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.

2w1y

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 05:01, 19 November 2020

THE INTERDEPENDENCE OF WAVELENGTH, REDUNDANCY AND DOSE IN SULFUR SAD EXPERIMENTS: 1.540 A wavelength 180 images data

Structural highlights

2w1y 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.
Ligands:	,
Related:	1w6z, 1kxx, 3lyo, 4lyo, 1t6v, 1kip, 1vds, 1ic7, 1lzt, 1kir, 1lys, 1e8l, 1bwj, 132l, 1yil, 1heo, 1sfg, 1kxw, 2c8o, 1sf4, 1g7l, 1yl1, 1ior, 1h87, 3lyt, 1ljg, 1dpx, 1iot, 1v7s, 1ja6, 1jis, 1ir8, 2w1m, 1uic, 1ykz, 1xgq, 1uie, 1lji, 1lj3, 8lyz, 1dpw, 2iff, 2lyo, 1bwi, 1g7h, 1jj0, 1lks, 1rfp, 5lyt, 1jiy, 1sfb, 1iee, 1xei, 1ir7, 1hel, 1xek, 1at6, 1ljf, 1mlc, 2b5z, 1f10, 1lsz, 193l, 1ljk, 6lyt, 1sq2, 1zmy, 1vdq, 1lje, 2d91, 1b2k, 1lze, 1aki, 1uia, 1hen, 1yik, 1xfp, 2d6b, 1ndg, 1lpi, 1flw, 1lsd, 2blx, 6lyz, 1lsg, 1nbz, 4lyt, 1ved, 3hfm, 1jit, 1lzn, 1lyz, 1ja2, 1wtn, 1uuz, 2d4i, 2fbb, 1fdl, 2lym, 1lse, 1lzh, 1gxx, 1lz9, 1lsm, 3lym, 7lyz, 1jj3, 1yky, 1t3p, 1heq, 1kiq, 1kxy, 2lzh, 1uih, 2w1l, 2bly, 1b0d, 1g7j, 1her, 1bhz, 1wtm, 1nby, 1hep, 1ioq, 1jtt, 1qio, 1lza, 1xgp, 1ps5, 1gwd, 1v7t, 1jpo, 1h6m, 1dqj, 1j1p, 2a7d, 1ljj, 1z55, 2c8p, 1lsb, 1f0w, 1lzg, 1flq, 1lzc, 1jj1, 1rcm, 1uid, 1yqv, 1hsx, 1bgi, 1lcn, 1lzd, 1hew, 2vb1, 2cds, 2aub, 1hf4, 1uib, 2cgi, 1ios, 1rjc, 1ir9, 1j1x, 1uc0, 1azf, 1ic4, 1ljh, 4lyz, 1gpq, 2a6u, 2d4k, 1xej, 1ja7, 1mel, 1ri8, 1bvx, 1uig, 1qtk, 1c10, 1lkr, 1lyo, 1n4f, 1hsw, 1g7m, 1jto, 1sf7, 1lsf, 1fn5, 2d4j, 5lyz, 1c08, 3lzt, 1ndm, 1sf6, 3lyz, 1bvk, 1uif, 1vau, 2lyz, 1lma, 1fly, 1hc0, 1yl0, 1j1o, 2lzt, 1a2y, 4lzt, 1uco, 1lsy, 1lsa, 5lym, 1gxv, 1p2c, 1ic5, 1ua6, 1at5, 1vat, 1f3j, 1vfb, 1lj4, 1hem, 1ja4, 2a7f, 4lym, 194l, 1flu, 1lz8, 1ykx, 1bwh, 2hfm, 1vdt, 1io5, 1lsn, 1lzb, 1g7i, 2bpu, 1lsc, 1vdp, 2w1x
Activity:	Lysozyme, with EC number 3.2.1.17
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

