8rxn

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(New page: 200px<br /><applet load="8rxn" size="450" color="white" frame="true" align="right" spinBox="true" caption="8rxn, resolution 1.0&Aring;" /> '''REFINEMENT OF RUBREDO...)
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[[Image:8rxn.jpg|left|200px]]<br /><applet load="8rxn" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="8rxn, resolution 1.0&Aring;" />
 
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'''REFINEMENT OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.0 ANGSTROMS WITH AND WITHOUT RESTRAINTS'''<br />
 
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==Overview==
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==REFINEMENT OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.0 ANGSTROMS WITH AND WITHOUT RESTRAINTS==
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X-ray data have been recorded from crystals of rubredoxin derived from the, bacterium Desulfovibrio vulgaris to a resolution of 1.0 A using in part, synchrotron radiation and in part X-rays from a sealed-tube Mo K alpha, source. In both cases an imaging-plate scanner was used as detector. The, space group of the crystals is P2(1) with cell dimensions a = 19.97, b =, 41.45, c = 24.41 A and beta = 108.3 degrees. The overall merging R(I), factor between symmetry-related reflections was 5.8%. The model was, refined by least-squares minimization initially with stereochemical, restraints to an R factor of 16.4%. Only atomic positional parameters and, isotropic temperature factors for non-H atoms were used in the refinement., There were 18,532 independent X-ray observations for a total of 1916, atomic parameters. A round of unrestrained refinement gave an R factor of, 16.0%, acceptable geometry for more than 90% of the protein atoms, but, emphasized the disorder inherent in eight of the residues. A final round, of restrained refinement gave an R factor of 14.7%. Three of the 389, protein atoms in the molecule, in the side chain of Lys2, have been, assigned zero occupancy in the model. A total of eight atoms in three side, chains have been assigned two conformations, giving 393 protein atomic, sites in the model. In addition there is one Fe atom, a sulfate ion and, 102 water sites. 339 H atoms were included at their calculated positions, which were not refined. There is clear evidence for anisotropic thermal, motion. This has not been incorporated in the present model.
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<StructureSection load='8rxn' size='340' side='right'caption='[[8rxn]], [[Resolution|resolution]] 1.00&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[8rxn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8RXN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8RXN 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&#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>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=8rxn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8rxn OCA], [https://pdbe.org/8rxn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8rxn RCSB], [https://www.ebi.ac.uk/pdbsum/8rxn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8rxn ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RUBR_DESVH RUBR_DESVH] 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/rx/8rxn_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=8rxn ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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8RXN 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 and SO4 as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=8RXN OCA].
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*[[Rubredoxin 3D structures|Rubredoxin 3D structures]]
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*[[Rubredoxin PDB structures|Rubredoxin PDB structures]]
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==Reference==
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__TOC__
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Refinement of rubredoxin from Desulfovibrio vulgaris at 1.0 A with and without restraints., Dauter Z, Sieker LC, Wilson KS, Acta Crystallogr B. 1992 Feb 1;48 ( Pt 1):42-59. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=1616692 1616692]
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</StructureSection>
[[Category: Desulfovibrio vulgaris]]
[[Category: Desulfovibrio vulgaris]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Dauter, Z.]]
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[[Category: Dauter Z]]
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[[Category: Sieker, L.]]
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[[Category: Sieker L]]
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[[Category: Wilson, K.]]
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[[Category: Wilson K]]
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[[Category: FE]]
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[[Category: SO4]]
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[[Category: electron transport(iron)]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:01:08 2007''
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Current revision

REFINEMENT OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.0 ANGSTROMS WITH AND WITHOUT RESTRAINTS

PDB ID 8rxn

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