6taa

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:12, 9 October 2024) (edit) (undo)
 
(9 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:6taa.gif|left|200px]]
 
-
{{Structure
+
==STRUCTURE AND MOLECULAR MODEL REFINEMENT OF ASPERGILLUS ORYZAE (TAKA) ALPHA-AMYLASE: AN APPLICATION OF THE SIMULATED-ANNEALING METHOD==
-
|PDB= 6taa |SIZE=350|CAPTION= <scene name='initialview01'>6taa</scene>, resolution 2.1&Aring;
+
<StructureSection load='6taa' size='340' side='right'caption='[[6taa]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>
+
<table><tr><td colspan='2'>[[6taa]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_oryzae Aspergillus oryzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TAA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TAA FirstGlance]. <br>
-
|ACTIVITY= <span class='plainlinks'>[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] </span>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-
|DOMAIN=
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6taa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6taa OCA], [https://pdbe.org/6taa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6taa RCSB], [https://www.ebi.ac.uk/pdbsum/6taa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6taa ProSAT]</span></td></tr>
-
|RELATEDENTRY=
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6taa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6taa OCA], [http://www.ebi.ac.uk/pdbsum/6taa PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=6taa RCSB]</span>
+
== Function ==
-
}}
+
[https://www.uniprot.org/uniprot/AMYA1_ASPOR AMYA1_ASPOR]
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ta/6taa_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=6taa ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
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 &amp; 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 &amp; 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).
-
'''STRUCTURE AND MOLECULAR MODEL REFINEMENT OF ASPERGILLUS ORYZAE (TAKA) ALPHA-AMYLASE: AN APPLICATION OF THE SIMULATED-ANNEALING METHOD'''
+
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<ref>PMID:1930835</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 6taa" style="background-color:#fffaf0;"></div>
-
==Overview==
+
==See Also==
-
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 &amp; 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 &amp; 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).
+
*[[Amylase 3D structures|Amylase 3D structures]]
-
 
+
== References ==
-
==About this Structure==
+
<references/>
-
6TAA is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Aspergillus_oryzae Aspergillus oryzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TAA OCA].
+
__TOC__
-
 
+
</StructureSection>
-
==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:[http://www.ncbi.nlm.nih.gov/pubmed/1930835 1930835]
+
-
[[Category: Alpha-amylase]]
+
[[Category: Aspergillus oryzae]]
[[Category: Aspergillus oryzae]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Brady, L.]]
+
[[Category: Brady L]]
-
[[Category: Derewenda, Z S.]]
+
[[Category: Derewenda ZS]]
-
[[Category: Dodson, E J.]]
+
[[Category: Dodson EJ]]
-
[[Category: Swift, H J.]]
+
[[Category: Swift HJ]]
-
[[Category: Turkenburg, J P.]]
+
[[Category: Turkenburg JP]]
-
[[Category: Wilkinson, A J.]]
+
[[Category: Wilkinson AJ]]
-
[[Category: hydrolase(o-glycosyl)]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:43:37 2008''
+

Current revision

STRUCTURE AND MOLECULAR MODEL REFINEMENT OF ASPERGILLUS ORYZAE (TAKA) ALPHA-AMYLASE: AN APPLICATION OF THE SIMULATED-ANNEALING METHOD

PDB ID 6taa

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6taa"
Personal tools