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.


1cad

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="1cad" size="450" color="white" frame="true" align="right" spinBox="true" caption="1cad, resolution 1.8&Aring;" /> '''X-RAY CRYSTAL STRUCTU...)
Current revision (06:41, 7 February 2024) (edit) (undo)
 
(16 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1cad.gif|left|200px]]<br /><applet load="1cad" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1cad, resolution 1.8&Aring;" />
 
-
'''X-RAY CRYSTAL STRUCTURES OF THE OXIDIZED AND REDUCED FORMS OF THE RUBREDOXIN FROM THE MARINE HYPERTHERMOPHILIC ARCHAEBACTERIUM PYROCOCCUS FURIOSUS'''<br />
 
-
==Overview==
+
==X-RAY CRYSTAL STRUCTURES OF THE OXIDIZED AND REDUCED FORMS OF THE RUBREDOXIN FROM THE MARINE HYPERTHERMOPHILIC ARCHAEBACTERIUM PYROCOCCUS FURIOSUS==
-
The structures of the oxidized and reduced forms of the rubredoxin from, the archaebacterium, Pyrococcus furiosus, an organism that grows optimally, at 100 degrees C, have been determined by X-ray crystallography to a, resolution of 1.8 A. Crystals of this rubredoxin grow in space group, P2(1)2(1)2(1) with room temperature cell dimensions a = 34.6 A, b = 35.5, A, and c = 44.4 A. Initial phases were determined by the method of, molecular replacement using the oxidized form of the rubredoxin from the, mesophilic eubacterium, Clostridium pasteurianum, as a starting model. The, oxidized and reduced models of P. furiosus rubredoxin each contain 414, nonhydrogen protein atoms comprising 53 residues. The model of the, oxidized form contains 61 solvent H2O oxygen atoms and has been refined, with X-PLOR and TNT to a final R = 0.178 with root mean square (rms), deviations from ideality in bond distances and bond angles of 0.014 A and, 2.06 degrees, respectively. The model of the reduced form contains 37, solvent H2O oxygen atoms and has been refined to R = 0.193 with rms, deviations from ideality in bond lengths of 0.012 A and in bond angles of, 1.95 degrees. The overall structure of P. furiosus rubredoxin is similar, to the structures of mesophilic rubredoxins, with the exception of a more, extensive hydrogen-bonding network in the beta-sheet region and multiple, electrostatic interactions (salt bridge, hydrogen bonds) of the Glu 14, side chain with groups on three other residues (the amino-terminal, nitrogen of Ala 1; the indole nitrogen of Trp 3; and the amide nitrogen, group of Phe 29). The influence of these and other features upon the, thermostability of the P. furiosus protein is discussed.
+
<StructureSection load='1cad' size='340' side='right'caption='[[1cad]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1cad]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CAD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CAD FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1cad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cad OCA], [https://pdbe.org/1cad PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cad RCSB], [https://www.ebi.ac.uk/pdbsum/1cad PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cad ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[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.
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ca/1cad_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</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=1cad ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
1CAD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus] with FE as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1CAD OCA].
+
*[[Rubredoxin 3D structures|Rubredoxin 3D structures]]
-
 
+
*[[Rubredoxin PDB structures|Rubredoxin PDB structures]]
-
==Reference==
+
__TOC__
-
X-ray crystal structures of the oxidized and reduced forms of the rubredoxin from the marine hyperthermophilic archaebacterium Pyrococcus furiosus., Day MW, Hsu BT, Joshua-Tor L, Park JB, Zhou ZH, Adams MW, Rees DC, Protein Sci. 1992 Nov;1(11):1494-507. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=1303768 1303768]
+
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Pyrococcus furiosus]]
[[Category: Pyrococcus furiosus]]
-
[[Category: Single protein]]
+
[[Category: Adams MWW]]
-
[[Category: Adams, M.W.W.]]
+
[[Category: Day MW]]
-
[[Category: Day, M.W.]]
+
[[Category: Hsu BT]]
-
[[Category: Hsu, B.T.]]
+
[[Category: Joshua-Tor L]]
-
[[Category: Joshua-Tor, L.]]
+
[[Category: Park JB]]
-
[[Category: Park, J.B.]]
+
[[Category: Rees DC]]
-
[[Category: Rees, D.C.]]
+
[[Category: Zhou ZH]]
-
[[Category: Zhou, Z.H.]]
+
-
[[Category: FE]]
+
-
[[Category: electron transport]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 12:18:14 2007''
+

Current revision

X-RAY CRYSTAL STRUCTURES OF THE OXIDIZED AND REDUCED FORMS OF THE RUBREDOXIN FROM THE MARINE HYPERTHERMOPHILIC ARCHAEBACTERIUM PYROCOCCUS FURIOSUS

PDB ID 1cad

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/1cad"
Personal tools