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| - | [[Image:119d.jpg|left|200px]] | |
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| - | <!--
| + | ==CRYSTAL AND MOLECULAR STRUCTURE OF D(CGTAGATCTACG) AT 2.25 ANGSTROMS RESOLUTION== |
| - | The line below this paragraph, containing "STRUCTURE_119d", creates the "Structure Box" on the page.
| + | <StructureSection load='119d' size='340' side='right'caption='[[119d]], [[Resolution|resolution]] 2.25Å' scene=''> |
| - | You may change the PDB parameter (which sets the PDB file loaded into the applet)
| + | == Structural highlights == |
| - | or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| + | <table><tr><td colspan='2'>[[119d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=119D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=119D FirstGlance]. <br> |
| - | or leave the SCENE parameter empty for the default display.
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.25Å</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=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | {{STRUCTURE_119d| PDB=119d | SCENE= }}
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=119d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=119d OCA], [https://pdbe.org/119d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=119d RCSB], [https://www.ebi.ac.uk/pdbsum/119d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=119d ProSAT]</span></td></tr> |
| - | | + | </table> |
| - | '''CRYSTAL AND MOLECULAR STRUCTURE OF D(CGTAGATCTACG) AT 2.25 ANGSTROMS RESOLUTION'''
| + | __TOC__ |
| - | | + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | ==Overview==
| + | [[Category: Hunter WN]] |
| - | Single crystal X-ray diffraction methods have been used to determine the structure of the synthetic DNA dodecamer d(CGTAGATCTACG). The dodecamer presents a new crystal form of B-DNA in the monoclinic system, space group C2 with a = 64.83 A, b = 35.36 A, c = 25.35 A and beta = 92.24 degrees. Structure solution was by molecular replacement and the refinement used a combination of rigid body treatment, molecular dynamics simulated annealing and restrained least-squares methods. The refinement has been concluded with an R-factor of 13.8% for 2120 reflections (78% of what is theoretically available) with F > or = 2 sigma (F) in the resolution range 7.0 to 2.25 A. The asymmetric unit comprises a B-form duplex (24 nucleotides, molecular weight 7.2 kDa), 136.5 water molecules and a single magnesium ion at 50% occupancy. The DNA model has root-mean-square derivations from standard bond lengths of 0.011 A. The central part of the structure is d(GATC), a tetrad sequence involved in methylation and mismatch repair. A comparison with other structures containing such a tetrad indicates polymorphism at the tetrad level. In our structure a narrow minor groove with a pronounced hydration pattern is observed. Such features may be of importance in the recognition of the sequence by specific enzymes. A noteworthy feature of the hydration is the identification of several pentagonal arrangements of hydrogen bonding groups. Details of conformational parameters, base stacking patterns, intermolecular interactions and hydration are presented and comparisons with related structures are given.
| + | [[Category: Leonard GA]] |
| - | | + | |
| - | ==About this Structure== | + | |
| - | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=119D OCA]. | + | |
| - | | + | |
| - | ==Reference== | + | |
| - | Crystal and molecular structure of d(CGTAGATCTACG) at 2.25 A resolution., Leonard GA, Hunter WN, J Mol Biol. 1993 Nov 5;234(1):198-208. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8230199 8230199]
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| - | [[Category: Hunter, W N.]] | + | |
| - | [[Category: Leonard, G A.]] | + | |
| - | [[Category: B-dna]] | + | |
| - | [[Category: Double helix]] | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 09:27:08 2008''
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