1vro
From Proteopedia
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|PDB= 1vro |SIZE=350|CAPTION= <scene name='initialview01'>1vro</scene>, resolution 1.10Å | |PDB= 1vro |SIZE=350|CAPTION= <scene name='initialview01'>1vro</scene>, resolution 1.10Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=GMS:2'-DEOXYGUANOSINE-5'-MONOSELENOPHOSPHATE'>GMS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1vro FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vro OCA], [http://www.ebi.ac.uk/pdbsum/1vro PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1vro RCSB]</span> | ||
}} | }} | ||
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[[Category: Wawrzak, Z.]] | [[Category: Wawrzak, Z.]] | ||
[[Category: Wilds, C J.]] | [[Category: Wilds, C J.]] | ||
| - | [[Category: MG]] | ||
| - | [[Category: SPM]] | ||
[[Category: covalent modification of oligonucleotide]] | [[Category: covalent modification of oligonucleotide]] | ||
[[Category: left-handed z-dna]] | [[Category: left-handed z-dna]] | ||
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[[Category: synchrotron]] | [[Category: synchrotron]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:27:45 2008'' |
Revision as of 21:27, 30 March 2008
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| , resolution 1.10Å | |||||||
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| Ligands: | , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Selenium-Assisted Nucleic Acid Crystallography: Use of Phosphoroselenoates for MAD Phasing of a DNA Structure
Overview
The combination of synchrotron radiation and a variety of atoms or ions (either covalently attached to the biomolecule prior to crystallization or soaked into crystals) that serve as anomalous scatterers constitutes a powerful tool in the X-ray crystallographer's repertoire of structure determination techniques. Phosphoroselenoates in which one of the nonbridging phosphate oxygens in the backbone is replaced by selenium offer a simplified means for introducing an anomalous scatterer into oligonucleotides by conventional solid-phase synthesis. Unlike other methods that are used to derivatize DNA or RNA by covalent attachment of a heavy atom (i.e., bromine at the C5 position of pyrimidines), tedious synthesis of specialized nucleosides is not required. Introduction of selenium is readily accomplished in solid-phase oligonucleotide synthesis by replacing the standard oxidation agent with a solution of potassium selenocyanide. This results in a diastereomeric mixture of phosphoroselenoates that can be separated by strong anion-exchange HPLC. As a test case, all 10 DNA hexamers of the sequence CGCGCG containing a single phosphoroselenoate linkage (PSe) were prepared. Crystals were grown for a subset of them, and the structure of [d(C(PSe)GCGCG)](2) was determined by the multiwavelength anomalous dispersion technique and refined to 1.1 A resolution.
About this Structure
1VRO is a Protein complex structure of sequences from [1]. This structure supersedes the now removed PDB entry 1N6S. Full crystallographic information is available from OCA.
Reference
Selenium-assisted nucleic acid crystallography: use of phosphoroselenoates for MAD phasing of a DNA structure., Wilds CJ, Pattanayek R, Pan C, Wawrzak Z, Egli M, J Am Chem Soc. 2002 Dec 18;124(50):14910-6. PMID:12475332
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