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[[Image:1gox.jpg|left|200px]]


{{Structure
==REFINED STRUCTURE OF SPINACH GLYCOLATE OXIDASE AT 2 ANGSTROMS RESOLUTION==
|PDB= 1gox |SIZE=350|CAPTION= <scene name='initialview01'>1gox</scene>, resolution 2.0&Aring;
<StructureSection load='1gox' size='340' side='right'caption='[[1gox]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene> and <scene name='pdbligand=FMN:FLAVIN MONONUCLEOTIDE'>FMN</scene>
<table><tr><td colspan='2'>[[1gox]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GOX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GOX FirstGlance]. <br>
|ACTIVITY= [http://en.wikipedia.org/wiki/(S)-2-hydroxy-acid_oxidase (S)-2-hydroxy-acid oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.15 1.1.3.15]
</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&#8491;</td></tr>
|GENE=
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</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=1gox FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gox OCA], [https://pdbe.org/1gox PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gox RCSB], [https://www.ebi.ac.uk/pdbsum/1gox PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gox ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/GOX_SPIOL GOX_SPIOL]
== 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/go/1gox_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=1gox ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The amino acid sequence of glycolate oxidase from spinach has been fitted to an electron density map of 2.0 A nominal resolution and the structure has been refined using the restrained parameter least-squares refinement of Hendrickson and Konnert. A final crystallographic R-factor of 18.9% was obtained for 32,888 independent reflections from 5.5 to 2 A resolution. The geometry of the model, consisting of 350 amino acid residues, the cofactor flavin mononucleotide and 298 solvent molecules, is close to ideal with root-mean-square deviations of 0.015 A in bond lengths and 2.6 degrees in bond angles. The expected trimodal distribution with preference for staggered conformation is obtained for the side-chain chi 1-angles. The core of the subunit is built up from the eight beta-strands in the beta/alpha-barrel. This core consists of two hydrophobic layers. One in the center is made up of residues pointing in from the beta-strands towards the barrel axis and the second, consisting of two segments of residues, pointing out from the beta-strands towards the eight alpha-helices of the barrel and pointing from the helices towards the strands. The hydrogen bond pattern for the beta-strands in the beta/alpha-barrel is described. There are a number of residues with 3(10)-helix conformation, in particular there is one left-handed helix. The ordered solvent molecules are organized mainly in clusters. The average isotropic temperature factor is quite high, 27.1 A2, perhaps a reflection of the high solvent content in the crystal. The octameric glycolate oxidase molecule, which has 422 symmetry, makes strong interactions around the 4-fold axis forming a tight tetramer, but only weak interactions between the two tetramers forming the octamer.


'''REFINED STRUCTURE OF SPINACH GLYCOLATE OXIDASE AT 2 ANGSTROMS RESOLUTION'''
Refined structure of spinach glycolate oxidase at 2 A resolution.,Lindqvist Y J Mol Biol. 1989 Sep 5;209(1):151-66. PMID:2681790<ref>PMID:2681790</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1gox" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
The amino acid sequence of glycolate oxidase from spinach has been fitted to an electron density map of 2.0 A nominal resolution and the structure has been refined using the restrained parameter least-squares refinement of Hendrickson and Konnert. A final crystallographic R-factor of 18.9% was obtained for 32,888 independent reflections from 5.5 to 2 A resolution. The geometry of the model, consisting of 350 amino acid residues, the cofactor flavin mononucleotide and 298 solvent molecules, is close to ideal with root-mean-square deviations of 0.015 A in bond lengths and 2.6 degrees in bond angles. The expected trimodal distribution with preference for staggered conformation is obtained for the side-chain chi 1-angles. The core of the subunit is built up from the eight beta-strands in the beta/alpha-barrel. This core consists of two hydrophobic layers. One in the center is made up of residues pointing in from the beta-strands towards the barrel axis and the second, consisting of two segments of residues, pointing out from the beta-strands towards the eight alpha-helices of the barrel and pointing from the helices towards the strands. The hydrogen bond pattern for the beta-strands in the beta/alpha-barrel is described. There are a number of residues with 3(10)-helix conformation, in particular there is one left-handed helix. The ordered solvent molecules are organized mainly in clusters. The average isotropic temperature factor is quite high, 27.1 A2, perhaps a reflection of the high solvent content in the crystal. The octameric glycolate oxidase molecule, which has 422 symmetry, makes strong interactions around the 4-fold axis forming a tight tetramer, but only weak interactions between the two tetramers forming the octamer.
*[[Glycolate oxidase 3D structures|Glycolate oxidase 3D structures]]
 
== References ==
==About this Structure==
<references/>
1GOX is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GOX OCA].
__TOC__
 
</StructureSection>
==Reference==
[[Category: Large Structures]]
Refined structure of spinach glycolate oxidase at 2 A resolution., Lindqvist Y, J Mol Biol. 1989 Sep 5;209(1):151-66. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/2681790 2681790]
[[Category: (S)-2-hydroxy-acid oxidase]]
[[Category: Single protein]]
[[Category: Spinacia oleracea]]
[[Category: Spinacia oleracea]]
[[Category: Lindqvist, Y.]]
[[Category: Lindqvist Y]]
[[Category: ACE]]
[[Category: FMN]]
[[Category: oxidoreductase (oxygen(a))]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 11:26:01 2008''

Latest revision as of 03:01, 21 November 2024

REFINED STRUCTURE OF SPINACH GLYCOLATE OXIDASE AT 2 ANGSTROMS RESOLUTIONREFINED STRUCTURE OF SPINACH GLYCOLATE OXIDASE AT 2 ANGSTROMS RESOLUTION

Structural highlights

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

Function

GOX_SPIOL

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

The amino acid sequence of glycolate oxidase from spinach has been fitted to an electron density map of 2.0 A nominal resolution and the structure has been refined using the restrained parameter least-squares refinement of Hendrickson and Konnert. A final crystallographic R-factor of 18.9% was obtained for 32,888 independent reflections from 5.5 to 2 A resolution. The geometry of the model, consisting of 350 amino acid residues, the cofactor flavin mononucleotide and 298 solvent molecules, is close to ideal with root-mean-square deviations of 0.015 A in bond lengths and 2.6 degrees in bond angles. The expected trimodal distribution with preference for staggered conformation is obtained for the side-chain chi 1-angles. The core of the subunit is built up from the eight beta-strands in the beta/alpha-barrel. This core consists of two hydrophobic layers. One in the center is made up of residues pointing in from the beta-strands towards the barrel axis and the second, consisting of two segments of residues, pointing out from the beta-strands towards the eight alpha-helices of the barrel and pointing from the helices towards the strands. The hydrogen bond pattern for the beta-strands in the beta/alpha-barrel is described. There are a number of residues with 3(10)-helix conformation, in particular there is one left-handed helix. The ordered solvent molecules are organized mainly in clusters. The average isotropic temperature factor is quite high, 27.1 A2, perhaps a reflection of the high solvent content in the crystal. The octameric glycolate oxidase molecule, which has 422 symmetry, makes strong interactions around the 4-fold axis forming a tight tetramer, but only weak interactions between the two tetramers forming the octamer.

Refined structure of spinach glycolate oxidase at 2 A resolution.,Lindqvist Y J Mol Biol. 1989 Sep 5;209(1):151-66. PMID:2681790[1]

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

See Also

References

  1. ↑ Lindqvist Y. Refined structure of spinach glycolate oxidase at 2 A resolution. J Mol Biol. 1989 Sep 5;209(1):151-66. PMID:2681790

1gox, resolution 2.00Å

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