- PDB-3uby: Crystal structure of human alklyadenine DNA glycosylase in a lowe... -
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基本情報
登録情報
データベース: PDB / ID: 3uby
タイトル
Crystal structure of human alklyadenine DNA glycosylase in a lower and higher-affinity complex with DNA
要素
DNA (5'-D(*GP*AP*CP*AP*TP*GP*(EDC)P*TP*TP*GP*CP*CP*T)-3')
DNA-3-methyladenine glycosylase
キーワード
HYDROLASE/DNA / alkyladenine DNA glycosylase fold / AAG / DNA repair / DNA binding / Nucleus / HYDROLASE-DNA complex
機能・相同性
機能・相同性情報
alkylbase DNA N-glycosylase activity / DNA-7-methyladenine glycosylase activity / DNA-3-methylguanine glycosylase activity / DNA-3-methyladenine glycosylase II / DNA-7-methylguanine glycosylase activity / DNA-3-methyladenine glycosylase activity / depurination / DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / DNA alkylation repair ...alkylbase DNA N-glycosylase activity / DNA-7-methyladenine glycosylase activity / DNA-3-methylguanine glycosylase activity / DNA-3-methyladenine glycosylase II / DNA-7-methylguanine glycosylase activity / DNA-3-methyladenine glycosylase activity / depurination / DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / DNA alkylation repair / mitochondrial nucleoid / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / base-excision repair / damaged DNA binding / nucleoplasm / cytosol 類似検索 - 分子機能
A: DNA-3-methyladenine glycosylase C: DNA (5'-D(*GP*AP*CP*AP*TP*GP*(EDC)P*TP*TP*GP*CP*CP*T)-3') D: DNA (5'-D(*GP*AP*CP*AP*TP*GP*(EDC)P*TP*TP*GP*CP*CP*T)-3')
温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 詳細: An equimolar ratio of delta79AAG and 13-mer single-stranded (ss) EDC DNA were mixed to form a protein-DNA complex concentration of 0.3 mM in the complex buffer (20 mM HEPES-NaOH, pH 7.5, 100 ...詳細: An equimolar ratio of delta79AAG and 13-mer single-stranded (ss) EDC DNA were mixed to form a protein-DNA complex concentration of 0.3 mM in the complex buffer (20 mM HEPES-NaOH, pH 7.5, 100 mM NaCl, 0.1 mM EDTA, 5% v/v glycerol and 1 mM DTT). The complex was incubated on ice for 15 min and used for crystallization. Crystals were obtained upon mixing 1 uL of protein-DNA complex and 1 uL of reservoir solution (100 mM BIS-TRIS, pH 5.5, 200 mM cesium chloride and 20% polyethylene glycol (PEG) 3350) over 0.5 ml of reservoir solution. Crystals appeared after incubation for 14 days at 22 degrees C, VAPOR DIFFUSION, HANGING DROP, temperature 298K
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データ収集
回折
平均測定温度: 100 K
放射光源
由来: シンクロトロン / サイト: ALS / ビームライン: 12.3.1 / 波長: 1.116 Å
検出器
タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2006年7月11日
放射
モノクロメーター: Double Crystal, Double Multilayer / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長
波長: 1.116 Å / 相対比: 1
反射
解像度: 2→66 Å / Num. all: 26998 / Num. obs: 26998 / % possible obs: 100 %
解像度: 2→65.65 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.904 / SU B: 12.087 / SU ML: 0.158 / 交差検証法: THROUGHOUT / ESU R Free: 0.208 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
反射数
%反射
Selection details
Rfree
0.26545
1375
5.1 %
RANDOM
Rwork
0.2194
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obs
0.22176
25556
92.12 %
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all
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26998
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溶媒の処理
イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.4 Å / 溶媒モデル: MASK