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5rub

From Proteopedia

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[[Image:5rub.jpg|left|200px]]
 
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{{Structure
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==CRYSTALLOGRAPHIC REFINEMENT AND STRUCTURE OF RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE FROM RHODOSPIRILLUM RUBRUM AT 1.7 ANGSTROMS RESOLUTION==
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|PDB= 5rub |SIZE=350|CAPTION= <scene name='initialview01'>5rub</scene>, resolution 1.7&Aring;
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<StructureSection load='5rub' size='340' side='right'caption='[[5rub]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND=
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<table><tr><td colspan='2'>[[5rub]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodospirillum_rubrum Rhodospirillum rubrum]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2rub 2rub]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5RUB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5RUB FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribulose-bisphosphate_carboxylase Ribulose-bisphosphate carboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.39 4.1.1.39] </span>
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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]] 1.7&#8491;</td></tr>
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|GENE=
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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=5rub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5rub OCA], [https://pdbe.org/5rub PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5rub RCSB], [https://www.ebi.ac.uk/pdbsum/5rub PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5rub ProSAT]</span></td></tr>
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|DOMAIN=
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</table>
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|RELATEDENTRY=
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== Function ==
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5rub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5rub OCA], [http://www.ebi.ac.uk/pdbsum/5rub PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=5rub RCSB]</span>
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[https://www.uniprot.org/uniprot/RBL2_RHORU RBL2_RHORU] RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate. Both reactions occur simultaneously and in competition at the same active site.[HAMAP-Rule:MF_01339]
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}}
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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/ru/5rub_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=5rub ConSurf].
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<div style="clear:both"></div>
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'''CRYSTALLOGRAPHIC REFINEMENT AND STRUCTURE OF RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE FROM RHODOSPIRILLUM RUBRUM AT 1.7 ANGSTROMS RESOLUTION'''
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==See Also==
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*[[RuBisCO 3D structures|RuBisCO 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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The amino acid sequence of ribulose-1,5-bisphosphate carboxylase/oxygenase from Rhodospirillum rubrum has been fitted to the electron density maps. The resulting protein model has been refined to a nominal resolution of 1.7 A using the constrained-restrained least-squares refinement program of Sussman and the restrained least-squares refinement program of Hendrickson &amp; Konnert. The crystallographic refinement, based on 76,452 reflections with F greater than sigma (F) in the resolution range 5.5 to 1.7 A resulted in a crystallographic R-factor of 18.0%. The asymmetric unit contains one dimeric ribulose-1,5-biphosphate carboxylase molecule, consisting of 869 amino acid residues and 736 water molecules. The geometry of the refined model is close to ideal, with root-mean-square deviations of 0.018 A in bond lengths and 2.7 degrees in bond angles. Two loop regions, comprising residues 54 to 63 and 324 to 335, and the last ten amino acid residues at the C terminus are disordered in our crystals. The expected trimodal distribution is obtained for the side-chain chi 1-angles with a marked preference for staggered conformation. The hydrogen-bonding pattern in the N-terminal beta-sheet and the parallel sheet in the beta/alpha-barrel is described. A number of hydrogen bonds and salt bridges are involved in domain-domain and subunit-subunit interactions. The subunit-subunit interface in the dimer covers an area of 2800 A2. Considerable deviations from the local 2-fold symmetry are found at both the N terminus (residues 2 to 5) and the C terminus (residues 422 to 457). Furthermore, loop 8 in the beta/alpha-barrel domain has a different conformation in the two subunits. A number of amino acid side-chains have different conformations in the two subunits. Most of these residues are located at the surface of the protein. An analysis of the individual temperature factors indicates a high mobility of the C-terminal region and for some of the loops at the active site. The positions and B-factors for 736 solvent sites have been refined (average B: 45.9 A2). Most of the solvent molecules are bound as clusters to the protein. The active site of the enzyme, especially the environment of the activator Lys191 in the non-activated enzyme is described. Crystallographic refinement at 1.7 A resolution clearly revealed the presence of a cis-proline at the active site. This residue is part of the highly conserved region Lys166-Pro167-Lys168.
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[[Category: Large Structures]]
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==About this Structure==
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5RUB is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rhodospirillum_rubrum Rhodospirillum rubrum]. This structure supersedes the now removed PDB entry 2RUB. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5RUB OCA].
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==Reference==
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Crystallographic refinement and structure of ribulose-1,5-bisphosphate carboxylase from Rhodospirillum rubrum at 1.7 A resolution., Schneider G, Lindqvist Y, Lundqvist T, J Mol Biol. 1990 Feb 20;211(4):989-1008. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/2107319 2107319]
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[[Category: Rhodospirillum rubrum]]
[[Category: Rhodospirillum rubrum]]
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[[Category: Ribulose-bisphosphate carboxylase]]
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[[Category: Lindqvist Y]]
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[[Category: Single protein]]
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[[Category: Lundqvist T]]
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[[Category: Lindqvist, Y.]]
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[[Category: Schneider G]]
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[[Category: Lundqvist, T.]]
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[[Category: Schneider, G.]]
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[[Category: lyase(carbon-carbon)]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:42:14 2008''
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Current revision

CRYSTALLOGRAPHIC REFINEMENT AND STRUCTURE OF RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE FROM RHODOSPIRILLUM RUBRUM AT 1.7 ANGSTROMS RESOLUTION

PDB ID 5rub

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