This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


3ss2

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (13:06, 14 March 2024) (edit) (undo)
 
(3 intermediate revisions not shown.)
Line 1: Line 1:
 +
==Neutron structure of perdeuterated rubredoxin using 48 hours 3rd pass data==
==Neutron structure of perdeuterated rubredoxin using 48 hours 3rd pass data==
-
<StructureSection load='3ss2' size='340' side='right' caption='[[3ss2]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
+
<StructureSection load='3ss2' size='340' side='right'caption='[[3ss2]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3ss2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus_dsm_3638 Pyrococcus furiosus dsm 3638]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SS2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SS2 FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3ss2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus_DSM_3638 Pyrococcus furiosus DSM 3638]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SS2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SS2 FirstGlance]. <br>
-
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene><br>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Neutron Diffraction, [[Resolution|Resolution]] 1.75&#8491;</td></tr>
-
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3kyx|3kyx]], [[3ryg|3ryg]], [[3rz6|3rz6]], [[3rzr|3rzr]], [[3rzt|3rzt]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
-
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PF1282, rub ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 Pyrococcus furiosus DSM 3638])</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=3ss2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ss2 OCA], [https://pdbe.org/3ss2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ss2 RCSB], [https://www.ebi.ac.uk/pdbsum/3ss2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ss2 ProSAT]</span></td></tr>
-
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ss2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ss2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ss2 RCSB], [http://www.ebi.ac.uk/pdbsum/3ss2 PDBsum]</span></td></tr>
+
</table>
-
<table>
+
== Function ==
-
<div style="background-color:#fffaf0;">
+
[https://www.uniprot.org/uniprot/RUBR_PYRFU RUBR_PYRFU] 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.
-
== Publication Abstract from PubMed ==
+
-
Neutron crystallography is a powerful technique for experimental visualization of the positions of light atoms, including hydrogen and its isotope deuterium. In recent years, structural biologists have shown increasing interest in the technique as it uniquely complements X-ray crystallographic data by revealing the positions of D atoms in macromolecules. With this regained interest, access to macromolecular neutron crystallography beamlines is becoming a limiting step. In this report, it is shown that a rapid data-collection strategy can be a valuable alternative to longer data-collection times in appropriate cases. Comparison of perdeuterated rubredoxin structures refined against neutron data sets collected over hours and up to 5 d shows that rapid neutron data collection in just 14 h is sufficient to provide the positions of 269 D atoms without ambiguity.
+
-
 
+
-
Rapid visualization of hydrogen positions in protein neutron crystallographic structures.,Munshi P, Chung SL, Blakeley MP, Weiss KL, Myles DA, Meilleur F Acta Crystallogr D Biol Crystallogr. 2012 Jan;68(Pt 1):35-41. Epub 2011, Dec 9. PMID:22194331<ref>PMID:22194331</ref>
+
-
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
+
==See Also==
-
</div>
+
*[[Rubredoxin 3D structures|Rubredoxin 3D structures]]
-
== References ==
+
*[[Rubredoxin PDB structures|Rubredoxin PDB structures]]
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Pyrococcus furiosus dsm 3638]]
+
[[Category: Large Structures]]
-
[[Category: Blakeley, M P.]]
+
[[Category: Pyrococcus furiosus DSM 3638]]
-
[[Category: Chung, C L.]]
+
[[Category: Blakeley MP]]
-
[[Category: Meilleur, F.]]
+
[[Category: Chung C-L]]
-
[[Category: Munshi, P.]]
+
[[Category: Meilleur F]]
-
[[Category: Myles, D A.A.]]
+
[[Category: Munshi P]]
-
[[Category: Weiss, K L.]]
+
[[Category: Myles DAA]]
-
[[Category: Electron transport]]
+
[[Category: Weiss KL]]
-
[[Category: Iron]]
+
-
[[Category: Metal-binding]]
+
-
[[Category: Transport]]
+

Current revision

Neutron structure of perdeuterated rubredoxin using 48 hours 3rd pass data

PDB ID 3ss2

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3ss2"
Personal tools