2r8w

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[[Image:2r8w.gif|left|200px]]<br /><applet load="2r8w" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2r8w, resolution 1.80&Aring;" />
 
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'''The crystal structure of dihydrodipicolinate synthase (Atu0899) from Agrobacterium tumefaciens str. C58'''<br />
 
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==Overview==
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==The crystal structure of dihydrodipicolinate synthase (Atu0899) from Agrobacterium tumefaciens str. C58==
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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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<StructureSection load='2r8w' size='340' side='right'caption='[[2r8w]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2r8w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_fabrum_str._C58 Agrobacterium fabrum str. C58]. 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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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
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<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>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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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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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q7D0E8_AGRFC Q7D0E8_AGRFC]
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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/initialview03.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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==About this Structure==
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==See Also==
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2R8W is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens_str._c58 Agrobacterium tumefaciens str. c58] with <scene name='pdbligand=ACT:'>ACT</scene> and <scene name='pdbligand=CL:'>CL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8W OCA].
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*[[Dihydrodipicolinate synthase|Dihydrodipicolinate synthase]]
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__TOC__
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==Reference==
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</StructureSection>
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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://ispc.weizmann.ac.il//pmbin/getpm?pmid=17982461 17982461]
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[[Category: Agrobacterium fabrum str. C58]]
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[[Category: Agrobacterium tumefaciens str. c58]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Dong A]]
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[[Category: Dong, A.]]
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[[Category: Edwards AM]]
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[[Category: Edwards, A M.]]
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[[Category: Gu J]]
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[[Category: Gu, J.]]
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[[Category: Joachimiak A]]
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[[Category: Joachimiak, A.]]
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[[Category: Savchenko A]]
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[[Category: MCSG, Midwest Center for Structural Genomics.]]
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[[Category: Tan K]]
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[[Category: Savchenko, A.]]
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[[Category: Xu X]]
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[[Category: Tan, K.]]
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[[Category: Zheng H]]
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[[Category: Xu, X.]]
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[[Category: Zheng, H.]]
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[[Category: ACT]]
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[[Category: CL]]
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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 genomics]]
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[[Category: protein structure initiative]]
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[[Category: psi-2]]
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[[Category: structural genomics]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:45:29 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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