1dyz

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:09, 6 December 2023) (edit) (undo)
 
(16 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1dyz.gif|left|200px]]<br /><applet load="1dyz" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1dyz, resolution 1.75&Aring;" />
 
-
'''OXIDISED AZURIN II FROM ALCALIGENES XYLOSOXIDANS'''<br />
 
-
==Overview==
+
==OXIDISED AZURIN II FROM ALCALIGENES XYLOSOXIDANS==
-
Crystallographic structures of oxidized and reduced forms of azurin II are, reported at 1.75 A resolution. Data were collected using one crystal in, each case and by translating the crystal after each oscillation range to, minimize photoreduction. Very small differences are observed at the Cu, site upon reduction and these cannot be determined with confidence at, current resolution. A comparison with the three-dimensional EXAFS reveals, a good correspondence for all the ligand distances except for Cu-His46, where a larger deviation of approximately 0.12-0.18 A is observed, indicating that this ligand is more tightly restrained in the, crystallographic refinement at the current resolution.
+
<StructureSection load='1dyz' size='340' side='right'caption='[[1dyz]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1dyz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Achromobacter_xylosoxidans Achromobacter xylosoxidans]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1arn 1arn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DYZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DYZ FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</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=1dyz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dyz OCA], [https://pdbe.org/1dyz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dyz RCSB], [https://www.ebi.ac.uk/pdbsum/1dyz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dyz ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/AZUR2_ALCXX AZUR2_ALCXX] Transfers electrons from cytochrome c551 to cytochrome oxidase.
 +
== 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/dy/1dyz_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=1dyz ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Crystallographic structures of oxidized and reduced forms of azurin II are reported at 1.75 A resolution. Data were collected using one crystal in each case and by translating the crystal after each oscillation range to minimize photoreduction. Very small differences are observed at the Cu site upon reduction and these cannot be determined with confidence at current resolution. A comparison with the three-dimensional EXAFS reveals a good correspondence for all the ligand distances except for Cu-His46, where a larger deviation of approximately 0.12-0.18 A is observed, indicating that this ligand is more tightly restrained in the crystallographic refinement at the current resolution.
-
==About this Structure==
+
Structures of oxidized and reduced azurin II from Alcaligenes xylosoxidans at 1.75 A resolution.,Dodd FE, Abraham ZH, Eady RR, Hasnain SS Acta Crystallogr D Biol Crystallogr. 2000 Jun;56(Pt 6):690-6. PMID:10818345<ref>PMID:10818345</ref>
-
1DYZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Achromobacter_xylosoxidans Achromobacter xylosoxidans] with <scene name='pdbligand=CU:'>CU</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. This structure superseeds the now removed PDB entry 1ARN. Known structural/functional Site: <scene name='pdbsite=CU1:Type+1+Cu+Site'>CU1</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DYZ OCA].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
Structures of oxidized and reduced azurin II from Alcaligenes xylosoxidans at 1.75 A resolution., Dodd FE, Abraham ZH, Eady RR, Hasnain SS, Acta Crystallogr D Biol Crystallogr. 2000 Jun;56(Pt 6):690-6. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10818345 10818345]
+
</div>
-
[[Category: Achromobacter xylosoxidans]]
+
<div class="pdbe-citations 1dyz" style="background-color:#fffaf0;"></div>
-
[[Category: Single protein]]
+
-
[[Category: Abraham, Z.H.L.]]
+
-
[[Category: Dodd, F.E.]]
+
-
[[Category: Eady, R.R.]]
+
-
[[Category: Hasnain, S.S.]]
+
-
[[Category: CU]]
+
-
[[Category: copper]]
+
-
[[Category: cupredoxin]]
+
-
[[Category: electron transport]]
+
-
[[Category: periplasmic]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb 3 09:36:08 2008''
+
==See Also==
 +
*[[Azurin 3D structures|Azurin 3D structures]]
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Achromobacter xylosoxidans]]
 +
[[Category: Large Structures]]
 +
[[Category: Abraham ZHL]]
 +
[[Category: Dodd FE]]
 +
[[Category: Eady RR]]
 +
[[Category: Hasnain SS]]

Current revision

OXIDISED AZURIN II FROM ALCALIGENES XYLOSOXIDANS

PDB ID 1dyz

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1dyz"
Personal tools