1xso: Difference between revisions

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THREE-DIMENSIONAL STRUCTURE OF XENOPUS LAEVIS CU,ZN SUPEROXIDE DISMUTASE B DETERMINED BY X-RAY CRYSTALLOGRAPHY AT 1.5 ANGSTROMS RESOLUTION

OverviewOverview

Xenopus laevis Cu,Zn superoxide dismutase (recombinant isoenzyme b) has been crystallized and the structure determined at 1.49 A resolution. The crystals belong to space group P2(1)2(1)2(1), with cell constants a = 73.33, b = 68.86, c = 59.73 A, and contain one dimeric molecule of M(r) 32 000 per asymmetric unit. The structure was solved by molecular-replacement techniques using the semisynthetic Cu,Co bovine enzyme as search model, and refined by molecular dynamics with a crystallographic pseudo-energy term. During the final steps, positional and anisotropic thermal parameters of the atoms were refined. The R factor for the 49 209 unique reflections in the 10.0-1.49 A resolution range is 0.104, for a model comprising 2023 protein atoms, two Cu(2+), two Zn(2+), and 353 water molecules. The overall temperature factor for the model, including solvent, is 20.3 A(2), while the calculated r.m.s. coordinate error for the refined model is 0.036 A. As suggested by the primary structure homology to any other known intracellular eukaryotic superoxide dismutase (> 50%), the typical structural scaffolding of flattened antiparallel eight-stranded (beta-barrel is well conserved in X. laevis Cu,Zn superoxide dismutase b, together with the coordination geometry of the metal centers in the active site. The higher thermal stability of the bb X. laevis superoxide dismutase homodimer, with respect to dimers involving the a-type isoenzyme subunit(s), can be related, on the basis of the high-resolution structure, to side-chain and solvent interactions centered on residue Tyr149, in both b-type subunits. The analysis of the overall solvent structure reveals a number of equivalent water molecule sites in the two subunits, and in homologous superoxide dismutase models. Their locations are discussed in detail and classified on the basis of their structural role.

About this StructureAbout this Structure

1XSO is a Single protein structure of sequence from Xenopus laevis with and as ligands. Active as Superoxide dismutase, with EC number 1.15.1.1 Full crystallographic information is available from OCA.

ReferenceReference

Three-dimensional structure of Xenopus laevis Cu,Zn superoxide dismutase b determined by X-ray crystallography at 1.5 A resolution., Djinovic Carugo K, Battistoni A, Carri MT, Polticelli F, Desideri A, Rotilio G, Coda A, Wilson KS, Bolognesi M, Acta Crystallogr D Biol Crystallogr. 1996 Jan 1;52(Pt 1):176-88. PMID:15299740

