2vb1: Difference between revisions

Revision as of 18:31, 4 May 2008

HEWL AT 0.65 ANGSTROM RESOLUTION

OverviewOverview

The crystal structure of triclinic hen egg-white lysozyme (HEWL) has been refined against diffraction data extending to 0.65 A resolution measured at 100 K using synchrotron radiation. Refinement with anisotropic displacement parameters and with the removal of stereochemical restraints for the well ordered parts of the structure converged with a conventional R factor of 8.39% and an R(free) of 9.52%. The use of full-matrix refinement provided an estimate of the variances in the derived parameters. In addition to the 129-residue protein, a total of 170 water molecules, nine nitrate ions, one acetate ion and three ethylene glycol molecules were located in the electron-density map. Eight sections of the main chain and many side chains were modeled with alternate conformations. The occupancies of the water sites were refined and this step is meaningful when assessed by use of the free R factor. A detailed description and comparison of the structure are made with reference to the previously reported triclinic HEWL structures refined at 0.925 A (at the low temperature of 120 K) and at 0.95 A resolution (at room temperature).

About this StructureAbout this Structure

2VB1 is a Single protein structure of sequence from Gallus gallus. Full crystallographic information is available from OCA.

ReferenceReference

Triclinic lysozyme at 0.65 A resolution., Wang J, Dauter M, Alkire R, Joachimiak A, Dauter Z, Acta Crystallogr D Biol Crystallogr. 2007 Dec;63(Pt 12):1254-68. Epub 2007, Nov 16. PMID:18084073 Page seeded by OCA on Sun May 4 18:31:25 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
 [[Image:2vb1.jpg|left|200px]]
- {{Structure
+<!--
-|PDB= 2vb1 |SIZE=350|CAPTION= <scene name='initialview01'>2vb1</scene>, resolution 0.65&Aring;
+The line below this paragraph, containing "STRUCTURE_2vb1", creates the "Structure Box" on the page.
-|SITE= <scene name='pdbsite=AC1:Act+Binding+Site+For+Chain+A'>AC1</scene>, <scene name='pdbsite=AC2:Edo+Binding+Site+For+Chain+A'>AC2</scene>, <scene name='pdbsite=AC3:Edo+Binding+Site+For+Chain+A'>AC3</scene>, <scene name='pdbsite=AC4:Edo+Binding+Site+For+Chain+A'>AC4</scene>, <scene name='pdbsite=AC5:No3+Binding+Site+For+Chain+A'>AC5</scene>, <scene name='pdbsite=AC6:No3+Binding+Site+For+Chain+A'>AC6</scene>, <scene name='pdbsite=AC7:No3+Binding+Site+For+Chain+A'>AC7</scene>, <scene name='pdbsite=AC8:No3+Binding+Site+For+Chain+A'>AC8</scene>, <scene name='pdbsite=AC9:No3+Binding+Site+For+Chain+A'>AC9</scene>, <scene name='pdbsite=BC1:No3+Binding+Site+For+Chain+A'>BC1</scene>, <scene name='pdbsite=BC2:No3+Binding+Site+For+Chain+A'>BC2</scene>, <scene name='pdbsite=BC3:No3+Binding+Site+For+Chain+A'>BC3</scene> and <scene name='pdbsite=BC4:No3+Binding+Site+For+Chain+A'>BC4</scene>
