- PDB-6neo: Crystal structure of PprA filament from Deinococcus radiodurans -
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Basic information
Entry
Database: PDB / ID: 6neo
Title
Crystal structure of PprA filament from Deinococcus radiodurans
Components
DNA repair protein PprA
Keywords
DNA BINDING PROTEIN / PROTEIN FIBRIL / DNA damage repair / Radiation induced / Genome segregation / Filament formation
Function / homology
cellular response to desiccation / positive regulation of DNA ligation / cellular response to gamma radiation / double-stranded DNA binding / damaged DNA binding / DNA repair / DNA repair protein PprA
Function and homology information
Biological species
Deinococcus radiodurans (radioresistant)
Method
X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 5.94 Å
Evidence: gel filtration, Purified PprA elutes from a gel filtration column at a broad distribution of retention volumes. The retention volume corresponds to an oligomeric size ranging from a ...Evidence: gel filtration, Purified PprA elutes from a gel filtration column at a broad distribution of retention volumes. The retention volume corresponds to an oligomeric size ranging from a tetramer to a 50-mer and larger., scanning transmission electron microscopy, In vitro, PprA exists as a long filament of varying length, as observed by TEM. This behavior is independent of Deinococcus species of origin., microscopy, In vivo, PprA forms a thin strand spanning the septum of dividing D. radiodurans cells. This was visualized by fluorescence microscopy., The repeating filament assembly present in the crystal has been observed in other crystal forms, despite different symmetries and crystal packing., Residues that are required for DNA binding all map to two distinct faces of this assembly.
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 4.55 Å3/Da / Density % sol: 72.96 % / Description: long hexagonal-base prism
Crystal grow
Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1:1 4.9 mg/mL protein in 150 mM potassium chloride, 20 mM Tris, pH 8.0 + Morpheus II-FX96 (Molecular Dimensions) condition H2 - 40 mM polyamines (spermine tetrahydrochloride, spermidine ...Details: 1:1 4.9 mg/mL protein in 150 mM potassium chloride, 20 mM Tris, pH 8.0 + Morpheus II-FX96 (Molecular Dimensions) condition H2 - 40 mM polyamines (spermine tetrahydrochloride, spermidine trihydrochloride, 1,4-diaminobutane dihydrochloride, DL-ornithine monohydrochloride), 50% v/v Precipitant Mix 6 (25% w/v PEG4000, 40% w/v 1,2,6-hexanetriol), 0.1 M Buffer System 4 (Gly-Gly, AMPD) at pH 6.5. The drop was suspended over a 1.5 M ammonium sulfate dehydrating solution and incubated at 20 degrees C for about 5 months. Temp details: Temperature-controlled incubator
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Data collection
Diffraction
Mean temperature: 100 K / Ambient temp details: Nitrogen gas cryostream / Serial crystal experiment: N
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