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3kyx

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Revision as of 11:03, 4 August 2016

Joint Xray/neutron crystal structure determination of fully perdeuterated rubredoxin at 295K

Structural highlights

3kyx is a 1 chain structure with sequence from Atcc 43587. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	3kyu, 3kyv, 3kyw, 3kyy
Gene:	rub, PF1282 (ATCC 43587)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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

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 locations of H atoms in biological structures can be difficult to determine using X-ray diffraction methods. Neutron diffraction offers a relatively greater scattering magnitude from H and D atoms. Here, 1.65 A resolution neutron diffraction studies of fully perdeuterated and selectively CH(3)-protonated perdeuterated crystals of Pyrococcus furiosus rubredoxin (D-rubredoxin and HD-rubredoxin, respectively) at room temperature (RT) are described, as well as 1.1 A resolution X-ray diffraction studies of the same protein at both RT and 100 K. The two techniques are quantitatively compared in terms of their power to directly provide atomic positions for D atoms and analyze the role played by atomic thermal motion by computing the sigma level at the D-atom coordinate in simulated-annealing composite D-OMIT maps. It is shown that 1.65 A resolution RT neutron data for perdeuterated rubredoxin are approximately 8 times more likely overall to provide high-confidence positions for D atoms than 1.1 A resolution X-ray data at 100 K or RT. At or above the 1.0sigma level, the joint X-ray/neutron (XN) structures define 342/378 (90%) and 291/365 (80%) of the D-atom positions for D-rubredoxin and HD-rubredoxin, respectively. The X-ray-only 1.1 A resolution 100 K structures determine only 19/388 (5%) and 8/388 (2%) of the D-atom positions above the 1.0sigma level for D-rubredoxin and HD-rubredoxin, respectively. Furthermore, the improved model obtained from joint XN refinement yielded improved electron-density maps, permitting the location of more D atoms than electron-density maps from models refined against X-ray data only.

Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallography.,Gardberg AS, Del Castillo AR, Weiss KL, Meilleur F, Blakeley MP, Myles DA Acta Crystallogr D Biol Crystallogr. 2010 May;66(Pt 5):558-67. Epub 2010, Apr 21. PMID:20445231^[1]

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

References

↑ Gardberg AS, Del Castillo AR, Weiss KL, Meilleur F, Blakeley MP, Myles DA. Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallography. Acta Crystallogr D Biol Crystallogr. 2010 May;66(Pt 5):558-67. Epub 2010, Apr 21. PMID:20445231 doi:10.1107/S0907444910005494

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/3kyx"

@@ Line 1: / Line 1: @@
 ==Joint Xray/neutron crystal structure determination of fully perdeuterated rubredoxin at 295K==
 <StructureSection load='3kyx' size='340' side='right' caption='[[3kyx]], [[Resolution|resolution]] 1.68&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3kyx]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KYX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KYX FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3kyx]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43587 Atcc 43587]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KYX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KYX FirstGlance]. <br>
 </td></tr><tr id='ligand'><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></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3kyu|3kyu]], [[3kyv|3kyv]], [[3kyw|3kyw]], [[3kyy|3kyy]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rub, PF1282 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 Pyrococcus furiosus])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rub, PF1282 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587])</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=3kyx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kyx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kyx RCSB], [http://www.ebi.ac.uk/pdbsum/3kyx 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=3kyx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kyx OCA], [http://pdbe.org/3kyx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kyx RCSB], [http://www.ebi.ac.uk/pdbsum/3kyx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3kyx ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 18: / Line 19: @@
     <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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=3kyx ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 28: / Line 29: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3kyx" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Pyrococcus furiosus]]
+[[Category: Atcc 43587]]
 [[Category: Gardberg, A S]]
 [[Category: Meilleur, F]]

3kyx

From Proteopedia

Revision as of 11:03, 4 August 2016

Joint Xray/neutron crystal structure determination of fully perdeuterated rubredoxin at 295K

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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