In the last decade, the popularity of sulfur SAD anomalous dispersion experiments has spread rapidly among synchrotron users as a quick and streamlined way of solving the phase problem in macromolecular crystallography. On beamline 10 at SRS (Daresbury Laboratory, UK), a versatile design has allowed test data sets to be collected at six wavelengths between 0.979 and 2.290 A in order to evaluate the importance and the interdependence of experimental variables such as the Bijvoet ratio, wavelength, resolution limit, data redundancy and absorbed X-ray dose in the sample per data set. All the samples used in the experiments were high-quality hen egg-white lysozyme crystals. X-radiation damage was found to affect disulfide bridges after the crystals had been given a total dose of 0.20 x 10(7) Gy. However, with such a total dose, it was still possible in all cases to find a strategy to collect data sets to determine the sulfur substructure and produce good-quality phases by choosing an optimum combination of wavelength, exposure time and redundancy. A |Delta(ano)|/sigma(Delta(ano)) greater than 1.5 for all resolution shells was a necessary requirement for successful sulfur SAD substructure location. Provided this is achieved, it seems possible to find an optimum compromise between wavelength, redundancy and dose to provide phasing information. The choice of the wavelength should then follow the sample composition and the diffracting properties of the crystal. For strongly diffracting crystals, wavelengths equal or shorter than 1.540 A can be selected to capture the available data (provided the Bijvoet ratio is reasonable), while a longer wavelength, to gain as high a Bijvoet ratio as possible, must be used for more weakly diffracting crystals. These results suggest that an approach to a sulfur SAD experiment based on a complete description of the crystal system and the instrument for data collection is useful.

The interdependence of wavelength, redundancy and dose in sulfur SAD experiments.,Cianci M, Helliwell JR, Suzuki A Acta Crystallogr D Biol Crystallogr. 2008 Dec;64(Pt 12):1196-209. Epub, 2008 Nov 18. PMID:19018096^[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
↑ Cianci M, Helliwell JR, Suzuki A. The interdependence of wavelength, redundancy and dose in sulfur SAD experiments. Acta Crystallogr D Biol Crystallogr. 2008 Dec;64(Pt 12):1196-209. Epub, 2008 Nov 18. PMID:19018096 doi:10.1107/S0907444908030503

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/2w1y"

