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| [[Image:123d.gif|left|200px]]
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| {{Structure
| | ==DNA HELIX STRUCTURE AND REFINEMENT ALGORITHM: COMPARISON OF MODELS FOR D(CCAGGCM==5==CTGG) DERIVED FROM NUCLSQ, TNT, AND X-PLOR== |
| |PDB= 123d |SIZE=350|CAPTION= <scene name='initialview01'>123d</scene>, resolution 1.700Å
| | <StructureSection load='123d' size='340' side='right'caption='[[123d]], [[Resolution|resolution]] 1.70Å' scene=''> |
| |SITE=
| | == Structural highlights == |
| |LIGAND= <scene name='pdbligand=5CM:5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE'>5CM</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>
| | <table><tr><td colspan='2'>[[123d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=123D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=123D 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]] 1.7Å</td></tr> |
| |GENE=
| | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</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=123d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=123d OCA], [https://pdbe.org/123d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=123d RCSB], [https://www.ebi.ac.uk/pdbsum/123d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=123d ProSAT]</span></td></tr> |
| |RELATEDENTRY=
| | </table> |
| |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=123d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=123d OCA], [http://www.ebi.ac.uk/pdbsum/123d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=123d RCSB]</span>
| | __TOC__ |
| }}
| | </StructureSection> |
| | | [[Category: Large Structures]] |
| '''DNA HELIX STRUCTURE AND REFINEMENT ALGORITHM: COMPARISON OF MODELS FOR D(CCAGGCM==5==CTGG) DERIVED FROM NUCLSQ, TNT, AND X-PLOR'''
| | [[Category: Hahn M]] |
| | | [[Category: Heinemann U]] |
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| ==Overview==
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| In an earlier study [Heinemann & Hahn (1992). J. Biol. Chem. 267, 7332-7341], the crystal structure of the double-stranded B-DNA decamer d(CCAGGCm(5)CTGG) was refined with NUCLSQ to R = 17.4% against 3799 2sigma structure amplitudes in the resolution range 8-1.7 A. This structure has now been re-refined against the same diffraction data using either TNT or X-PLOR in order to determine to what extent the resulting DNA conformations would differ and to examine the suitability of these programs for the refinement of oligonucleotide structures. The R value from the NUCLSQ refinement could not be reached with either TNT or X-PLOR, although both programs yield reasonably refined DNA models showing root-mean-square deviations against the NUCLSQ model of the decamer duplex of 0.25 and 0.32 A, respectively. Some derived local structure parameters differ depending on the refinement procedure used. This holds true for several exocyclic torsion angles of the sugar-phosphate backbone, whereas sugar puckers as well as helical and base-pair stacking parameters are only weakly influenced. A subset of 15 solvent sites with low temperature factors is conserved in all three models.
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| ==About this Structure==
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| 123D 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=123D OCA].
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| ==Reference==
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| DNA helix structure and refinement algorithm: comparison of models for d(CCAGGCm5CTGG) derived from NUCLSQ, TNT and X-PLOR., Hahn M, Heinemann U, Acta Crystallogr D Biol Crystallogr. 1993 Sep 1;49(Pt 5):468-77. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15299506 15299506]
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| [[Category: Protein complex]] | |
| [[Category: Hahn, M.]] | |
| [[Category: Heinemann, U.]] | |
| [[Category: b-dna]]
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| [[Category: double helix]]
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| [[Category: modified]]
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| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:27:13 2008''
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