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2r8w

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[[Image:2r8w.gif|left|200px]]
 
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{{Structure
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==The crystal structure of dihydrodipicolinate synthase (Atu0899) from Agrobacterium tumefaciens str. C58==
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|PDB= 2r8w |SIZE=350|CAPTION= <scene name='initialview01'>2r8w</scene>, resolution 1.80&Aring;
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<StructureSection load='2r8w' size='340' side='right'caption='[[2r8w]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>
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<table><tr><td colspan='2'>[[2r8w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrfc Agrfc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R8W FirstGlance]. <br>
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|ACTIVITY=
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</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>
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|GENE= AGR_C_1641 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=176299 Agrobacterium tumefaciens str. C58])
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=COG0329 DapA], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd00408 DHDPS-like]</span>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AGR_C_1641 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=176299 AGRFC])</td></tr>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2r8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8w OCA], [http://www.ebi.ac.uk/pdbsum/2r8w PDBsum], [http://www.fli-leibniz.de/cgi-bin/ImgLib.pl?CODE=1kfv JenaLib], [http://www.rcsb.org/pdb/explore.do?structureId=2r8w RCSB]</span>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2r8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8w OCA], [https://pdbe.org/2r8w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r8w RCSB], [https://www.ebi.ac.uk/pdbsum/2r8w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r8w ProSAT], [https://www.topsan.org/Proteins/MCSG/2r8w TOPSAN]</span></td></tr>
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}}
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</table>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r8/2r8w_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2r8w ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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We tested the general applicability of in situ proteolysis to form protein crystals suitable for structure determination by adding a protease (chymotrypsin or trypsin) digestion step to crystallization trials of 55 bacterial and 14 human proteins that had proven recalcitrant to our best efforts at crystallization or structure determination. This is a work in progress; so far we determined structures of 9 bacterial proteins and the human aminoimidazole ribonucleotide synthetase (AIRS) domain.
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'''The crystal structure of dihydrodipicolinate synthase (Atu0899) from Agrobacterium tumefaciens str. C58'''
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In situ proteolysis for protein crystallization and structure determination.,Dong A, Xu X, Edwards AM, Chang C, Chruszcz M, Cuff M, Cymborowski M, Di Leo R, Egorova O, Evdokimova E, Filippova E, Gu J, Guthrie J, Ignatchenko A, Joachimiak A, Klostermann N, Kim Y, Korniyenko Y, Minor W, Que Q, Savchenko A, Skarina T, Tan K, Yakunin A, Yee A, Yim V, Zhang R, Zheng H, Akutsu M, Arrowsmith C, Avvakumov GV, Bochkarev A, Dahlgren LG, Dhe-Paganon S, Dimov S, Dombrovski L, Finerty P Jr, Flodin S, Flores A, Graslund S, Hammerstrom M, Herman MD, Hong BS, Hui R, Johansson I, Liu Y, Nilsson M, Nedyalkova L, Nordlund P, Nyman T, Min J, Ouyang H, Park HW, Qi C, Rabeh W, Shen L, Shen Y, Sukumard D, Tempel W, Tong Y, Tresagues L, Vedadi M, Walker JR, Weigelt J, Welin M, Wu H, Xiao T, Zeng H, Zhu H Nat Methods. 2007 Dec;4(12):1019-21. Epub 2007 Nov 4. PMID:17982461<ref>PMID:17982461</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2r8w" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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We tested the general applicability of in situ proteolysis to form protein crystals suitable for structure determination by adding a protease (chymotrypsin or trypsin) digestion step to crystallization trials of 55 bacterial and 14 human proteins that had proven recalcitrant to our best efforts at crystallization or structure determination. This is a work in progress; so far we determined structures of 9 bacterial proteins and the human aminoimidazole ribonucleotide synthetase (AIRS) domain.
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*[[Dihydrodipicolinate synthase|Dihydrodipicolinate synthase]]
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== References ==
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==About this Structure==
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<references/>
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2R8W is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens_str._c58 Agrobacterium tumefaciens str. c58]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8W OCA].
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__TOC__
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</StructureSection>
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==Reference==
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[[Category: Agrfc]]
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In situ proteolysis for protein crystallization and structure determination., Dong A, Xu X, Edwards AM, Chang C, Chruszcz M, Cuff M, Cymborowski M, Di Leo R, Egorova O, Evdokimova E, Filippova E, Gu J, Guthrie J, Ignatchenko A, Joachimiak A, Klostermann N, Kim Y, Korniyenko Y, Minor W, Que Q, Savchenko A, Skarina T, Tan K, Yakunin A, Yee A, Yim V, Zhang R, Zheng H, Akutsu M, Arrowsmith C, Avvakumov GV, Bochkarev A, Dahlgren LG, Dhe-Paganon S, Dimov S, Dombrovski L, Finerty P Jr, Flodin S, Flores A, Graslund S, Hammerstrom M, Herman MD, Hong BS, Hui R, Johansson I, Liu Y, Nilsson M, Nedyalkova L, Nordlund P, Nyman T, Min J, Ouyang H, Park HW, Qi C, Rabeh W, Shen L, Shen Y, Sukumard D, Tempel W, Tong Y, Tresagues L, Vedadi M, Walker JR, Weigelt J, Welin M, Wu H, Xiao T, Zeng H, Zhu H, Nat Methods. 2007 Dec;4(12):1019-21. Epub 2007 Nov 4. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17982461 17982461]
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[[Category: Large Structures]]
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[[Category: Dong, A]]
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[[Category: Edwards, A M]]
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[[Category: Gu, J]]
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[[Category: Joachimiak, A]]
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[[Category: Structural genomic]]
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[[Category: Savchenko, A]]
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[[Category: Tan, K]]
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[[Category: Xu, X]]
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[[Category: Zheng, H]]
[[Category: Agrobacterium tumefaciens str. c58]]
[[Category: Agrobacterium tumefaciens str. c58]]
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[[Category: Single protein]]
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[[Category: Apc7498]]
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[[Category: Dong, A.]]
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[[Category: Dihydrodipicolinate synthase]]
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[[Category: Edwards, A M.]]
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[[Category: Lyase]]
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[[Category: Gu, J.]]
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[[Category: Mcsg]]
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[[Category: Joachimiak, A.]]
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[[Category: PSI, Protein structure initiative]]
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[[Category: MCSG, Midwest Center for Structural Genomics.]]
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[[Category: Savchenko, A.]]
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[[Category: Tan, K.]]
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[[Category: Xu, X.]]
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[[Category: Zheng, H.]]
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[[Category: agrobacterium tumefaciens str. c58]]
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[[Category: apc7498]]
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[[Category: dihydrodipicolinate synthase]]
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[[Category: lyase]]
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[[Category: mcsg]]
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[[Category: midwest center for structural genomic]]
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[[Category: protein structure initiative]]
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[[Category: psi-2]]
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[[Category: structural genomic]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 26 06:45:33 2008''
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Current revision

The crystal structure of dihydrodipicolinate synthase (Atu0899) from Agrobacterium tumefaciens str. C58

PDB ID 2r8w

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