This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


2gjp

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:41, 30 August 2023) (edit) (undo)
 
(12 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2gjp.gif|left|200px]]
 
-
<!--
+
==Structure of Bacillus halmapalus alpha-amylase, crystallized with the substrate analogue acarbose and maltose==
-
The line below this paragraph, containing "STRUCTURE_2gjp", creates the "Structure Box" on the page.
+
<StructureSection load='2gjp' size='340' side='right'caption='[[2gjp]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[2gjp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sutcliffiella_halmapala Sutcliffiella halmapala]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GJP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GJP FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DAF:4,6-DIDEOXY-4-{[(1S,5R,6S)-3-FORMYL-5,6-DIHYDROXY-4-OXOCYCLOHEX-2-EN-1-YL]AMINO}-ALPHA-D-XYLO-HEX-5-ENOPYRANOSE'>DAF</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PRD_900001:alpha-maltose'>PRD_900001</scene></td></tr>
-
{{STRUCTURE_2gjp| PDB=2gjp | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2gjp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gjp OCA], [https://pdbe.org/2gjp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gjp RCSB], [https://www.ebi.ac.uk/pdbsum/2gjp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gjp ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/AMT6_BACS7 AMT6_BACS7]
 +
== 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/gj/2gjp_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2gjp ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Recombinant Bacillus halmapalus alpha-amylase (BHA) was studied in two different crystal forms. The first crystal form was obtained by crystallization of BHA at room temperature in the presence of acarbose and maltose; data were collected at cryogenic temperature to a resolution of 1.9 A. It was found that the crystal belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 47.0, b = 73.5, c = 151.1 A. A maltose molecule was observed and found to bind to BHA and previous reports of the binding of a nonasaccharide were confirmed. The second crystal form was obtained by pH-induced crystallization of BHA in a MES-HEPES-boric acid buffer (MHB buffer) at 303 K; the solubility of BHA in MHB has a retrograde temperature dependency and crystallization of BHA was only possible by raising the temperature to at least 298 K. Data were collected at cryogenic temperature to a resolution of 2.0 A. The crystal belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 38.6, b = 59.0, c = 209.8 A. The structure was solved using molecular replacement. The maltose-binding site is described and the two structures are compared. No significant changes were seen in the structure upon binding of the substrates.
-
'''Structure of Bacillus halmapalus alpha-amylase, crystallized with the substrate analogue acarbose and maltose'''
+
Structure of Bacillus halmapalus alpha-amylase crystallized with and without the substrate analogue acarbose and maltose.,Lyhne-Iversen L, Hobley TJ, Kaasgaard SG, Harris P Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Sep 1;62(Pt, 9):849-54. Epub 2006 Aug 26. PMID:16946462<ref>PMID:16946462</ref>
-
 
+
-
 
+
-
==Overview==
+
-
Recombinant Bacillus halmapalus alpha-amylase (BHA) was studied in two different crystal forms. The first crystal form was obtained by crystallization of BHA at room temperature in the presence of acarbose and maltose; data were collected at cryogenic temperature to a resolution of 1.9 A. It was found that the crystal belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 47.0, b = 73.5, c = 151.1 A. A maltose molecule was observed and found to bind to BHA and previous reports of the binding of a nonasaccharide were confirmed. The second crystal form was obtained by pH-induced crystallization of BHA in a MES-HEPES-boric acid buffer (MHB buffer) at 303 K; the solubility of BHA in MHB has a retrograde temperature dependency and crystallization of BHA was only possible by raising the temperature to at least 298 K. Data were collected at cryogenic temperature to a resolution of 2.0 A. The crystal belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 38.6, b = 59.0, c = 209.8 A. The structure was solved using molecular replacement. The maltose-binding site is described and the two structures are compared. No significant changes were seen in the structure upon binding of the substrates.
+
-
==About this Structure==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
2GJP is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_halmapalus Bacillus halmapalus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GJP OCA].
+
</div>
 +
<div class="pdbe-citations 2gjp" style="background-color:#fffaf0;"></div>
-
==Reference==
+
==See Also==
-
Structure of Bacillus halmapalus alpha-amylase crystallized with and without the substrate analogue acarbose and maltose., Lyhne-Iversen L, Hobley TJ, Kaasgaard SG, Harris P, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Sep 1;62(Pt, 9):849-54. Epub 2006 Aug 26. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16946462 16946462]
+
*[[Amylase 3D structures|Amylase 3D structures]]
-
[[Category: Alpha-amylase]]
+
== References ==
-
[[Category: Bacillus halmapalus]]
+
<references/>
-
[[Category: Single protein]]
+
__TOC__
-
[[Category: Harris, P.]]
+
</StructureSection>
-
[[Category: Hobley, T J.]]
+
[[Category: Large Structures]]
-
[[Category: Kaasgaard, S G.]]
+
[[Category: Sutcliffiella halmapala]]
-
[[Category: Lyhne-Iversen, L.]]
+
[[Category: Harris P]]
-
[[Category: Alpha-amylase]]
+
[[Category: Hobley TJ]]
-
[[Category: Bacillus halmapalus]]
+
[[Category: Kaasgaard SG]]
-
[[Category: Maltose binding site]]
+
[[Category: Lyhne-Iversen L]]
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 05:11:03 2008''
+

Current revision

Structure of Bacillus halmapalus alpha-amylase, crystallized with the substrate analogue acarbose and maltose

PDB ID 2gjp

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/2gjp"
Personal tools