1p7g
From Proteopedia
(New page: 200px<br /><applet load="1p7g" size="450" color="white" frame="true" align="right" spinBox="true" caption="1p7g, resolution 1.80Å" /> '''Crystal structure of...) |
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| - | [[Image:1p7g.gif|left|200px]]<br /><applet load="1p7g" size=" | + | [[Image:1p7g.gif|left|200px]]<br /><applet load="1p7g" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1p7g, resolution 1.80Å" /> | caption="1p7g, resolution 1.80Å" /> | ||
'''Crystal structure of superoxide dismutase from Pyrobaculum aerophilum'''<br /> | '''Crystal structure of superoxide dismutase from Pyrobaculum aerophilum'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The crystal structure of superoxide dismutase from the hyperthermophilic | + | The crystal structure of superoxide dismutase from the hyperthermophilic crenarchaeon Pyrobaculum aerophilum was determined by molecular replacement at 1.8 A resolution. The structure determination was made especially challenging by the large number of molecules (24) in the asymmetric unit, the presence of a pseudo-crystallographic twofold operator close to a twinning operator and the inability to detect twinning by conventional means. Molecular replacement proceeded at low resolution in pseudo (apparent) space group P3(2)12 and was facilitated by examination of the self-rotation function and native Patterson map. Refinement, however, stalled at an R factor of 40% when high-resolution data were included. Expanding to the lower symmetry space group P3(2) decreased R (to 22%) and R(free) (to 26%), but not by as much as expected for the quality of data. Finally, despite the apparent lack of evidence from conventional twinning tests [i.e. plots of the second moment of I and N(Z) distributions], a twinning operator was included in the refinement, lowering R and R(free) to 16.2 and 21.7%, respectively. The early detection of twinning appears to have been masked by a deviation in the expected intensity distribution caused by the presence of non-crystallographic translational symmetry. These findings suggest the importance of testing twinning operators in cases where pseudo-translational symmetry can explain negative results from conventional twinning tests. The structure reveals a tetrameric assembly with 222 symmetry, similar to superoxide dismutase structures from other organisms. The current structural model represents the metal-free state of the enzyme. |
==About this Structure== | ==About this Structure== | ||
| - | 1P7G is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrobaculum_aerophilum Pyrobaculum aerophilum] with ACT and BME 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:// | + | 1P7G is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrobaculum_aerophilum Pyrobaculum aerophilum] with <scene name='pdbligand=ACT:'>ACT</scene> and <scene name='pdbligand=BME:'>BME</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=1P7G OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Eisenberg, D.]] | [[Category: Eisenberg, D.]] | ||
[[Category: Lee, S.]] | [[Category: Lee, S.]] | ||
| - | [[Category: Sawaya, M | + | [[Category: Sawaya, M R.]] |
[[Category: ACT]] | [[Category: ACT]] | ||
[[Category: BME]] | [[Category: BME]] | ||
[[Category: alpha-beta]] | [[Category: alpha-beta]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:25:57 2008'' |
Revision as of 12:25, 21 February 2008
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Crystal structure of superoxide dismutase from Pyrobaculum aerophilum
Overview
The crystal structure of superoxide dismutase from the hyperthermophilic crenarchaeon Pyrobaculum aerophilum was determined by molecular replacement at 1.8 A resolution. The structure determination was made especially challenging by the large number of molecules (24) in the asymmetric unit, the presence of a pseudo-crystallographic twofold operator close to a twinning operator and the inability to detect twinning by conventional means. Molecular replacement proceeded at low resolution in pseudo (apparent) space group P3(2)12 and was facilitated by examination of the self-rotation function and native Patterson map. Refinement, however, stalled at an R factor of 40% when high-resolution data were included. Expanding to the lower symmetry space group P3(2) decreased R (to 22%) and R(free) (to 26%), but not by as much as expected for the quality of data. Finally, despite the apparent lack of evidence from conventional twinning tests [i.e. plots of the second moment of I and N(Z) distributions], a twinning operator was included in the refinement, lowering R and R(free) to 16.2 and 21.7%, respectively. The early detection of twinning appears to have been masked by a deviation in the expected intensity distribution caused by the presence of non-crystallographic translational symmetry. These findings suggest the importance of testing twinning operators in cases where pseudo-translational symmetry can explain negative results from conventional twinning tests. The structure reveals a tetrameric assembly with 222 symmetry, similar to superoxide dismutase structures from other organisms. The current structural model represents the metal-free state of the enzyme.
About this Structure
1P7G is a Single protein structure of sequence from Pyrobaculum aerophilum with and as ligands. Active as Superoxide dismutase, with EC number 1.15.1.1 Full crystallographic information is available from OCA.
Reference
Structure of superoxide dismutase from Pyrobaculum aerophilum presents a challenging case in molecular replacement with multiple molecules, pseudo-symmetry and twinning., Lee S, Sawaya MR, Eisenberg D, Acta Crystallogr D Biol Crystallogr. 2003 Dec;59(Pt 12):2191-9. Epub 2003, Nov 27. PMID:14646077
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