1yk5

From Proteopedia

(Difference between revisions)

Revision as of 08:47, 20 January 2021

Pyrococcus abyssi rubredoxin

Structural highlights

1yk5 is a 4 chain structure with sequence from "pyrococcus_abyssi"_erauso_et_al._1993 "pyrococcus abyssi" erauso et al. 1993. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	1yk4
Gene:	rub ("Pyrococcus abyssi" Erauso et al. 1993)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RUBR_PYRAB] 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 (By similarity).

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 Pyrococcus abyssi rubredoxin mutant W4L/R5S was solved by direct methods. The model of the air-oxidized protein was refined by partially restrained full-matrix least-squares refinement against intensity data to 0.69 A resolution. This first ultrahigh-resolution structure of a rubredoxin provides very detailed and precise information about the Fe(SCys)(4) centre and its environment, the peptide-backbone stereochemistry, H atoms and hydrogen bonds, static and dynamic disorder, the solvent structure and the electron-density distribution. P. abyssi rubredoxin W4L/R5S is the first of a series of mutants studied by atomic and ultrahigh-resolution X-ray crystallography which are expected to contribute to the understanding of structure-function relationships in iron-sulfur proteins.

Ultrahigh-resolution study on Pyrococcus abyssi rubredoxin. I. 0.69 A X-ray structure of mutant W4L/R5S.,Bonisch H, Schmidt CL, Bianco P, Ladenstein R Acta Crystallogr D Biol Crystallogr. 2005 Jul;61(Pt 7):990-1004. Epub 2005, Jun 24. PMID:15983423^[1]

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

References

↑ Bonisch H, Schmidt CL, Bianco P, Ladenstein R. Ultrahigh-resolution study on Pyrococcus abyssi rubredoxin. I. 0.69 A X-ray structure of mutant W4L/R5S. Acta Crystallogr D Biol Crystallogr. 2005 Jul;61(Pt 7):990-1004. Epub 2005, Jun 24. PMID:15983423 doi:10.1107/S090744490501293X

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/1yk5"

@@ Line 1: / Line 1: @@
 ==Pyrococcus abyssi rubredoxin==
-<StructureSection load='1yk5' size='340' side='right' caption='[[1yk5]], [[Resolution|resolution]] 1.79&Aring;' scene=''>
+<StructureSection load='1yk5' size='340' side='right'caption='[[1yk5]], [[Resolution|resolution]] 1.79&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1yk5]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"pyrococcus_abyssi"_erauso_et_al._1993 "pyrococcus abyssi" erauso et al. 1993]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YK5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YK5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1yk5]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"pyrococcus_abyssi"_erauso_et_al._1993 "pyrococcus abyssi" erauso et al. 1993]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YK5 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1YK5 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>
+</td></tr><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>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1yk4|1yk4]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1yk4|1yk4]]</div></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rub ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29292 "Pyrococcus abyssi" Erauso et al. 1993])</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=1yk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yk5 OCA], [http://pdbe.org/1yk5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yk5 RCSB], [http://www.ebi.ac.uk/pdbsum/1yk5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yk5 ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1yk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yk5 OCA], [http://pdbe.org/1yk5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yk5 RCSB], [http://www.ebi.ac.uk/pdbsum/1yk5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yk5 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 35: / Line 35: @@
 </StructureSection>
 [[Category: Pyrococcus abyssi erauso et al. 1993]]
+[[Category: Large Structures]]
 [[Category: Bianco, P]]
 [[Category: Bonisch, H]]

1yk5

From Proteopedia

Revision as of 08:47, 20 January 2021

Pyrococcus abyssi rubredoxin

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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