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| - | [[Image:1zf7.gif|left|200px]] | |
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| - | {{Structure
| + | ==GAC Duplex B-DNA== |
| - | |PDB= 1zf7 |SIZE=350|CAPTION= <scene name='initialview01'>1zf7</scene>, resolution 1.05Å
| + | <StructureSection load='1zf7' size='340' side='right'caption='[[1zf7]], [[Resolution|resolution]] 1.05Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>
| + | <table><tr><td colspan='2'>[[1zf7]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZF7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZF7 FirstGlance]. <br> |
| - | |ACTIVITY=
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.05Å</td></tr> |
| - | |GENE=
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> |
| - | |DOMAIN=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1zf7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zf7 OCA], [https://pdbe.org/1zf7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zf7 RCSB], [https://www.ebi.ac.uk/pdbsum/1zf7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zf7 ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=[[1p4y|1P4Y]], [[1p4z|1P4Z]], [[1dcw|1DCW]], [[1dcv|1DCV]], [[1zew|1ZEW]], [[1zex|1ZEX]], [[1zey|1ZEY]], [[1zez|1ZEZ]], [[1zf0|1ZF0]], [[1zf1|1ZF1]], [[1zf2|1ZF2]], [[1zf3|1ZF3]], [[1zf4|1ZF4]], [[1zf5|1ZF5]], [[1zf6|1ZF6]], [[1zf8|1ZF8]], [[1zf9|1ZF9]], [[1zfa|1ZFA]], [[1zfb|1ZFB]], [[1zfc|1ZFC]], [[1zfe|1ZFE]], [[1zff|1ZFF]], [[1zfg|1ZFG]], [[1zfh|1ZFH]], [[1zfm|1ZFM]]
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1zf7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zf7 OCA], [http://www.ebi.ac.uk/pdbsum/1zf7 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1zf7 RCSB]</span>
| + | __TOC__ |
| - | }}
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | '''GAC Duplex B-DNA'''
| + | [[Category: Cavaliere E]] |
| - | | + | [[Category: Harms M]] |
| - | | + | [[Category: Hays FA]] |
| - | ==Overview==
| + | [[Category: Ho PS]] |
| - | The fundamental question of how sequence defines conformation is explicitly answered if the structures of all possible sequences of a macromolecule are determined. We present here a crystallographic screen of all permutations of the inverted repeat DNA sequence d(CCnnnN6N7N8GG), where N6, N7, and N8 are any of the four naturally occurring nucleotides. At this point, 63 of the 64 possible permutations have been crystallized from a defined set of solutions. When combined with previous work, we have assembled a data set of 37 single-crystal structures from 29 of the sequences in this motif, representing three structural classes of DNA (B-DNA, A-DNA, and four-stranded Holliday junctions). This data set includes a unique set of amphimorphic sequence, those that crystallize in two different conformations and serve to bridge the three structural phases. We have thus constructed a map of DNA structures that can be walked through in single nucleotide steps. Finally, the resulting data set allows us to dissect in detail the stabilization of and conformational variations within structural classes and identify significant conformational deviations within a particular structural class that result from sequence rather than crystal or crystallization effects.
| + | [[Category: Jones ZJR]] |
| - | | + | [[Category: Raup D]] |
| - | ==About this Structure==
| + | [[Category: Teegarden AT]] |
| - | 1ZF7 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZF7 OCA].
| + | [[Category: Watson J]] |
| - | | + | |
| - | ==Reference==
| + | |
| - | How sequence defines structure: a crystallographic map of DNA structure and conformation., Hays FA, Teegarden A, Jones ZJ, Harms M, Raup D, Watson J, Cavaliere E, Ho PS, Proc Natl Acad Sci U S A. 2005 May 17;102(20):7157-62. Epub 2005 May 3. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15870206 15870206]
| + | |
| - | [[Category: Protein complex]] | + | |
| - | [[Category: Cavaliere, E.]] | + | |
| - | [[Category: Harms, M.]] | + | |
| - | [[Category: Hays, F A.]] | + | |
| - | [[Category: Ho, P S.]] | + | |
| - | [[Category: Jones, Z J.R.]] | + | |
| - | [[Category: Raup, D.]] | + | |
| - | [[Category: Teegarden, A T.]] | + | |
| - | [[Category: Watson, J.]] | + | |
| - | [[Category: crystallographic screen]]
| + | |
| - | [[Category: dna structure]]
| + | |
| - | [[Category: holliday junction]]
| + | |
| - | [[Category: molecular structure]]
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| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:35:08 2008''
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