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY= <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>
+or leave the SCENE parameter empty for the default display.
-|GENE=
+-->
-|DOMAIN=
+{{STRUCTURE_2vb1|  PDB=2vb1  |  SCENE=  }}
-|RELATEDENTRY=[[1aki|1AKI]], [[1azf|1AZF]], [[1b2k|1B2K]], [[1bgi|1BGI]], [[1bvx|1BVX]], [[1bwj|1BWJ]], [[1c10|1C10]], [[1dpw|1DPW]], [[1dqj|1DQJ]], [[1f0w|1F0W]], [[1f10|1F10]], [[1fdl|1FDL]], [[1flq|1FLQ]], [[1flu|1FLU]], [[1flw|1FLW]], [[1fn5|1FN5]], [[1g7i|1G7I]], [[1g7l|1G7L]], [[1gwd|1GWD]], [[1gxv|1GXV]], [[1h6m|1H6M]], [[1hc0|1HC0]], [[1hel|1HEL]], [[1hen|1HEN]], [[1heo|1HEO]], [[132l|132L]], [[193l|193L]], [[194l|194L]], [[1a2y|1A2Y]], [[1at5|1AT5]], [[1at6|1AT6]], [[1b0d|1B0D]], [[1bhz|1BHZ]], [[1bvk|1BVK]], [[1bwh|1BWH]], [[1bwi|1BWI]], [[1c08|1C08]], [[1dpx|1DPX]], [[1e8l|1E8L]], [[1f3j|1F3J]], [[1fly|1FLY]], [[1g7h|1G7H]], [[1g7j|1G7J]], [[1g7m|1G7M]], [[1gpq|1GPQ]], [[1gxx|1GXX]], [[1h87|1H87]], [[1hem|1HEM]], [[1heq|1HEQ]], [[1her|1HER]], [[1hsw|1HSW]], [[1hep|1HEP]], [[1hew|1HEW]], [[1hf4|1HF4]], [[1ic4|1IC4]], [[1ic5|1IC5]], [[1ic7|1IC7]], [[1iee|1IEE]], [[1io5|1IO5]], [[1ioq|1IOQ]], [[1ios|1IOS]], [[1iot|1IOT]], [[1ir7|1IR7]], [[1ir9|1IR9]], [[1j1x|1J1X]], [[1ja2|1JA2]], [[1ja6|1JA6]], [[1jis|1JIS]], [[1jit|1JIT]], [[1jj0|1JJ0]], [[1jj1|1JJ1]], [[1jj3|1JJ3]], [[1kip|1KIP]], [[1kir|1KIR]], [[1lcn|1LCN]], [[1hsx|1HSX]], [[1ior|1IOR]], [[1ir8|1IR8]], [[1j1o|1J1O]], [[1j1p|1J1P]], [[1ja4|1JA4]], [[1ja7|1JA7]], [[1jiy|1JIY]], [[1jpo|1JPO]], [[1jto|1JTO]], [[1jtt|1JTT]], [[1kiq|1KIQ]], [[1kxw|1KXW]], [[1kxx|1KXX]], [[1kxy|1KXY]], [[1lj3|1LJ3]], [[1lj4|1LJ4]], [[1ljf|1LJF]], [[1ljh|1LJH]], [[1ljj|1LJJ]], [[1ljk|1LJK]], [[1lkr|1LKR]], [[1lks|1LKS]], [[1lpi|1LPI]], [[1lsa|1LSA]], [[1lse|1LSE]], [[1lje|1LJE]], [[1ljg|1LJG]], [[1lji|1LJI]], [[1lma|1LMA]], [[1lsb|1LSB]], [[1lsc|1LSC]], [[1lsd|1LSD]], [[1lsf|1LSF]], [[1lsm|1LSM]], [[1lsn|1LSN]], [[1lsy|1LSY]], [[1lys|1LYS]], [[1lz9|1LZ9]], [[1lzc|1LZC]], [[1lze|1LZE]], [[1lzg|1LZG]], [[1lzh|1LZH]], [[1mel|1MEL]], [[1n4f|1N4F]], [[1nby|1NBY]], [[1ndg|1NDG]], [[1qio|1QIO]], [[1ri8|1RI8]], [[1rjc|1RJC]], [[1sf6|1SF6]], [[1sfg|1SFG]], [[1lsg|1LSG]], [[1lsz|