Page seeded by OCA on Thu Feb 21 15:58:20 2008

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OCA

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-[[Image:1xso.jpg|left|200px]]<br /><applet load="1xso" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1xso.jpg|left|200px]]<br /><applet load="1xso" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1xso, resolution 1.49&Aring;" />
 '''THREE-DIMENSIONAL STRUCTURE OF XENOPUS LAEVIS CU,ZN SUPEROXIDE DISMUTASE B DETERMINED BY X-RAY CRYSTALLOGRAPHY AT 1.5 ANGSTROMS RESOLUTION'''<br />
 ==Overview==
-Xenopus laevis Cu,Zn superoxide dismutase (recombinant isoenzyme b) has, been crystallized and the structure determined at 1.49 A resolution. The, crystals belong to space group P2(1)2(1)2(1), with cell constants a =, 73.33, b = 68.86, c = 59.73 A, and contain one dimeric molecule of M(r) 32, 000 per asymmetric unit. The structure was solved by molecular-replacement, techniques using the semisynthetic Cu,Co bovine enzyme as search model, and refined by molecular dynamics with a crystallographic pseudo-energy, term. During the final steps, positional and anisotropic thermal, parameters of the atoms were refined. The R factor for the 49 209 unique, reflections in the 10.0-1.49 A resolution range is 0.104, for a model, comprising 2023 protein atoms, two Cu(2+), two Zn(2+), and 353 water, molecules. The overall temperature factor for the model, including, solvent, is 20.3 A(2), while the calculated r.m.s. coordinate error for, the refined model is 0.036 A. As suggested by the primary structure, homology to any other known intracellular eukaryotic superoxide dismutase, (&gt; 50%), the typical structural scaffolding of flattened antiparallel, eight-stranded (beta-barrel is well conserved in X. laevis Cu,Zn, superoxide dismutase b, together with the coordination geometry of the, metal centers in the active site. The higher thermal stability of the bb, X. laevis superoxide dismutase homodimer, with respect to dimers involving, the a-type isoenzyme subunit(s), can be related, on the basis of the, high-resolution structure, to side-chain and solvent interactions centered, on residue Tyr149, in both b-type subunits. The analysis of the overall, solvent structure reveals a number of equivalent water molecule sites in, the two subunits, and in homologous superoxide dismutase models. Their, locations are discussed in detail and classified on the basis of their, structural role.
+Xenopus laevis Cu,Zn superoxide dismutase (recombinant isoenzyme b) has been crystallized and the structure determined at 1.49 A resolution. The crystals belong to space group P2(1)2(1)2(1), with cell constants a = 73.33, b = 68.86, c = 59.73 A, and contain one dimeric molecule of M(r) 32 000 per asymmetric unit. The structure was solved by molecular-replacement techniques using the semisynthetic Cu,Co bovine enzyme as search model, and refined by molecular dynamics with a crystallographic pseudo-energy term. During the final steps, positional and anisotropic thermal parameters of the atoms were refined. The R factor for the 49 209 unique reflections in the 10.0-1.49 A resolution range is 0.104, for a model comprising 2023 protein atoms, two Cu(2+), two Zn(2+), and 353 water molecules. The overall temperature factor for the model, including solvent, is 20.3 A(2), while the calculated r.m.s. coordinate error for the refined model is 0.036 A. As suggested by the primary structure homology to any other known intracellular eukaryotic superoxide dismutase (&gt; 50%), the typical structural scaffolding of flattened antiparallel eight-stranded (beta-barrel is well conserved in X. laevis Cu,Zn superoxide dismutase b, together with the coordination geometry of the metal centers in the active site. The higher thermal stability of the bb X. laevis superoxide dismutase homodimer, with respect to dimers involving the a-type isoenzyme subunit(s), can be related, on the basis of the high-resolution structure, to side-chain and solvent interactions centered on residue Tyr149, in both b-type subunits. The analysis of the overall solvent structure reveals a number of equivalent water molecule sites in the two subunits, and in homologous superoxide dismutase models. Their locations are discussed in detail and classified on the basis of their structural role.
 ==About this Structure==
-XSO is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis] with CU and ZN as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1XSO OCA].
+XSO is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis] with <scene name='pdbligand=CU:'>CU</scene> and <scene name='pdbligand=ZN:'>ZN</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XSO OCA].
 ==Reference==
-Three-dimensional structure of Xenopus laevis Cu,Zn superoxide dismutase b determined by X-ray crystallography at 1.5 A resolution., Carugo KD, Battistoni A, Carri MT, Polticelli F, Desideri A, Rotilio G, Coda A, Wilson KS, Bolognesi M, Acta Crystallogr D Biol Crystallogr. 1996 Jan 1;52(Pt 1):176-88. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15299740 15299740]
+Three-dimensional structure of Xenopus laevis Cu,Zn superoxide dismutase b determined by X-ray crystallography at 1.5 A resolution., Djinovic Carugo K, Battistoni A, Carri MT, Polticelli F, Desideri A, Rotilio G, Coda A, Wilson KS, Bolognesi M, Acta Crystallogr D Biol Crystallogr. 1996 Jan 1;52(Pt 1):176-88. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15299740 15299740]
 [[Category: Single protein]]
 [[Category: Superoxide dismutase]]
@@ Line 16: / Line 16: @@
 [[Category: Battistoni, A.]]
 [[Category: Bolognesi, M.]]
-[[Category: Carri, M.T.]]
+[[Category: Carri, M T.]]
-[[Category: Carugo, K.Djinovic.]]
+[[Category: Carugo, K Djinovic.]]
 [[Category: Coda, A.]]
 [[Category: Desideri, A.]]
 [[Category: Polticelli, F.]]
 [[Category: Rotilio, G.]]
-[[Category: Wilson, K.S.]]
+[[Category: Wilson, K S.]]
 [[Category: CU]]
 [[Category: ZN]]
 [[Category: oxidoreductase (superoxide acceptor)]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 06:19:16 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:58:20 2008''