1.9, A resolution to an R value of 17.5%. In form II, there are three molecules, in the asymmetric unit with the molecules related by a, non-crystallographic 32 symmetry axis. In both crystal forms, it was found, that only a few residues effectively participate in the formation of, intermolecular contacts along both the crystallographic (form I) and the, non-crystallographic (form II) 32 axes. The crystal structure of the form, II crystal is compared with those of other rubredoxin molecules from, anaerobic bacteria. From this comparison, a similarity in the core region, which is composed of aromatic residues and includes the active centre, has, been revealed.
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<StructureSection load='2rdv' size='340' side='right'caption='[[2rdv]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2rdv]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_str._'Miyazaki_F' Desulfovibrio vulgaris str. 'Miyazaki F']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RDV FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2rdv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdv OCA], [https://pdbe.org/2rdv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rdv RCSB], [https://www.ebi.ac.uk/pdbsum/2rdv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rdv ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RUBR_DESVM RUBR_DESVM] 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. Electron acceptor for cytoplasmic lactate dehydrogenase.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rd/2rdv_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2rdv ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The structures of two crystal forms (form I, P3221, a = b = 43.7, c = 50.7 A; form II, P21, a = 27.3, b = 44.9, c = 51.2 A and beta = 90. 6 degrees ) of the rubredoxin from Desulfovibrio vulgaris Miyazaki F have been solved by the molecular-replacement method. Form I has been refined at a resolution of 2.0 A to an R value of 20.8% and includes 32 water molecules. Form II includes 86 water molecules and has been refined at 1.9 A resolution to an R value of 17.5%. In form II, there are three molecules in the asymmetric unit with the molecules related by a non-crystallographic 32 symmetry axis. In both crystal forms, it was found that only a few residues effectively participate in the formation of intermolecular contacts along both the crystallographic (form I) and the non-crystallographic (form II) 32 axes. The crystal structure of the form II crystal is compared with those of other rubredoxin molecules from anaerobic bacteria. From this comparison, a similarity in the core region, which is composed of aromatic residues and includes the active centre, has been revealed.
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==About this Structure==
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Structure determination of rubredoxin from Desulfovibrio vulgaris Miyazaki F in two crystal forms.,Misaki S, Morimoto Y, Ogata M, Yagi T, Higuchi Y, Yasuoka N Acta Crystallogr D Biol Crystallogr. 1999 Feb;55(Pt 2):408-13. PMID:10089348<ref>PMID:10089348</ref>
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2RDV is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris] with FE as [http://en.wikipedia.org/wiki/ligand ligand]. Structure known Active Sites: FEA, FEB and FEC. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2RDV OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Structure determination of rubredoxin from Desulfovibrio vulgaris Miyazaki F in two crystal forms., Misaki S, Morimoto Y, Ogata M, Yagi T, Higuchi Y, Yasuoka N, Acta Crystallogr D Biol Crystallogr. 1999 Feb;55(Pt 2):408-13. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10089348 10089348]
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</div>
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[[Category: Desulfovibrio vulgaris]]
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<div class="pdbe-citations 2rdv" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: Higuchi, Y.]]
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[[Category: Yasuoka, N.]]
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[[Category: FE]]
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[[Category: compnd]]
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[[Category: electron transfer protein]]
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[[Category: metalloprotein]]
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[[Category: rubredoxin]]
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[[Category: sulfate-reducing bacterium]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 5 18:37:25 2007''
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==See Also==
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*[[Rubredoxin 3D structures|Rubredoxin 3D structures]]
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*[[Rubredoxin PDB structures|Rubredoxin PDB structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Desulfovibrio vulgaris str. 'Miyazaki F']]
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[[Category: Large Structures]]
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[[Category: Higuchi Y]]
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[[Category: Yasuoka N]]

Current revision

RUBREDOXIN FROM DESULFOVIBRIO VULGARIS MIYAZAKI F, MONOCLINIC CRYSTAL FORM

PDB ID 2rdv

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