2gjp: Difference between revisions

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Line 1:

~~[[Image:2gjp.gif|left|200px]]<br /><applet load="2gjp" size="450" color="white" frame="true" align="right" spinBox="true"~~

~~caption="2gjp, resolution 1.90Å" />~~

~~'''Structure of Bacillus halmapalus alpha-amylase, crystallized with the substrate analogue acarbose and maltose'''<br />~~

==~~Overview~~==

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

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.

== Structural highlights ==

<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>

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</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>

<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>

<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].

== 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.

~~==About this~~ Structure==

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>

~~2GJP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure~~ of ~~sequence from [http://en.wikipedia.org/wiki/Bacillus_halmapalus~~ Bacillus halmapalus] with ~~MAL~~, ~~GLC~~, ~~CA and NA as [http://en~~.~~wikipedia.org/wiki/ligands ligands]. 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~~:/~~/ispc.weizmann.ac.il/oca-bin/ocashort?id=2GJP OCA].~~

~~==Reference==~~

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

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 Crystallograph Sect F Struct Biol Cryst Commun. 2006 Sep 1;~~62(Pt, 9):849-54. Epub 2006 Aug 26. PMID:[http:~~/~~/ispc.weizmann.ac.il//pmbin/getpm?pmid=16946462 16946462]~~

</div>

~~[[Category: Alpha-amylase]]~~

~~[[Category: Bacillus halmapalus]]~~

~~[[Category: Single protein]]~~

~~[[Category: Harris~~, P.]]

~~[[Category: Hobley, T~~.J.]]

~~[[Category: Kaasgaard, S.G.]]~~

~~[[Category: Lyhne~~-~~Iversen, L.]]~~

~~[[Category: CA]]~~

~~[[Category: GLC]]~~

~~[[Category: MAL]]~~

~~[[Category: NA]]~~

~~[[Category: alpha~~-~~amylase]]~~

~~[[Category~~: ~~bacillus halmapalus]]~~

~~[[Category: maltose binding site]]~~

~~''Page seeded by~~ [~~http:~~//~~ispc.weizmann.ac.il/oca OCA~~ ] ~~on Wed Nov 21 11~~:14:~~37 2007''~~

==See Also==

*[[Amylase 3D structures|Amylase 3D structures]]

== References ==

__TOC__

</StructureSection>

[[Category: Large Structures]]

[[Category: Sutcliffiella halmapala]]

[[Category: Harris P]]

[[Category: Hobley TJ]]

[[Category: Kaasgaard SG]]

[[Category: Lyhne-Iversen L]]

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@@ Line 1: / Line 1: @@
-[[Image:2gjp.gif|left|200px]]<br /><applet load="2gjp" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="2gjp, resolution 1.90&Aring;" />
-'''Structure of Bacillus halmapalus alpha-amylase, crystallized with the substrate analogue acarbose and maltose'''<br />
-==Overview==
+==Structure of Bacillus halmapalus alpha-amylase, crystallized with the substrate analogue acarbose and maltose==
-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.
+<StructureSection load='2gjp' size='340' side='right'caption='[[2gjp]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+== Structural highlights ==
+<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>
+</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>
+<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.
-==About this Structure==
+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>
-GJP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_halmapalus Bacillus halmapalus] with MAL, GLC, CA and NA as [http://en.wikipedia.org/wiki/ligands ligands]. 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=2GJP OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-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 Crystallograph Sect F Struct Biol Cryst Commun. 2006 Sep 1;62(Pt, 9):849-54. Epub 2006 Aug 26. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16946462 16946462]
+</div>
-[[Category: Alpha-amylase]]
+<div class="pdbe-citations 2gjp" style="background-color:#fffaf0;"></div>
-[[Category: Bacillus halmapalus]]
-[[Category: Single protein]]
-[[Category: Harris, P.]]
-[[Category: Hobley, T.J.]]
-[[Category: Kaasgaard, S.G.]]
-[[Category: Lyhne-Iversen, L.]]
-[[Category: CA]]
-[[Category: GLC]]
-[[Category: MAL]]
-[[Category: NA]]
-[[Category: alpha-amylase]]
-[[Category: bacillus halmapalus]]
-[[Category: maltose binding site]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 11:14:37 2007''
+==See Also==
+*[[Amylase 3D structures|Amylase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Sutcliffiella halmapala]]
+[[Category: Harris P]]
+[[Category: Hobley TJ]]
+[[Category: Kaasgaard SG]]
+[[Category: Lyhne-Iversen L]]