1LSZ]], [[1lyo|1LYO]], [[1lyz|1LYZ]], [[1lz8|1LZ8]], [[1lza|1LZA]], [[1lzb|1LZB]], [[1lzd|1LZD]], [[1lzn|1LZN]], [[1lzt|1LZT]], [[1mlc|1MLC]], [[1nbz|1NBZ]], [[1ndm|1NDM]], [[1p2c|1P2C]], [[1ps5|1PS5]], [[1qtk|1QTK]], [[1rcm|1RCM]], [[1rfp|1RFP]], [[1sf4|1SF4]], [[1sf7|1SF7]], [[1sfb|1SFB]], [[1sq2|1SQ2]], [[1t3p|1T3P]], [[1t6v|1T6V]], [[1ua6|1UA6]], [[1uc0|1UC0]], [[1uco|1UCO]], [[1uib|1UIB]], [[1uif|1UIF]], [[1vat|1VAT]], [[1vdp|1VDP]], [[1vds|1VDS]], [[1vdt|1VDT]], [[1ved|1VED]], [[1vfb|1VFB]], [[1w6z|1W6Z]], [[1wtm|1WTM]], [[1wtn|1WTN]], [[1xej|1XEJ]], [[1xgq|1XGQ]], [[1yik|1YIK]], [[1ykx|1YKX]], [[1yl0|1YL0]], [[1yqv|1YQV]], [[1zmy|1ZMY]], [[2aub|2AUB]], [[2bly|2BLY]], [[2bpu|2BPU]], [[1uia|1UIA]], [[1uic|1UIC]], [[1uid|1UID]], [[1uie|1UIE]], [[1uig|1UIG]], [[1uih|1UIH]], [[1uuz|1UUZ]], [[1v7s|1V7S]], [[1v7t|1V7T]], [[1vau|1VAU]], [[1vdq|1VDQ]], [[1xei|1XEI]], [[1xek|1XEK]], [[1xfp|1XFP]], [[1xgp|1XGP]], [[1yil|1YIL]], [[1yky|1YKY]], [[1ykz|1YKZ]], [[1yl1|1YL1]], [[1z55|1Z55]], [[2a6u|2A6U]], [[2a7d|2A7D]], [[2a7f|2A7F]], [[2b5z|2B5Z]], [[2blx|2BLX]], [[2c8o|2C8O]], [[2c8p|2C8P]], [[2cds|2CDS]], [[2d4i|2D4I]], [[2d6b|2D6B]], [[2d91|2D91]], [[2lyo|2LYO]], [[3hfm|3HFM]], [[3lyt|3LYT]], [[3lyz|3LYZ]], [[4lyo|4LYO]], [[5lyz|5LYZ]], [[6lyt|6LYT]], [[6lyz|6LYZ]], [[7lyz|7LYZ]], [[8lyz|8LYZ]], [[2cgi|2CGI]], [[2d4j|2D4J]], [[2d4k|2D4K]], [[2fbb|2FBB]], [[2hfm|2HFM]], [[2iff|2IFF]], [[2lym|2LYM]], [[2lyz|2LYZ]], [[2lzh|2LZH]], [[2lzt|2LZT]], [[3lym|3LYM]], [[3lyo|3LYO]], [[3lzt|3LZT]], [[4lym|4LYM]], [[4lyt|4LYT]], [[4lyz|4LYZ]], [[4lzt|4LZT]], [[5lym|5LYM]], [[5lyt|5LYT]]
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2vb1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vb1 OCA], [http://www.ebi.ac.uk/pdbsum/2vb1 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2vb1 RCSB]</span>
-}}
 '''HEWL AT 0.65 ANGSTROM RESOLUTION'''
@@ Line 31: / Line 28: @@
 [[Category: Joachimiak, A.]]
 [[Category: Wang, J.]]
-[[Category: allergen]]
+[[Category: Allergen]]
-[[Category: antimicrobial]]
+[[Category: Antimicrobial]]
-[[Category: atomic resolution]]
+[[Category: Atomic resolution]]
-[[Category: bacteriolytic enzyme]]
+[[Category: Bacteriolytic enzyme]]
-[[Category: glycosidase]]
+[[Category: Glycosidase]]
-[[Category: hydrolase]]
+[[Category: Hydrolase]]
-[[Category: lysozyme]]
+[[Category: Lysozyme]]
-[[Category: triclinic hewl]]
+[[Category: Triclinic hewl]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 18:31:25 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:10:35 2008''