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


{{Structure
==Crystal structure of H168A mutant of phospholipase D from Streptomyces antibioticus, as a complex with phosphatidylcholine==
|PDB= 2ze9 |SIZE=350|CAPTION= <scene name='initialview01'>2ze9</scene>, resolution 2.30&Aring;
<StructureSection load='2ze9' size='340' side='right'caption='[[2ze9]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <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>
<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>
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Phospholipase_D Phospholipase D], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.4 3.1.4.4] </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]] 2.3&#8491;</td></tr>
|GENE=
<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>
|DOMAIN=
<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>
|RELATEDENTRY=[[2ze4|2ZE4]]
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ze9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ze9 OCA], [http://www.ebi.ac.uk/pdbsum/2ze9 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2ze9 RCSB]</span>
== 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>


==Overview==
==See Also==
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.
*[[Phospholipase D 3D structures|Phospholipase D 3D structures]]
 
== References ==
==About this Structure==
<references/>
2ZE9 is a [[Single protein]] structure of 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].
__TOC__
 
</StructureSection>
==Reference==
[[Category: Large Structures]]
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:[http://www.ncbi.nlm.nih.gov/pubmed/10089437 10089437]
[[Category: Phospholipase D]]
[[Category: Single protein]]
[[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]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:20:39 2008''

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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