@@ Line 5: / Line 5: @@
 <table><tr><td colspan='2'>[[2w1y]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W1Y OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2W1Y FirstGlance]. <br>
 </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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1w6z|1w6z]], [[1kxx|1kxx]], [[3lyo|3lyo]], [[4lyo|4lyo]], [[1t6v|1t6v]], [[1kip|1kip]], [[1vds|1vds]], [[1ic7|1ic7]], [[1lzt|1lzt]], [[1kir|1kir]], [[1lys|1lys]], [[1e8l|1e8l]], [[1bwj|1bwj]], [[132l|132l]], [[1yil|1yil]], [[1heo|1heo]], [[1sfg|1sfg]], [[1kxw|1kxw]], [[2c8o|2c8o]], [[1sf4|1sf4]], [[1g7l|1g7l]], [[1yl1|1yl1]], [[1ior|1ior]], [[1h87|1h87]], [[3lyt|3lyt]], [[1ljg|1ljg]], [[1dpx|1dpx]], [[1iot|1iot]], [[1v7s|1v7s]], [[1ja6|1ja6]], [[1jis|1jis]], [[1ir8|1ir8]], [[2w1m|2w1m]], [[1uic|1uic]], [[1ykz|1ykz]], [[1xgq|1xgq]], [[1uie|1uie]], [[1lji|1lji]], [[1lj3|1lj3]], [[8lyz|8lyz]], [[1dpw|1dpw]], [[2iff|2iff]], [[2lyo|2lyo]], [[1bwi|1bwi]], [[1g7h|1g7h]], [[1jj0|1jj0]], [[1lks|1lks]], [[1rfp|1rfp]], [[5lyt|5lyt]], [[1jiy|1jiy]], [[1sfb|1sfb]], [[1iee|1iee]], [[1xei|1xei]], [[1ir7|1ir7]], [[1hel|1hel]], [[1xek|1xek]], [[1at6|1at6]], [[1ljf|1ljf]], [[1mlc|1mlc]], [[2b5z|2b5z]], [[1f10|1f10]], [[1lsz|1lsz]], [[193l|193l]], [[1ljk|1ljk]], [[6lyt|6lyt]], [[1sq2|1sq2]], [[1zmy|1zmy]], [[1vdq|1vdq]], [[1lje|1lje]], [[2d91|2d91]], [[1b2k|1b2k]], [[1lze|1lze]], [[1aki|1aki]], [[1uia|1uia]], [[1hen|1hen]], [[1yik|1yik]], [[1xfp|1xfp]], [[2d6b|2d6b]], [[1ndg|1ndg]], [[1lpi|1lpi]], [[1flw|1flw]], [[1lsd|1lsd]], [[2blx|2blx]], [[6lyz|6lyz]], [[1lsg|1lsg]], [[1nbz|1nbz]], [[4lyt|4lyt]], [[1ved|1ved]], [[3hfm|3hfm]], [[1jit|1jit]], [[1lzn|1lzn]], [[1lyz|1lyz]], [[1ja2|1ja2]], [[1wtn|1wtn]], [[1uuz|1uuz]], [[2d4i|2d4i]], [[2fbb|2fbb]], [[1fdl|1fdl]], [[2lym|2lym]], [[1lse|1lse]], [[1lzh|1lzh]], [[1gxx|1gxx]], [[1lz9|1lz9]], [[1lsm|1lsm]], [[3lym|3lym]], [[7lyz|7lyz]], [[1jj3|1jj3]], [[1yky|1yky]], [[1t3p|1t3p]], [[1heq|1heq]], [[1kiq|1kiq]], [[1kxy|1kxy]], [[2lzh|2lzh]], [[1uih|1uih]], [[2w1l|2w1l]], [[2bly|2bly]], [[1b0d|1b0d]], [[1g7j|1g7j]], [[1her|1her]], [[1bhz|1bhz]], [[1wtm|1wtm]], [[1nby|1nby]], [[1hep|1hep]], [[1ioq|1ioq]], [[1jtt|1jtt]], [[1qio|1qio]], [[1lza|1lza]], [[1xgp|1xgp]], [[1ps5|1ps5]], [[1gwd|1gwd]], [[1v7t|1v7t]], [[1jpo|1jpo]], [[1h6m|1h6m]], [[1dqj|1dqj]], [[1j1p|1j1p]], [[2a7d|2a7d]], [[1ljj|1ljj]], [[1z55|1z55]], [[2c8p|2c8p]], [[1lsb|1lsb]], [[1f0w|1f0w]], [[1lzg|1lzg]], [[1flq|1flq]], [[1lzc|1lzc]], [[1jj1|1jj1]], [[1rcm|1rcm]], [[1uid|1uid]], [[1yqv|1yqv]], [[1hsx|1hsx]], [[1bgi|1bgi]], [[1lcn|1lcn]], [[1lzd|1lzd]], [[1hew|1hew]], [[2vb1|2vb1]], [[2cds|2cds]], [[2aub|2aub]], [[1hf4|1hf4]], [[1uib|1uib]], [[2cgi|2cgi]], [[1ios|1