5lag: Difference between revisions

(3 intermediate revisions by the same user not shown)

Line 1:

~~'''Unreleased structure'''~~

~~The entry~~ 5lag is ~~ON HOLD until Paper~~ Publication

==Room temperature X-ray diffraction of tetragonal HEWL with 1M of uridine. Second data set (0.62 MGy)==

== Structural highlights ==

<table><tr><td colspan='2'>[[5lag]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LAG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LAG 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]] 1.6Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=5lag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lag OCA], [https://pdbe.org/5lag PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5lag RCSB], [https://www.ebi.ac.uk/pdbsum/5lag PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5lag ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/LYSC_CHICK LYSC_CHICK] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Has bacteriolytic activity against M.luteus.<ref>PMID:22044478</ref>

== Publication Abstract from PubMed ==

Macromolecular crystallography (MX) and small-angle X-ray scattering (SAXS) studies on proteins at synchrotron light sources are commonly limited by the structural damage produced by the intense X-ray beam. Several effects, such as aggregation in protein solutions and global and site-specific damage in crystals, reduce the data quality or even introduce artefacts that can result in a biologically misguiding structure. One strategy to reduce these negative effects is the inclusion of an additive in the buffer solution to act as a free radical scavenger. Here the properties of uridine as a scavenger for both SAXS and MX experiments on lysozyme at room temperature are examined. In MX experiments, upon addition of uridine at 1 M, the critical dose D1/2 is increased by a factor of approximately 1.7, a value similar to that obtained in the presence of the most commonly used scavengers such as ascorbate and sodium nitrate. Other figures of merit to assess radiation damage show a similar trend. In SAXS experiments, the scavenging effect of 40 mM uridine is similar to that of 5% v/v glycerol, and greater than 2 mM DTT and 1 mM ascorbic acid. In all cases, the protective effect of uridine is proportional to its concentration.

~~Authors:~~ Castellvi, A., Juanhuix, J.

Uridine as a new scavenger for synchrotron-based structural biology techniques.,Crosas E, Castellvi A, Crespo I, Fulla D, Gil-Ortiz F, Fuertes G, Kamma-Lorger CS, Malfois M, Aranda MA, Juanhuix J J Synchrotron Radiat. 2017 Jan 1;24(Pt 1):53-62. doi: 10.1107/S1600577516018452. , Epub 2017 Jan 1. PMID:28009546<ref>PMID:28009546</ref>

~~Description: Room temperature X-ray diffraction~~ of ~~tetragonal HEWL with 1M~~ of ~~uridine~~. ~~Second data set (0.62 MGy)~~

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

[[Category: ~~Unreleased Structures~~]]

</div>

[[Category: ~~Juanhuix, J~~]]

[[Category: Castellvi, A]]

== References ==

__TOC__

</StructureSection>

[[Category: Gallus gallus]]

[[Category: Large Structures]]

[[Category: Castellvi A]]

[[Category: Juanhuix J]]

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5lag is ON HOLD  until Paper Publication
+==Room temperature X-ray diffraction of tetragonal HEWL with 1M of uridine. Second data set (0.62 MGy)==
+<StructureSection load='5lag' size='340' side='right'caption='[[5lag]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5lag]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LAG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LAG 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]] 1.6&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=5lag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lag OCA], [https://pdbe.org/5lag PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5lag RCSB], [https://www.ebi.ac.uk/pdbsum/5lag PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5lag ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/LYSC_CHICK LYSC_CHICK] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Has bacteriolytic activity against M.luteus.<ref>PMID:22044478</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Macromolecular crystallography (MX) and small-angle X-ray scattering (SAXS) studies on proteins at synchrotron light sources are commonly limited by the structural damage produced by the intense X-ray beam. Several effects, such as aggregation in protein solutions and global and site-specific damage in crystals, reduce the data quality or even introduce artefacts that can result in a biologically misguiding structure. One strategy to reduce these negative effects is the inclusion of an additive in the buffer solution to act as a free radical scavenger. Here the properties of uridine as a scavenger for both SAXS and MX experiments on lysozyme at room temperature are examined. In MX experiments, upon addition of uridine at 1 M, the critical dose D1/2 is increased by a factor of approximately 1.7, a value similar to that obtained in the presence of the most commonly used scavengers such as ascorbate and sodium nitrate. Other figures of merit to assess radiation damage show a similar trend. In SAXS experiments, the scavenging effect of 40 mM uridine is similar to that of 5% v/v glycerol, and greater than 2 mM DTT and 1 mM ascorbic acid. In all cases, the protective effect of uridine is proportional to its concentration.
-Authors: Castellvi, A., Juanhuix, J.
+Uridine as a new scavenger for synchrotron-based structural biology techniques.,Crosas E, Castellvi A, Crespo I, Fulla D, Gil-Ortiz F, Fuertes G, Kamma-Lorger CS, Malfois M, Aranda MA, Juanhuix J J Synchrotron Radiat. 2017 Jan 1;24(Pt 1):53-62. doi: 10.1107/S1600577516018452. , Epub 2017 Jan 1. PMID:28009546<ref>PMID:28009546</ref>
-Description: Room temperature X-ray diffraction of tetragonal HEWL with 1M of uridine. Second data set (0.62 MGy)
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Juanhuix, J]]
+<div class="pdbe-citations 5lag" style="background-color:#fffaf0;"></div>
-[[Category: Castellvi, A]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Gallus gallus]]
+[[Category: Large Structures]]
+[[Category: Castellvi A]]
+[[Category: Juanhuix J]]