2chr

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[[Image:2chr.gif|left|200px]]
 
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==A RE-EVALUATION OF THE CRYSTAL STRUCTURE OF CHLOROMUCONATE CYCLOISOMERASE==
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The line below this paragraph, containing "STRUCTURE_2chr", creates the "Structure Box" on the page.
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<StructureSection load='2chr' size='340' side='right'caption='[[2chr]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<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>
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or leave the SCENE parameter empty for the default display.
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</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>
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<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>
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{{STRUCTURE_2chr| PDB=2chr | SCENE= }}
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<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>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/TFDD1_CUPPJ TFDD1_CUPPJ]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ch/2chr_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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].
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<div style="clear:both"></div>
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'''A RE-EVALUATION OF THE CRYSTAL STRUCTURE OF CHLOROMUCONATE CYCLOISOMERASE'''
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==See Also==
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*[[Muconate cycloisomerase|Muconate cycloisomerase]]
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__TOC__
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==Overview==
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</StructureSection>
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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).
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==About this Structure==
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2CHR is a [[Single protein]] structure of sequence from [http://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].
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==Reference==
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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://www.ncbi.nlm.nih.gov/pubmed/15299651 15299651]
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[[Category: Chloromuconate cycloisomerase]]
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[[Category: Cupriavidus necator]]
[[Category: Cupriavidus necator]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Jones, T A.]]
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[[Category: Jones TA]]
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[[Category: Kleywegt, G J.]]
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[[Category: Kleywegt GJ]]
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[[Category: Isomerase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 22:10:24 2008''
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Current revision

A RE-EVALUATION OF THE CRYSTAL STRUCTURE OF CHLOROMUCONATE CYCLOISOMERASE

PDB ID 2chr

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