6taa
From Proteopedia
(New page: 200px<br /><applet load="6taa" size="450" color="white" frame="true" align="right" spinBox="true" caption="6taa, resolution 2.1Å" /> '''STRUCTURE AND MOLECUL...) |
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| - | [[Image:6taa.gif|left|200px]]<br /><applet load="6taa" size=" | + | [[Image:6taa.gif|left|200px]]<br /><applet load="6taa" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="6taa, resolution 2.1Å" /> | caption="6taa, resolution 2.1Å" /> | ||
'''STRUCTURE AND MOLECULAR MODEL REFINEMENT OF ASPERGILLUS ORYZAE (TAKA) ALPHA-AMYLASE: AN APPLICATION OF THE SIMULATED-ANNEALING METHOD'''<br /> | '''STRUCTURE AND MOLECULAR MODEL REFINEMENT OF ASPERGILLUS ORYZAE (TAKA) ALPHA-AMYLASE: AN APPLICATION OF THE SIMULATED-ANNEALING METHOD'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Monoclinic crystals of a neutral alpha-amylase from Aspergillus oryzae, containing three molecules in the asymmetric unit, have been reported | + | Monoclinic crystals of a neutral alpha-amylase from Aspergillus oryzae, containing three molecules in the asymmetric unit, have been reported previously and studied at 3 A resolution [Matsuura, Kunusoki, Harada & Kakudo (1984). J. Biochem. 95, 697-702]. Here we report the solution of the structure of this enzyme in a different crystal form (space group P2(1)2(1)2(1), a = 50.9, b = 67.2, c = 132.7 A), with only one molecule in the asymmetric unit. The structure was solved by the molecular replacement method, using a model of acid alpha-amylase from a related fungus A. niger [Brady, Brzozowski, Derewenda, Dodson & Dodson (1991). Acta Cryst. B47, 527-535]. Conventional least-squares crystallographic refinement failed to converge in a satisfactory manner, and the technique of molecular dynamics in the form of the XPLOR package [Brunger (1988). XPLOR Manual. Yale Univ., USA] was used to overcome the problem. A large rigid-body type movement of the C-terminal domain was identified and accounted for. The final round of restrained least-squares refinement (at 2.1 A resolution) including 3675 protein atoms and 247 water molecules resulted in a conventional crystallographic R factor of 0.183 and an atomic model which conforms well to standard stereochemical parameters (standard deviation of bond lengths from their expected values is 0.028 A, while that for planar groups is 0.029 A). |
==About this Structure== | ==About this Structure== | ||
| - | 6TAA is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aspergillus_oryzae Aspergillus oryzae] with CA as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.1 3.2.1.1] Full crystallographic information is available from [http:// | + | 6TAA is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aspergillus_oryzae Aspergillus oryzae] with <scene name='pdbligand=CA:'>CA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.1 3.2.1.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TAA OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Brady, L.]] | [[Category: Brady, L.]] | ||
| - | [[Category: Derewenda, Z | + | [[Category: Derewenda, Z S.]] |
| - | [[Category: Dodson, E | + | [[Category: Dodson, E J.]] |
| - | [[Category: Swift, H | + | [[Category: Swift, H J.]] |
| - | [[Category: Turkenburg, J | + | [[Category: Turkenburg, J P.]] |
| - | [[Category: Wilkinson, A | + | [[Category: Wilkinson, A J.]] |
[[Category: CA]] | [[Category: CA]] | ||
[[Category: hydrolase(o-glycosyl)]] | [[Category: hydrolase(o-glycosyl)]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:16:45 2008'' |
Revision as of 17:16, 21 February 2008
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STRUCTURE AND MOLECULAR MODEL REFINEMENT OF ASPERGILLUS ORYZAE (TAKA) ALPHA-AMYLASE: AN APPLICATION OF THE SIMULATED-ANNEALING METHOD
Overview
Monoclinic crystals of a neutral alpha-amylase from Aspergillus oryzae, containing three molecules in the asymmetric unit, have been reported previously and studied at 3 A resolution [Matsuura, Kunusoki, Harada & Kakudo (1984). J. Biochem. 95, 697-702]. Here we report the solution of the structure of this enzyme in a different crystal form (space group P2(1)2(1)2(1), a = 50.9, b = 67.2, c = 132.7 A), with only one molecule in the asymmetric unit. The structure was solved by the molecular replacement method, using a model of acid alpha-amylase from a related fungus A. niger [Brady, Brzozowski, Derewenda, Dodson & Dodson (1991). Acta Cryst. B47, 527-535]. Conventional least-squares crystallographic refinement failed to converge in a satisfactory manner, and the technique of molecular dynamics in the form of the XPLOR package [Brunger (1988). XPLOR Manual. Yale Univ., USA] was used to overcome the problem. A large rigid-body type movement of the C-terminal domain was identified and accounted for. The final round of restrained least-squares refinement (at 2.1 A resolution) including 3675 protein atoms and 247 water molecules resulted in a conventional crystallographic R factor of 0.183 and an atomic model which conforms well to standard stereochemical parameters (standard deviation of bond lengths from their expected values is 0.028 A, while that for planar groups is 0.029 A).
About this Structure
6TAA is a Single protein structure of sequence from Aspergillus oryzae with as ligand. Active as Alpha-amylase, with EC number 3.2.1.1 Full crystallographic information is available from OCA.
Reference
Structure and molecular model refinement of Aspergillus oryzae (TAKA) alpha-amylase: an application of the simulated-annealing method., Swift HJ, Brady L, Derewenda ZS, Dodson EJ, Dodson GG, Turkenburg JP, Wilkinson AJ, Acta Crystallogr B. 1991 Aug 1;47 ( Pt 4):535-44. PMID:1930835
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