1rdv

From Proteopedia

(Difference between revisions)

Revision as of 07:39, 28 February 2018

RUBREDOXIN FROM DESULFOVIBRIO VULGARIS MIYAZAKI F, TRIGONAL CRYSTAL FORM

Structural highlights

1rdv is a 1 chain structure with sequence from Desulfovibrio vulgaris str. 'miyazaki f'. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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.

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 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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Misaki S, Morimoto Y, Ogata M, Yagi T, Higuchi Y, Yasuoka N. Structure determination of rubredoxin from Desulfovibrio vulgaris Miyazaki F in two crystal forms. Acta Crystallogr D Biol Crystallogr. 1999 Feb;55(Pt 2):408-13. PMID:10089348

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1rdv"

@@ Line 1: / Line 1: @@
 ==RUBREDOXIN FROM DESULFOVIBRIO VULGARIS MIYAZAKI F, TRIGONAL CRYSTAL FORM==
 <StructureSection load='1rdv' size='340' side='right' caption='[[1rdv]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1rdv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desvm Desvm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RDV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RDV FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1rdv]] is a 1 chain structure with sequence from [http://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=1RDV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RDV FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></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=1rdv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rdv OCA], [http://pdbe.org/1rdv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rdv RCSB], [http://www.ebi.ac.uk/pdbsum/1rdv PDBsum]</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=1rdv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rdv OCA], [http://pdbe.org/1rdv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rdv RCSB], [http://www.ebi.ac.uk/pdbsum/1rdv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1rdv ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 12: / Line 13: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rd/1rdv_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rd/1rdv_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 31: / Line 32: @@
 __TOC__
 </StructureSection>
-[[Category: Desvm]]
+[[Category: Desulfovibrio vulgaris str. 'miyazaki f']]
 [[Category: Higuchi, Y]]
 [[Category: Yasuoka, N]]

1rdv

From Proteopedia

Revision as of 07:39, 28 February 2018

RUBREDOXIN FROM DESULFOVIBRIO VULGARIS MIYAZAKI F, TRIGONAL CRYSTAL FORM

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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