1oad

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:58, 9 May 2024) (edit) (undo)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1oad.gif|left|200px]]<br /><applet load="1oad" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1oad, resolution 1.5&Aring;" />
 
-
'''GLUCOSE ISOMERASE FROM STREPTOMYCES RUBIGINOSUS IN P21212 CRYSTAL FORM'''<br />
 
-
==Overview==
+
==Glucose isomerase from Streptomyces rubiginosus in P21212 crystal form==
-
Glucose isomerase from Streptomyces rubiginosus was crystallized in two, forms: I222, with one molecule of 44 kDa in the asymmetric unit, and, P2(1)2(1)2, with two unique molecules. The I222 structure is known, but, the P2(1)2(1)2 form has not been solved before. X-ray diffraction data for, the P2(1)2(1)2 form were collected at a wavelength of 1.54 A and data for, the I222 form were collected at three different wavelengths: 1.34, 1.07, and 0.98 A. The amount of anomalous signal from one Mn and eight S atoms, in these data sets varies from 1.24% to as low as 0.56%. The dual-space, direct-methods program SHELXD, run against the Bijvoet differences, gave a, clear solution of all anomalous scatterers for all data sets. The Mn, positions only were used for SAD phasing of all four data sets. The, electron-density map after density modification, resulting from the, phasing of a single-wavelength data set and based purely on the anomalous, deltaf" contribution, was clearly interpretable; an almost complete model, of the protein was built by wARP without human intervention in all four, cases. As far as is known, this is the first time that an anomalous signal, as low as 0.6% has successfully been used to determine the structure of a, macromolecule.
+
<StructureSection load='1oad' size='340' side='right'caption='[[1oad]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1oad]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_rubiginosus Streptomyces rubiginosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OAD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OAD 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]] 1.5&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MQD:2-METHYLPENTANE-1,2,4-TRIOL'>MQD</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=1oad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oad OCA], [https://pdbe.org/1oad PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oad RCSB], [https://www.ebi.ac.uk/pdbsum/1oad PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oad ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/XYLA_STRRU XYLA_STRRU] Involved in D-xylose catabolism.
 +
== 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/oa/1oad_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=1oad ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Glucose isomerase from Streptomyces rubiginosus was crystallized in two forms: I222, with one molecule of 44 kDa in the asymmetric unit, and P2(1)2(1)2, with two unique molecules. The I222 structure is known, but the P2(1)2(1)2 form has not been solved before. X-ray diffraction data for the P2(1)2(1)2 form were collected at a wavelength of 1.54 A and data for the I222 form were collected at three different wavelengths: 1.34, 1.07 and 0.98 A. The amount of anomalous signal from one Mn and eight S atoms in these data sets varies from 1.24% to as low as 0.56%. The dual-space direct-methods program SHELXD, run against the Bijvoet differences, gave a clear solution of all anomalous scatterers for all data sets. The Mn positions only were used for SAD phasing of all four data sets. The electron-density map after density modification, resulting from the phasing of a single-wavelength data set and based purely on the anomalous deltaf" contribution, was clearly interpretable; an almost complete model of the protein was built by wARP without human intervention in all four cases. As far as is known, this is the first time that an anomalous signal as low as 0.6% has successfully been used to determine the structure of a macromolecule.
-
==About this Structure==
+
SAD manganese in two crystal forms of glucose isomerase.,Ramagopal UA, Dauter M, Dauter Z Acta Crystallogr D Biol Crystallogr. 2003 May;59(Pt 5):868-75. Epub 2003, Apr 25. PMID:12777803<ref>PMID:12777803</ref>
-
1OAD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_rubiginosus Streptomyces rubiginosus] with <scene name='pdbligand=MN:'>MN</scene>, <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=MRD:'>MRD</scene>, <scene name='pdbligand=MQD:'>MQD</scene>, <scene name='pdbligand=TRS:'>TRS</scene> and <scene name='pdbligand=MPD:'>MPD</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.5 5.3.1.5] Known structural/functional Site: <scene name='pdbsite=AC1:Mpd+Binding+Site+For+Chain+B'>AC1</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OAD OCA].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
SAD manganese in two crystal forms of glucose isomerase., Ramagopal UA, Dauter M, Dauter Z, Acta Crystallogr D Biol Crystallogr. 2003 May;59(Pt 5):868-75. Epub 2003, Apr 25. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12777803 12777803]
+
</div>
-
[[Category: Single protein]]
+
<div class="pdbe-citations 1oad" style="background-color:#fffaf0;"></div>
-
[[Category: Streptomyces rubiginosus]]
+
-
[[Category: Xylose isomerase]]
+
-
[[Category: Dauter, M.]]
+
-
[[Category: Dauter, Z.]]
+
-
[[Category: Ramagopal, U.A.]]
+
-
[[Category: MG]]
+
-
[[Category: MN]]
+
-
[[Category: MPD]]
+
-
[[Category: MQD]]
+
-
[[Category: MRD]]
+
-
[[Category: TRS]]
+
-
[[Category: glucose isomerase]]
+
-
[[Category: isomerase]]
+
-
[[Category: xylose isomerase]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb 3 09:55:31 2008''
+
==See Also==
 +
*[[D-xylose isomerase 3D structures|D-xylose isomerase 3D structures]]
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
 +
[[Category: Streptomyces rubiginosus]]
 +
[[Category: Dauter M]]
 +
[[Category: Dauter Z]]
 +
[[Category: Ramagopal UA]]

Current revision

Glucose isomerase from Streptomyces rubiginosus in P21212 crystal form

PDB ID 1oad

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools