1rdg
From Proteopedia
(New page: 200px<br /><applet load="1rdg" size="450" color="white" frame="true" align="right" spinBox="true" caption="1rdg, resolution 1.4Å" /> '''RUBREDOXIN FROM DESUL...) |
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| - | [[Image:1rdg.gif|left|200px]]<br /><applet load="1rdg" size=" | + | [[Image:1rdg.gif|left|200px]]<br /><applet load="1rdg" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1rdg, resolution 1.4Å" /> | caption="1rdg, resolution 1.4Å" /> | ||
'''RUBREDOXIN FROM DESULFOVIBRIO GIGAS. A MOLECULAR MODEL OF THE OXIDIZED FORM AT 1.4 ANGSTROMS RESOLUTION'''<br /> | '''RUBREDOXIN FROM DESULFOVIBRIO GIGAS. A MOLECULAR MODEL OF THE OXIDIZED FORM AT 1.4 ANGSTROMS RESOLUTION'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The crystal structure of rubredoxin from the sulfate-reducing bacterium | + | The crystal structure of rubredoxin from the sulfate-reducing bacterium Desulfovibrio gigas has been determined at 1.4 A resolution (1 A = 0.1 nm) by X-ray diffraction methods; starting with a model of the isostructural rubredoxin from Desulfovibrio vulgaris. Refinement of the molecular model has been carried out by restrained least-squares techniques and Fourier series calculations. The present model includes a formyl at the N-terminal end and 121 possible sites for solvent molecules with full or partial occupancy, which corresponds to the modeling of nearly all the solvent medium. The crystallographic R factor against the data with 10 A greater than d greater than 1.4 A with F greater than 2 sig(F), is 0.136; and R = 0.140 when all the data are considered. The estimated average root-mean-square (r.m.s.) error on the positional parameters is about 0.12 A. The overall structural features of this molecule are close to those of the two highly refined rubredoxins from Clostridium pasteurianum and D. vulgaris. Superposition of these two molecules on the rubredoxin from D. gigas shows in both cases an overall r.m.s. deviation of 0.5 A for the atoms in the main-chain and of 0.4 A for the atoms in the side-chains that make up the hydrophobic core. The iron atom is co-ordinated to four cysteine sulfur atoms forming an almost regular tetrahedron, with Fe-SG distances ranging from 2.27 A to 2.31 A and angles varying from 103 degrees to 115 degrees. The intramolecular hydrogen-bonding pattern is quite comparable to those found in other proteins refined at high resolution. All the polar groups are involved in hydrogen bonds: intramolecular, intermolecular or with solvent molecules. The main structural differences from the other rubredoxins are in the nature and the distribution of some of the charged residues over the molecular surface. The possible influence of several structural factors on the intramolecular and intermolecular electron transfer properties such as the NH...SG bonds, the solvent exposure of the redox center, and the aromatic core is discussed. The conservation, during evolution, of a ring of acidic residues in the proximity of the FeSG4 center suggests that this ring may be implicated in the recognition processes between rubredoxins and their functional partners. |
==About this Structure== | ==About this Structure== | ||
| - | 1RDG is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_gigas Desulfovibrio gigas] with FE and FOR as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http:// | + | 1RDG is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_gigas Desulfovibrio gigas] with <scene name='pdbligand=FE:'>FE</scene> and <scene name='pdbligand=FOR:'>FOR</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RDG OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Frey, M.]] | [[Category: Frey, M.]] | ||
[[Category: Payan, F.]] | [[Category: Payan, F.]] | ||
| - | [[Category: Sieker, L | + | [[Category: Sieker, L C.]] |
[[Category: FE]] | [[Category: FE]] | ||
[[Category: FOR]] | [[Category: FOR]] | ||
[[Category: electron transfer(iron-sulfur protein)]] | [[Category: electron transfer(iron-sulfur protein)]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:49:42 2008'' |
Revision as of 12:49, 21 February 2008
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RUBREDOXIN FROM DESULFOVIBRIO GIGAS. A MOLECULAR MODEL OF THE OXIDIZED FORM AT 1.4 ANGSTROMS RESOLUTION
Overview
The crystal structure of rubredoxin from the sulfate-reducing bacterium Desulfovibrio gigas has been determined at 1.4 A resolution (1 A = 0.1 nm) by X-ray diffraction methods; starting with a model of the isostructural rubredoxin from Desulfovibrio vulgaris. Refinement of the molecular model has been carried out by restrained least-squares techniques and Fourier series calculations. The present model includes a formyl at the N-terminal end and 121 possible sites for solvent molecules with full or partial occupancy, which corresponds to the modeling of nearly all the solvent medium. The crystallographic R factor against the data with 10 A greater than d greater than 1.4 A with F greater than 2 sig(F), is 0.136; and R = 0.140 when all the data are considered. The estimated average root-mean-square (r.m.s.) error on the positional parameters is about 0.12 A. The overall structural features of this molecule are close to those of the two highly refined rubredoxins from Clostridium pasteurianum and D. vulgaris. Superposition of these two molecules on the rubredoxin from D. gigas shows in both cases an overall r.m.s. deviation of 0.5 A for the atoms in the main-chain and of 0.4 A for the atoms in the side-chains that make up the hydrophobic core. The iron atom is co-ordinated to four cysteine sulfur atoms forming an almost regular tetrahedron, with Fe-SG distances ranging from 2.27 A to 2.31 A and angles varying from 103 degrees to 115 degrees. The intramolecular hydrogen-bonding pattern is quite comparable to those found in other proteins refined at high resolution. All the polar groups are involved in hydrogen bonds: intramolecular, intermolecular or with solvent molecules. The main structural differences from the other rubredoxins are in the nature and the distribution of some of the charged residues over the molecular surface. The possible influence of several structural factors on the intramolecular and intermolecular electron transfer properties such as the NH...SG bonds, the solvent exposure of the redox center, and the aromatic core is discussed. The conservation, during evolution, of a ring of acidic residues in the proximity of the FeSG4 center suggests that this ring may be implicated in the recognition processes between rubredoxins and their functional partners.
About this Structure
1RDG is a Single protein structure of sequence from Desulfovibrio gigas with and as ligands. Full crystallographic information is available from OCA.
Reference
Rubredoxin from Desulfovibrio gigas. A molecular model of the oxidized form at 1.4 A resolution., Frey M, Sieker L, Payan F, Haser R, Bruschi M, Pepe G, LeGall J, J Mol Biol. 1987 Oct 5;197(3):525-41. PMID:3441010
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