ios]], [[1rjc|1rjc]], [[1ir9|1ir9]], [[1j1x|1j1x]], [[1uc0|1uc0]], [[1azf|1azf]], [[1ic4|1ic4]], [[1ljh|1ljh]], [[4lyz|4lyz]], [[1gpq|1gpq]], [[2a6u|2a6u]], [[2d4k|2d4k]], [[1xej|1xej]], [[1ja7|1ja7]], [[1mel|1mel]], [[1ri8|1ri8]], [[1bvx|1bvx]], [[1uig|1uig]], [[1qtk|1qtk]], [[1c10|1c10]], [[1lkr|1lkr]], [[1lyo|1lyo]], [[1n4f|1n4f]], [[1hsw|1hsw]], [[1g7m|1g7m]], [[1jto|1jto]], [[1sf7|1sf7]], [[1lsf|1lsf]], [[1fn5|1fn5]], [[2d4j|2d4j]], [[5lyz|5lyz]], [[1c08|1c08]], [[3lzt|3lzt]], [[1ndm|1ndm]], [[1sf6|1sf6]], [[3lyz|3lyz]], [[1bvk|1bvk]], [[1uif|1uif]], [[1vau|1vau]], [[2lyz|2lyz]], [[1lma|1lma]], [[1fly|1fly]], [[1hc0|1hc0]], [[1yl0|1yl0]], [[1j1o|1j1o]], [[2lzt|2lzt]], [[1a2y|1a2y]], [[4lzt|4lzt]], [[1uco|1uco]], [[1lsy|1lsy]], [[1lsa|1lsa]], [[5lym|5lym]], [[1gxv|1gxv]], [[1p2c|1p2c]], [[1ic5|1ic5]], [[1ua6|1ua6]], [[1at5|1at5]], [[1vat|1vat]], [[1f3j|1f3j]], [[1vfb|1vfb]], [[1lj4|1lj4]], [[1hem|1hem]], [[1ja4|1ja4]], [[2a7f|2a7f]], [[4lym|4lym]], [[194l|194l]], [[1flu|1flu]], [[1lz8|1lz8]], [[1ykx|1ykx]], [[1bwh|1bwh]], [[2hfm|2hfm]], [[1vdt|1vdt]], [[1io5|1io5]], [[1lsn|1lsn]], [[1lzb|1lzb]], [[1g7i|1g7i]], [[2bpu|2bpu]], [[1lsc|1lsc]], [[1vdp|1vdp]], [[2w1x|2w1x]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1w6z|1w6z]], [[1kxx|1kxx]], [[3lyo|3lyo]], [[4lyo|4lyo]], [[1t6v|1t6v]], [[1kip|1kip]], [[1vds|1vds]], [[1ic7|1ic7]], [[1lzt|1lzt]], [[1kir|1kir]], [[1lys|1lys]], [[1e8l|1e8l]], [[1bwj|1bwj]], [[132l|132l]], [[1yil|1yil]], [[1heo|1heo]], [[1sfg|1sfg]], [[1kxw|1kxw]], [[2c8o|2c8o]], [[1sf4|1sf4]], [[1g7l|1g7l]], [[1yl1|1yl1]], [[1ior|1ior]], [[1h87|1h87]], [[3lyt|3lyt]], [[1ljg|1ljg]], [[1dpx|1dpx]], [[1iot|1iot]], [[1v7s|1v7s]], [[1ja6|1ja6]], [[1jis|1jis]], [[1ir8|1ir8]], [[2w1m|2w1m]], [[1uic|1uic]], [[1ykz|1ykz]], [[1xgq|1xgq]], [[1uie|1uie]], [[1lji|1lji]], [[1lj3|1lj3]], [[8lyz|8lyz]], [[1dpw|1dpw]], [[2iff|2iff]], [[2lyo|2lyo]], [[1bwi|1bwi]], [[1g7h|1g7h]], [[1jj0|1jj0]], [[1lks|1lks]], [[1rfp|1rfp]], [[5lyt|5lyt]], [[1jiy|1jiy]], [[1sfb|1sfb]], [[1iee|1iee]], [[1xei|1xei]], [[1ir7|1ir7]], [[1hel|1hel]], [[1xek|1xek]], [[1at6|1at6]], [[1ljf|1ljf]], [[1mlc|1mlc]], [[2b5z|2b5z]], [[1f10|1f10]], [[1lsz|1lsz]], [[193l|193l]], [[1ljk|1ljk]], [[6lyt|6lyt]], [[1sq2|1sq2]], [[1zmy|1zmy]], [[1vdq|1vdq]], [[1lje|1lje]], [[2d91|2d91]], [[1b2k|1b2k]], [[1lze|1lze]], [[1aki|1aki]], [[1uia|1uia]], [[1hen|1hen]], [[1yik|1yik]], [[1xfp|1xfp]], [[2d6b|2d6b]], [[1ndg|1ndg]], [[1lpi|1lpi]], [[1flw|1flw]], [[1lsd|1lsd]], [[2blx|2blx]], [[6lyz|6lyz]], [[1lsg|1lsg]], [[1nbz|1nbz]], [[4lyt|4lyt]], [[1ved|1ved]], [[3hfm|3hfm]], [[1jit|1jit]], [[1lzn|1lzn]], [[1lyz|1lyz]], [[1ja2|1ja2]], [[1wtn|1wtn]], [[1uuz|1uuz]], [[2d4i|2d4i]], [[2fbb|2fbb]], [[1fdl|1fdl]], [[2lym|2lym]], [[1lse|1lse]], [[1lzh|1lzh]], [[1gxx|1gxx]], [[1lz9|1lz9]], [[1lsm|1lsm]], [[3lym|3lym]], [[7lyz|7lyz]], [[1jj3|1jj3]], [[1yky|1yky]], [[1t3p|1t3p]], [[1heq|1heq]], [[1kiq|1kiq]], [[1kxy|1kxy]], [[2lzh|2lzh]], [[1uih|1uih]], [[2w1l|2w1l]], [[2bly|2bly]], [[1b0d|1b0d]], [[1g7j|1g7j]], [[1her|1her]], [[1bhz|1bhz]], [[1wtm|1wtm]], [[1nby|1nby]], [[1hep|1hep]], [[1ioq|1ioq]], [[1jtt|1jtt]], [[1qio|1qio]], [[1lza|1lza]], [[1xgp|1xgp]], [[1ps5|1ps5]], [[1gwd|1gwd]], [[1v7t|1v7t]], [[1jpo|1jpo]], [[1h6m|1h6m]], [[1dqj|1dqj]], [[1j1p|1j1p]], [[2a7d|2a7d]], [[1ljj|1ljj]], [[1z55|1z55]], [[2c8p|2c8p]], [[1lsb|1lsb]], [[1f0w|1f0w]], [[1lzg|1lzg]], [[1flq|1flq]], [[1lzc|1lzc]], [[1jj1|1jj1]], [[1rcm|1rcm]], [[1uid|1uid]], [[1yqv|1yqv]], [[1hsx|1hsx]], [[1bgi|1bgi]], [[1lcn|1lcn]], [[1lzd|1lzd]], [[1hew|1hew]], [[2vb1|2vb1]], [[2cds|2cds]], [[2aub|2aub]], [[1hf4|1hf4]], [[1uib|1uib]], [[2cgi|2cgi]], [[1ios|1ios]], [[1rjc|1rjc]], [[1ir9|1ir9]], [[1j1x|1j1x]], [[1uc0|1uc0]], [[1azf|1azf]], [[1ic4|1ic4]], [[1ljh|1ljh]], [[4lyz|4lyz]], [[1gpq|1gpq]], [[2a6u|2a6u]], [[2d4k|2d4k]], [[1xej|1xej]], [[1ja7|1ja7]], [[1mel|1mel]], [[1ri8|1ri8]], [[1bvx|1bvx]], [[1uig|1uig]], [[1qtk|1qtk]], [[1c10|1c10]], [[1lkr|1lkr]], [[1lyo|1lyo]], [[1n4f|1n4f]], [[1hsw|1hsw]], [[1g7m|1g7m]], [[1jto|1jto]], [[1sf7|1sf7]], [[1lsf|1lsf]], [[1fn5|1fn5]], [[2d4j|2d4j]], [[5lyz|5lyz]], [[1c08|1c08]], [[3lzt|3lzt]], [[1ndm|1ndm]], [[1sf6|1sf6]], [[3lyz|3lyz]], [[1bvk|1bvk]], [[1uif|1uif]], [[1vau|1vau]], [[2lyz|2lyz]], [[1lma|1lma]], [[1fly|1fly]], [[1hc0|1hc0]], [[1yl0|1yl0]], [[1j1o|1j1o]], [[2lzt|2lzt]], [[1a2y|1a2y]], [[4lzt|4lzt]], [[1uco|1uco]], [[1lsy|1lsy]], [[1lsa|1lsa]], [[5lym|5lym]], [[1gxv|1gxv]], [[1p2c|1p2c]], [[1ic5|1ic5]], [[1ua6|1ua6]], [[1at5|1at5]], [[1vat|1vat]], [[1f3j|1f3j]], [[1vfb|1vfb]], [[1lj4|1lj4]], [[1hem|1hem]], [[1ja4|1ja4]], [[2a7f|2a7f]], [[4lym|4lym]], [[194l|194l]], [[1flu|1flu]], [[1lz8|1lz8]], [[1ykx|1ykx]], [[1bwh|1bwh]], [[2hfm|2hfm]], [[1vdt|1vdt]], [[1io5|1io5]], [[1lsn|1lsn]], [[1lzb|1lzb]], [[1g7i|1g7i]], [[2bpu|2bpu]], [[1lsc|1lsc]], [[1vdp|1vdp]], [[2w1x|2w1x]]</div></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2w1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w1y OCA], [http://pdbe.org/2w1y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2w1y RCSB], [http://www.ebi.ac.uk/pdbsum/2w1y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2w1y ProSAT]</span></td></tr>

2w1y

From Proteopedia

Revision as of 05:01, 19 November 2020

THE INTERDEPENDENCE OF WAVELENGTH, REDUNDANCY AND DOSE IN SULFUR SAD EXPERIMENTS: 1.540 A wavelength 180 images data

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