This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

6irj

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Crystal structure of lysozyme by fixed-target serial femtosecond crystallography

Structural highlights

6irj is a 1 chain structure with sequence from Gallus gallus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.65Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[1]

Publication Abstract from PubMed

Fixed-target serial femtosecond crystallography (FT-SFX) was an important advance in crystallography by dramatically reducing sample consumption, while maintaining the benefits of SFX for obtaining crystal structures at room temperature without radiation damage. Despite a number of advantages, preparation of a sample holder for the sample delivery in FT-SFX with the use of many crystals in a single mount at ambient temperature is challenging as it can be complicated and costly, and thus, development of an efficient sample holder is essential. In this study, we introduced a nylon mesh-based sample holder enclosed by a polyimide film. This sample holder can be rapidly manufactured using a commercially available nylon mesh with pores of a desired size at a low cost without challenging technology. Furthermore, this simple device is highly efficient in data acquisition. We performed FT-SFX using a nylon mesh-based sample holder and collected over 130,000 images on a single sample holder using a 30 Hz X-ray pulse for 1.2 h. We determined the crystal structures of lysozyme and glucose isomerase using the nylon mesh at 1.65 and 1.75 A, respectively. The nylon mesh exposed to X-rays produced very low levels of background scattering at 3.75 and 4.30 A, which are negligible for data analysis. Our method provides a simple and rapid but highly efficient way to deliver samples for FT-SFX.

Nylon mesh-based sample holder for fixed-target serial femtosecond crystallography.,Lee D, Baek S, Park J, Lee K, Kim J, Lee SJ, Chung WK, Lee JL, Cho Y, Nam KH Sci Rep. 2019 May 6;9(1):6971. doi: 10.1038/s41598-019-43485-z. PMID:31061502^[2]

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

References

↑ Maehashi K, Matano M, Irisawa T, Uchino M, Kashiwagi Y, Watanabe T. Molecular characterization of goose- and chicken-type lysozymes in emu (Dromaius novaehollandiae): evidence for extremely low lysozyme levels in emu egg white. Gene. 2012 Jan 15;492(1):244-9. doi: 10.1016/j.gene.2011.10.021. Epub 2011 Oct, 25. PMID:22044478 doi:10.1016/j.gene.2011.10.021
↑ Lee D, Baek S, Park J, Lee K, Kim J, Lee SJ, Chung WK, Lee JL, Cho Y, Nam KH. Nylon mesh-based sample holder for fixed-target serial femtosecond crystallography. Sci Rep. 2019 May 6;9(1):6971. doi: 10.1038/s41598-019-43485-z. PMID:31061502 doi:http://dx.doi.org/10.1038/s41598-019-43485-z

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6irj"

Categories: Gallus gallus | Large Structures | Nam KH

@@ Line 3: / Line 3: @@
 <StructureSection load='6irj' size='340' side='right'caption='[[6irj]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6irj]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IRJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IRJ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6irj]] 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=6IRJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IRJ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.65&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></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=NA:SODIUM+ION'>NA</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6irj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6irj OCA], [http://pdbe.org/6irj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6irj RCSB], [http://www.ebi.ac.uk/pdbsum/6irj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6irj ProSAT]</span></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=6irj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6irj OCA], [https://pdbe.org/6irj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6irj RCSB], [https://www.ebi.ac.uk/pdbsum/6irj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6irj ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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>
+[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 ==
@@ Line 19: / Line 19: @@
 </div>
 <div class="pdbe-citations 6irj" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Lysozyme 3D structures|Lysozyme 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Gallus gallus]]
 [[Category: Large Structures]]
-[[Category: Lysozyme]]
+[[Category: Nam KH]]
-[[Category: Nam, K H]]
-[[Category: Hydrolase]]
-[[Category: Serial femtosecond crystallography]]
-[[Category: Sfx]]

6irj

From Proteopedia

Current revision

Crystal structure of lysozyme by fixed-target serial femtosecond crystallography

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox