2z8d: Difference between revisions

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[[Image:2z8d.jpg|left|200px]]


{{Structure
==The galacto-N-biose-/lacto-N-biose I-binding protein (GL-BP) of the ABC transporter from Bifidobacterium longum in complex with lacto-N-biose==
|PDB= 2z8d |SIZE=350|CAPTION= <scene name='initialview01'>2z8d</scene>, resolution 1.85&Aring;
<StructureSection load='2z8d' size='340' side='right'caption='[[2z8d]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
|SITE= <scene name='pdbsite=AC1:Nag+Binding+Site+For+Residue+A+2'>AC1</scene>, <scene name='pdbsite=AC2:Gal+Binding+Site+For+Residue+A+1'>AC2</scene>, <scene name='pdbsite=AC3:Nag+Binding+Site+For+Residue+B+2'>AC3</scene>, <scene name='pdbsite=AC4:Gal+Binding+Site+For+Residue+B+1'>AC4</scene>, <scene name='pdbsite=AC5:Zn+Binding+Site+For+Residue+A+3'>AC5</scene>, <scene name='pdbsite=AC6:Zn+Binding+Site+For+Residue+B+3'>AC6</scene>, <scene name='pdbsite=AC7:Zn+Binding+Site+For+Residue+A+4'>AC7</scene>, <scene name='pdbsite=AC8:Zn+Binding+Site+For+Residue+B+4'>AC8</scene>, <scene name='pdbsite=AC9:Zn+Binding+Site+For+Residue+B+5'>AC9</scene>, <scene name='pdbsite=BC1:Zn+Binding+Site+For+Residue+B+6'>BC1</scene>, <scene name='pdbsite=BC2:Zn+Binding+Site+For+Residue+B+7'>BC2</scene>, <scene name='pdbsite=BC3:Mes+Binding+Site+For+Residue+A+11'>BC3</scene> and <scene name='pdbsite=BC4:Mes+Binding+Site+For+Residue+B+12'>BC4</scene>
== Structural highlights ==
|LIGAND= <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
<table><tr><td colspan='2'>[[2z8d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bifidobacterium_longum Bifidobacterium longum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z8D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z8D FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.85&#8491;</td></tr>
|GENE= gltA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=216816 Bifidobacterium longum])
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=2z8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z8d OCA], [https://pdbe.org/2z8d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z8d RCSB], [https://www.ebi.ac.uk/pdbsum/2z8d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z8d ProSAT]</span></td></tr>
|RELATEDENTRY=[[2z8e|2Z8E]], [[2z8f|2Z8F]]
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2z8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z8d OCA], [http://www.ebi.ac.uk/pdbsum/2z8d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2z8d RCSB]</span>
== Function ==
}}
[https://www.uniprot.org/uniprot/A8W790_BIFLN A8W790_BIFLN]
== 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/z8/2z8d_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=2z8d ConSurf].
<div style="clear:both"></div>


'''The galacto-N-biose-/lacto-N-biose I-binding protein (GL-BP) of the ABC transporter from Bifidobacterium longum in complex with lacto-N-biose'''
==See Also==
 
*[[ABC transporter 3D structures|ABC transporter 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
A recombinant galacto-N-biose-/lacto-N-biose I-binding protein (GL-BP) from Bifidobacterium longum JCM1217 has been prepared and crystallized by the hanging-drop vapour-diffusion method using 10 mg ml(-1) purified enzyme, 0.01 M zinc sulfate, 0.1 M MES buffer pH 5.9-6.4 and 20-22%(v/v) PEG MME 550 in the presence of 5 mM disaccharide ligands. Suitable crystals grew after 10 d incubation at 293 K. The crystals belong to space group C222(1), with unit-cell parameters a = 106.3, b = 143.6, c = 114.6 A for the lacto-N-biose I complex and a = 106.4, b = 143.4, c = 115.5 A for the galacto-N-biose complex, and diffracted to 1.85 and 1.99 A resolution, respectively.
 
==About this Structure==
2Z8D is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bifidobacterium_longum Bifidobacterium longum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z8D OCA].
 
==Reference==
Purification, crystallization and preliminary X-ray analysis of the galacto-N-biose-/lacto-N-biose I-binding protein (GL-BP) of the ABC transporter from Bifidobacterium longum JCM1217., Wada J, Suzuki R, Fushinobu S, Kitaoka M, Wakagi T, Shoun H, Ashida H, Kumagai H, Katayama T, Yamamoto K, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 Sep 1;63(Pt, 9):751-3. Epub 2007 Aug 10. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17768345 17768345]
[[Category: Bifidobacterium longum]]
[[Category: Bifidobacterium longum]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Fushinobu, S.]]
[[Category: Fushinobu S]]
[[Category: Katayama, T.]]
[[Category: Katayama T]]
[[Category: Suzuki, R.]]
[[Category: Suzuki R]]
[[Category: Wada, J.]]
[[Category: Wada J]]
[[Category: abc transporter]]
[[Category: human milk oligosacchalide]]
[[Category: mucin core-1]]
[[Category: sugar binding protein]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:19:22 2008''

Latest revision as of 16:56, 13 March 2024

The galacto-N-biose-/lacto-N-biose I-binding protein (GL-BP) of the ABC transporter from Bifidobacterium longum in complex with lacto-N-bioseThe galacto-N-biose-/lacto-N-biose I-binding protein (GL-BP) of the ABC transporter from Bifidobacterium longum in complex with lacto-N-biose

Structural highlights

2z8d is a 2 chain structure with sequence from Bifidobacterium longum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.85Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A8W790_BIFLN

Evolutionary Conservation

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

See Also

2z8d, resolution 1.85Å

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