1r76: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
New page: left|200px<br /><applet load="1r76" size="450" color="white" frame="true" align="right" spinBox="true" caption="1r76, resolution 2.65Å" /> '''Structure of a pecta...
 
No edit summary
 
(15 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1r76.jpg|left|200px]]<br /><applet load="1r76" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1r76, resolution 2.65&Aring;" />
'''Structure of a pectate lyase from Azospirillum irakense'''<br />


==Overview==
==Structure of a pectate lyase from Azospirillum irakense==
The three-dimensional structure of Azospirillum irakense pectate lyase, (PelA) has been determined at a resolution of 2.65 A. The crystals are, hexagonal, belonging to space group P6(5)22, with unit-cell parameters a =, b = 85.37, c = 231.32 angstroms. Phase information was derived from a, multiple-wavelength anomalous dispersion (MAD) experiment using a Hg, derivative. Refinement of the model converged to Rcryst = 20.08% and Rfree, = 25.87%. The overall structure of PelA does not adopt the characteristic, parallel beta-helix fold displayed by pectate lyases from polysaccharide, lyase (PL) families PL1, PL3 and PL9. Instead, it displays a predominantly, alpha-helical structure with irregular coils and short beta-strands, similar to the recently reported structure of the catalytic module of the, Cellvibrio japonicus pectate lyase Pel10Acm. The topologies of the two, structures have been compared. They show two 'domains' with the interface, between them being a wide-open central groove in which the active site is, located. The active sites of the crystal structures are also compared and, their similarities and differences are discussed.
<StructureSection load='1r76' size='340' side='right'caption='[[1r76]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1r76]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Niveispirillum_irakense Niveispirillum irakense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R76 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R76 FirstGlance]. <br>
1R76 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Azospirillum_irakense Azospirillum irakense] with HG, CL, IPA and GOL as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Pectate_lyase Pectate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.2 4.2.2.2] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1R76 OCA].  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.65&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></td></tr>
==Reference==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1r76 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r76 OCA], [https://pdbe.org/1r76 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r76 RCSB], [https://www.ebi.ac.uk/pdbsum/1r76 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r76 ProSAT]</span></td></tr>
Azospirillum irakense pectate lyase displays a toroidal fold., Novoa De Armas H, Verboven C, De Ranter C, Desair J, Vande Broek A, Vanderleyden J, Rabijns A, Acta Crystallogr D Biol Crystallogr. 2004 Jun;60(Pt 6):999-1007. Epub 2004, May 21. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15159558 15159558]
</table>
[[Category: Azospirillum irakense]]
== Function ==
[[Category: Pectate lyase]]
[https://www.uniprot.org/uniprot/Q9X592_NIVIR Q9X592_NIVIR]  
[[Category: Single protein]]
== Evolutionary Conservation ==
[[Category: Armas, H.Novoa.de.]]
[[Image:Consurf_key_small.gif|200px|right]]
[[Category: Broek, A.Vande.]]
Check<jmol>
[[Category: Desair, J.]]
  <jmolCheckbox>
[[Category: Rabijns, A.]]
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r7/1r76_consurf.spt"</scriptWhenChecked>
[[Category: Ranter, C.De.]]
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
[[Category: Vanderleyden, J.]]
    <text>to colour the structure by Evolutionary Conservation</text>
[[Category: Verboven, C.]]
  </jmolCheckbox>
[[Category: CL]]
</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=1r76 ConSurf].
[[Category: GOL]]
<div style="clear:both"></div>
[[Category: HG]]
__TOC__
[[Category: IPA]]
</StructureSection>
[[Category: a-helical structure]]
[[Category: Large Structures]]
 
[[Category: Niveispirillum irakense]]
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 22:16:31 2007''
[[Category: De Ranter C]]
[[Category: Desair J]]
[[Category: Novoa de Armas H]]
[[Category: Rabijns A]]
[[Category: Vande Broek A]]
[[Category: Vanderleyden J]]
[[Category: Verboven C]]

Latest revision as of 11:21, 14 February 2024

Structure of a pectate lyase from Azospirillum irakenseStructure of a pectate lyase from Azospirillum irakense

Structural highlights

1r76 is a 1 chain structure with sequence from Niveispirillum irakense. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.65Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q9X592_NIVIR

Evolutionary Conservation

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

1r76, resolution 2.65Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=1r76&oldid=4054214"