2ze9: Difference between revisions

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[[Image:2ze9.png|left|200px]]


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==Crystal structure of H168A mutant of phospholipase D from Streptomyces antibioticus, as a complex with phosphatidylcholine==
The line below this paragraph, containing "STRUCTURE_2ze9", creates the "Structure Box" on the page.
<StructureSection load='2ze9' size='340' side='right'caption='[[2ze9]], [[Resolution|resolution]] 2.30&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'>[[2ze9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_antibioticus Streptomyces antibioticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZE9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZE9 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]] 2.3&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=PD7:(2R)-3-(PHOSPHONOOXY)PROPANE-1,2-DIYL+DIHEPTANOATE'>PD7</scene></td></tr>
{{STRUCTURE_2ze9|  PDB=2ze9  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ze9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ze9 OCA], [https://pdbe.org/2ze9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ze9 RCSB], [https://www.ebi.ac.uk/pdbsum/2ze9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ze9 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/PLD_STRAT PLD_STRAT]
== 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/ze/2ze9_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=2ze9 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Phospholipase D (E.C. 3.1.4.4) from Streptomyces antibioticus has been crystallized in six crystal forms using the hanging-drop vapour-diffusion method. The type III and V crystals belong to monoclinic and hexagonal systems, respectively. All of the other crystal forms, types I, II, IV and VI, belong to orthorhombic space group P212121. Of these four types, the type VI crystals are suitable for X-ray structure determination. Crystal data for type VI crystals are: a = 50.1, b = 98.7, c = 107.6 A, V = 532100 A3, Z = 4 and Vm = 2.47 A3 Da-1. Type VI crystals diffract to at least 2.3 A resolution. A total of 11295 independent reflections to 3 A resolution have been collected from a type VI crystal using a conventional X-ray source, and its structural analysis is currently being conducted using isomorphous replacement methods.


===Crystal structure of H168A mutant of phospholipase D from Streptomyces antibioticus, as a complex with phosphatidylcholine===
Crystallization and preliminary X-ray diffraction studies of phospholipase D from Streptomyces antibioticus.,Suzuki A, Kakuno K, Iwasaki Y, Yamane T, Yamane T Acta Crystallogr D Biol Crystallogr. 1999 Jan;55(Pt 1):317-9. Epub 1999, Jan 1. PMID:010089437<ref>PMID:010089437</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2ze9" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_10089437}}, adds the Publication Abstract to the page
*[[Phospholipase D 3D structures|Phospholipase D 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 10089437 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_10089437}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
[[2ze9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_antibioticus Streptomyces antibioticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZE9 OCA].
 
==Reference==
<ref group="xtra">PMID:10089437</ref><ref group="xtra">PMID:18338352</ref><references group="xtra"/>
[[Category: Phospholipase D]]
[[Category: Streptomyces antibioticus]]
[[Category: Streptomyces antibioticus]]
[[Category: Iwasaki, Y.]]
[[Category: Iwasaki Y]]
[[Category: Suzuki, A.]]
[[Category: Suzuki A]]
[[Category: Toda, H.]]
[[Category: Toda H]]
[[Category: Yamane, T.]]
[[Category: Yamane T]]
[[Category: Alpha-beta-beta-alpha sandwich]]
[[Category: Hydrolase]]
[[Category: Lipid degradation]]
[[Category: Secreted]]

Latest revision as of 04:33, 21 November 2024

Crystal structure of H168A mutant of phospholipase D from Streptomyces antibioticus, as a complex with phosphatidylcholineCrystal structure of H168A mutant of phospholipase D from Streptomyces antibioticus, as a complex with phosphatidylcholine

Structural highlights

2ze9 is a 1 chain structure with sequence from Streptomyces antibioticus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.3Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PLD_STRAT

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Phospholipase D (E.C. 3.1.4.4) from Streptomyces antibioticus has been crystallized in six crystal forms using the hanging-drop vapour-diffusion method. The type III and V crystals belong to monoclinic and hexagonal systems, respectively. All of the other crystal forms, types I, II, IV and VI, belong to orthorhombic space group P212121. Of these four types, the type VI crystals are suitable for X-ray structure determination. Crystal data for type VI crystals are: a = 50.1, b = 98.7, c = 107.6 A, V = 532100 A3, Z = 4 and Vm = 2.47 A3 Da-1. Type VI crystals diffract to at least 2.3 A resolution. A total of 11295 independent reflections to 3 A resolution have been collected from a type VI crystal using a conventional X-ray source, and its structural analysis is currently being conducted using isomorphous replacement methods.

Crystallization and preliminary X-ray diffraction studies of phospholipase D from Streptomyces antibioticus.,Suzuki A, Kakuno K, Iwasaki Y, Yamane T, Yamane T Acta Crystallogr D Biol Crystallogr. 1999 Jan;55(Pt 1):317-9. Epub 1999, Jan 1. PMID:010089437[1]

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

See Also

References

  1. ↑ Suzuki A, Kakuno K, Iwasaki Y, Yamane T, Yamane T. Crystallization and preliminary X-ray diffraction studies of phospholipase D from Streptomyces antibioticus. Acta Crystallogr D Biol Crystallogr. 1999 Jan;55(Pt 1):317-9. Epub 1999, Jan 1. PMID:10089437 doi:10.1107/S0907444998010592

2ze9, resolution 2.30Å

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