5rub
From Proteopedia
(New page: 200px<br /><applet load="5rub" size="450" color="white" frame="true" align="right" spinBox="true" caption="5rub, resolution 1.7Å" /> '''CRYSTALLOGRAPHIC REFI...) |
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| - | [[Image:5rub.jpg|left|200px]]<br /><applet load="5rub" size=" | + | [[Image:5rub.jpg|left|200px]]<br /><applet load="5rub" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="5rub, resolution 1.7Å" /> | caption="5rub, resolution 1.7Å" /> | ||
'''CRYSTALLOGRAPHIC REFINEMENT AND STRUCTURE OF RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE FROM RHODOSPIRILLUM RUBRUM AT 1.7 ANGSTROMS RESOLUTION'''<br /> | '''CRYSTALLOGRAPHIC REFINEMENT AND STRUCTURE OF RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE FROM RHODOSPIRILLUM RUBRUM AT 1.7 ANGSTROMS RESOLUTION'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The amino acid sequence of ribulose-1,5-bisphosphate carboxylase/oxygenase | + | 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 & 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. |
==About this Structure== | ==About this Structure== | ||
| - | 5RUB is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rhodospirillum_rubrum Rhodospirillum rubrum]. This structure | + | 5RUB is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rhodospirillum_rubrum Rhodospirillum rubrum]. This structure supersedes the now removed PDB entry 2RUB. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5RUB OCA]. |
==Reference== | ==Reference== | ||
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[[Category: lyase(carbon-carbon)]] | [[Category: lyase(carbon-carbon)]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:15:50 2008'' |
Revision as of 17:15, 21 February 2008
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CRYSTALLOGRAPHIC REFINEMENT AND STRUCTURE OF RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE FROM RHODOSPIRILLUM RUBRUM AT 1.7 ANGSTROMS RESOLUTION
Overview
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 & 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.
About this Structure
5RUB is a Single protein structure of sequence from Rhodospirillum rubrum. This structure supersedes the now removed PDB entry 2RUB. Active as Ribulose-bisphosphate carboxylase, with EC number 4.1.1.39 Full crystallographic information is available from OCA.
Reference
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:2107319
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