2npz: Difference between revisions
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|PDB= 2npz |SIZE=350|CAPTION= <scene name='initialview01'>2npz</scene>, resolution 3.35Å | |PDB= 2npz |SIZE=350|CAPTION= <scene name='initialview01'>2npz</scene>, resolution 3.35Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=NCO:COBALT+HEXAMMINE+ION'>NCO</scene> | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</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=DU:2'-DEOXYURIDINE-5'-MONOPHOSPHATE'>DU</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE+ION'>NCO</scene>, <scene name='pdbligand=PDI:PHOSPHORIC+ACID+MONO-(3-HYDROXY-PROPYL)+ESTER'>PDI</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY=[[1zfr|1ZFR]], [[2npy|2NPY]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2npz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2npz OCA], [http://www.ebi.ac.uk/pdbsum/2npz PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2npz RCSB]</span> | |||
}} | }} | ||
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[[Category: MacElrevey, C.]] | [[Category: MacElrevey, C.]] | ||
[[Category: Wedekind, J E.]] | [[Category: Wedekind, J E.]] | ||
[[Category: e loop]] | [[Category: e loop]] | ||
[[Category: hairpin]] | [[Category: hairpin]] | ||
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[[Category: s turn]] | [[Category: s turn]] | ||
''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 04:06:38 2008'' | ||
Revision as of 04:06, 31 March 2008
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| , resolution 3.35Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , , , , , | ||||||
| Related: | 1ZFR, 2NPY
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of junctioned hairpin ribozyme incorporating synthetic propyl linker
OverviewOverview
The hairpin ribozyme is a small catalytic RNA comprising two helix-loop-helix domains linked by a four-way helical junction (4WJ). In its most basic form, each domain can be formed independently and reconstituted without a 4WJ to yield an active enzyme. The production of such minimal junctionless hairpin ribozymes is achievable by chemical synthesis, which has allowed structures to be determined for numerous nucleotide variants. However, abasic and other destabilizing core modifications hinder crystallization. This investigation describes the use of a dangling 5'-U to form an intermolecular U.U mismatch, as well as the use of synthetic linkers to tether the loop A and B domains, including (i) a three-carbon propyl linker (C3L) and (ii) a nine-atom triethylene glycol linker (S9L). Both linker constructs demonstrated similar enzymatic activity, but S9L constructs yielded crystals that diffracted to 2.65 A resolution or better. In contrast, C3L variants diffracted to 3.35 A and exhibited a 15 A expansion of the c axis. Crystal packing of the C3L construct showed a paucity of 6(1) contacts, which comprise numerous backbone to 2'-OH hydrogen bonds in junctionless and S9L complexes. Significantly, the crystal packing in minimal structures mimics stabilizing features observed in the 4WJ hairpin ribozyme structure. The results demonstrate how knowledge-based design can be used to improve diffraction and overcome otherwise destabilizing defects.
About this StructureAbout this Structure
2NPZ is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
ReferenceReference
A posteriori design of crystal contacts to improve the X-ray diffraction properties of a small RNA enzyme., MacElrevey C, Spitale RC, Krucinska J, Wedekind JE, Acta Crystallogr D Biol Crystallogr. 2007 Jul;63(Pt 7):812-25. Epub 2007, Jun 15. PMID:17582172
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