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New page: left|200px<br /><applet load="2chr" size="450" color="white" frame="true" align="right" spinBox="true" caption="2chr, resolution 3.0Å" /> '''A RE-EVALUATION OF TH...
 
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[[Image:2chr.gif|left|200px]]<br /><applet load="2chr" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2chr, resolution 3.0&Aring;" />
'''A RE-EVALUATION OF THE CRYSTAL STRUCTURE OF CHLOROMUCONATE CYCLOISOMERASE'''<br />


==Overview==
==A RE-EVALUATION OF THE CRYSTAL STRUCTURE OF CHLOROMUCONATE CYCLOISOMERASE==
It is shown here that the reported 3 A crystal structure of chloromuconate, cycloisomerase from Alcaligenes eutrophus [Hoier, Schlomann, Hammer, Glusker, Carrell, Goldman, Stezowski &amp; Heinemann (1994). Acta Cryst. D50, 75-84] was refined in the incorrect space group I4. In addition, a stretch, of about 25 residues near the N-terminus is out-of-register with the, density in the original structure. From the coordinates and structure, factors deposited in the Protein Data Bank (PDB), it was possible to, determine the correct space group to be I422. The structure was then, re-refined, using the original data reduced to I422, to a crystallographic, free R factor of 0.264 at 3 A resolution (conventional R factor 0.189)., With conservative refinement and rebuilding methods, the errors in the, chain tracing could be identified and remedied. Since the two molecules, per asymmetric unit in the original structure are actually related by, crystallographic symmetry, the observed differences between them are, artefacts. In particular, the differences between, and peculiarities of, the metal-binding sites are unreal. This case shows the dangers of, crystallographic refinement in cases with unfavourable data-to-parameter, ratios, and the importance of reducing the number of parameters in such, cases to prevent gross errors (for instance, by using NCS constraints). It, also demonstrates how the evaluation and monitoring of model quality, during the entire refinement and rebuilding process can be used to detect, and remedy serious errors. Finally, it presents a strong case in favour of, depositing not only model coordinates, but also experimental data, (preferably, both merged and unmerged data).
<StructureSection load='2chr' size='340' side='right'caption='[[2chr]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2chr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cupriavidus_necator Cupriavidus necator]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CHR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CHR 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]] 3&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=2chr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2chr OCA], [https://pdbe.org/2chr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2chr RCSB], [https://www.ebi.ac.uk/pdbsum/2chr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2chr ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/TFDD1_CUPPJ TFDD1_CUPPJ]
== 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/ch/2chr_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=2chr ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
2CHR is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Cupriavidus_necator Cupriavidus necator] with MN and CL as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Chloromuconate_cycloisomerase Chloromuconate cycloisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.5.1.7 5.5.1.7] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2CHR OCA].
*[[Muconate cycloisomerase|Muconate cycloisomerase]]
 
__TOC__
==Reference==
</StructureSection>
A re-evaluation of the crystal structure of chloromuconate cycloisomerase., Kleywegt GJ, Hoier H, Jones TA, Acta Crystallogr D Biol Crystallogr. 1996 Jul 1;52(Pt 4):858-63. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15299651 15299651]
[[Category: Chloromuconate cycloisomerase]]
[[Category: Cupriavidus necator]]
[[Category: Cupriavidus necator]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Jones, T.A.]]
[[Category: Jones TA]]
[[Category: Kleywegt, G.J.]]
[[Category: Kleywegt GJ]]
[[Category: CL]]
[[Category: MN]]
[[Category: isomerase]]
 
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