1aho
From Proteopedia
(New page: 200px<br /><applet load="1aho" size="450" color="white" frame="true" align="right" spinBox="true" caption="1aho, resolution 0.96Å" /> '''THE AB INITIO STRUCT...) |
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| - | [[Image:1aho.gif|left|200px]]<br /><applet load="1aho" size=" | + | [[Image:1aho.gif|left|200px]]<br /><applet load="1aho" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1aho, resolution 0.96Å" /> | caption="1aho, resolution 0.96Å" /> | ||
'''THE AB INITIO STRUCTURE DETERMINATION AND REFINEMENT OF A SCORPION PROTEIN TOXIN'''<br /> | '''THE AB INITIO STRUCTURE DETERMINATION AND REFINEMENT OF A SCORPION PROTEIN TOXIN'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The structure of toxin II from the scorpion Androctonus australis Hector | + | The structure of toxin II from the scorpion Androctonus australis Hector has been determined ab initio by direct methods using SnB at 0.96 A resolution. For the purpose of this structure redetermination, undertaken as a test of the minimal function and the SnB program, the identity and sequence of the protein was withheld from part of the research team. A single solution obtained from 1 619 random atom trials was clearly revealed by the bimodal distribution of the final value of the minimal function associated with each individual trial. Five peptide fragments were identified from a conservative analysis of the initial E-map, and following several refinement cycles with X-PLOR, a model was built of the complete structure. At the end of the X-PLOR refinement, the sequence was compared with the published sequence and 57 of the 64 residues had been correctly identified. Two errors in sequence resulted from side chains with similar size while the rest of the errors were a result of severe disorder or high thermal motion in the side chains. Given the amino-acid sequence, it is estimated that the initial E-map could have produced a model containing 99% of all main-chain and 81% of side-chain atoms. The structure refinement was completed with PROFFT, including the contributions of protein H atoms, and converged at a residual of 0.158 for 30 609 data with F >or= 2sigma(F) in the resolution range 8.0-0.964 A. The final model consisted of 518 non-H protein atoms (36 disordered), 407 H atoms, and 129 water molecules (43 with occupancies less than unity). This total of 647 non-H atoms represents the largest light-atom structure solved to date. |
==About this Structure== | ==About this Structure== | ||
| - | 1AHO is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Androctonus_australis_hector Androctonus australis hector]. Full crystallographic information is available from [http:// | + | 1AHO is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Androctonus_australis_hector Androctonus australis hector]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AHO OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Androctonus australis hector]] | [[Category: Androctonus australis hector]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Blessing, R | + | [[Category: Blessing, R H.]] |
| - | [[Category: Ealick, S | + | [[Category: Ealick, S E.]] |
| - | [[Category: Fontecilla-Camps, J | + | [[Category: Fontecilla-Camps, J C.]] |
| - | [[Category: Hauptman, H | + | [[Category: Hauptman, H A.]] |
[[Category: Housset, D.]] | [[Category: Housset, D.]] | ||
| - | [[Category: Langs, D | + | [[Category: Langs, D A.]] |
[[Category: Miller, R.]] | [[Category: Miller, R.]] | ||
| - | [[Category: Smith, G | + | [[Category: Smith, G D.]] |
[[Category: ab initio phasing]] | [[Category: ab initio phasing]] | ||
[[Category: neurotoxin]] | [[Category: neurotoxin]] | ||
| Line 26: | Line 26: | ||
[[Category: toxin ii]] | [[Category: toxin ii]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:44:35 2008'' |
Revision as of 09:44, 21 February 2008
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THE AB INITIO STRUCTURE DETERMINATION AND REFINEMENT OF A SCORPION PROTEIN TOXIN
Overview
The structure of toxin II from the scorpion Androctonus australis Hector has been determined ab initio by direct methods using SnB at 0.96 A resolution. For the purpose of this structure redetermination, undertaken as a test of the minimal function and the SnB program, the identity and sequence of the protein was withheld from part of the research team. A single solution obtained from 1 619 random atom trials was clearly revealed by the bimodal distribution of the final value of the minimal function associated with each individual trial. Five peptide fragments were identified from a conservative analysis of the initial E-map, and following several refinement cycles with X-PLOR, a model was built of the complete structure. At the end of the X-PLOR refinement, the sequence was compared with the published sequence and 57 of the 64 residues had been correctly identified. Two errors in sequence resulted from side chains with similar size while the rest of the errors were a result of severe disorder or high thermal motion in the side chains. Given the amino-acid sequence, it is estimated that the initial E-map could have produced a model containing 99% of all main-chain and 81% of side-chain atoms. The structure refinement was completed with PROFFT, including the contributions of protein H atoms, and converged at a residual of 0.158 for 30 609 data with F >or= 2sigma(F) in the resolution range 8.0-0.964 A. The final model consisted of 518 non-H protein atoms (36 disordered), 407 H atoms, and 129 water molecules (43 with occupancies less than unity). This total of 647 non-H atoms represents the largest light-atom structure solved to date.
About this Structure
1AHO is a Single protein structure of sequence from Androctonus australis hector. Full crystallographic information is available from OCA.
Reference
Ab initio structure determination and refinement of a scorpion protein toxin., Smith GD, Blessing RH, Ealick SE, Fontecilla-Camps JC, Hauptman HA, Housset D, Langs DA, Miller R, Acta Crystallogr D Biol Crystallogr. 1997 Sep 1;53(Pt 5):551-7. PMID:15299886
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