- PDB-4fxd: Crystal structure of yeast DNA polymerase alpha bound to DNA/RNA -
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基本情報
登録情報
データベース: PDB / ID: 4fxd
タイトル
Crystal structure of yeast DNA polymerase alpha bound to DNA/RNA
要素
DNA (5'-D(*TP*TP*TP*TP*CP*GP*CP*TP*GP*CP*CP*CP*GP*CP*CP*T)-3')
DNA polymerase alpha catalytic subunit A
RNA (5'-R(*AP*GP*GP*CP*GP*GP*GP*CP*AP*G)-3')
キーワード
TRANSFERASE/DNA/RNA / DNA polymerase / DNA replication / TRANSFERASE-DNA-RNA complex
機能・相同性
機能・相同性情報
Inhibition of replication initiation of damaged DNA by RB1/E2F1 / RNA-templated DNA biosynthetic process / DNA replication initiation / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching / premeiotic DNA replication / alpha DNA polymerase:primase complex / Activation of the pre-replicative complex / lagging strand elongation ...Inhibition of replication initiation of damaged DNA by RB1/E2F1 / RNA-templated DNA biosynthetic process / DNA replication initiation / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching / premeiotic DNA replication / alpha DNA polymerase:primase complex / Activation of the pre-replicative complex / lagging strand elongation / mitotic DNA replication initiation / DNA synthesis involved in DNA repair / leading strand elongation / DNA replication origin binding / DNA replication initiation / replication fork / double-strand break repair / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / chromatin binding / mitochondrion / metal ion binding 類似検索 - 分子機能
B family DNA polymerase, thumb domain, four helix bundle / Helicase, Ruva Protein; domain 3 - #100 / Alpha-Beta Plaits - #2820 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #730 / B family DNA polymerase, thumb domain / Helicase, Ruva Protein; domain 3 / DNA polymerase alpha catalytic subunit, N-terminal domain / DNA polymerase alpha, zinc finger domain superfamily / DNA Polymerase alpha zinc finger / DNA polymerase alpha subunit p180 N terminal ...B family DNA polymerase, thumb domain, four helix bundle / Helicase, Ruva Protein; domain 3 - #100 / Alpha-Beta Plaits - #2820 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #730 / B family DNA polymerase, thumb domain / Helicase, Ruva Protein; domain 3 / DNA polymerase alpha catalytic subunit, N-terminal domain / DNA polymerase alpha, zinc finger domain superfamily / DNA Polymerase alpha zinc finger / DNA polymerase alpha subunit p180 N terminal / Zinc finger, DNA-directed DNA polymerase, family B, alpha / DNA polymerase alpha catalytic subunit, catalytic domain / Topoisomerase I; Chain A, domain 4 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / Monooxygenase / DNA polymerase family B, thumb domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H-like superfamily/Ribonuclease H / Helix non-globular / Special / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Helix Hairpins / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / Alpha-Beta Complex / Up-down Bundle / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta 類似検索 - ドメイン・相同性
DNA / DNA (> 10) / RNA / DNA polymerase alpha catalytic subunit A 類似検索 - 構成要素
A: DNA polymerase alpha catalytic subunit A B: DNA polymerase alpha catalytic subunit A C: DNA (5'-D(*TP*TP*TP*TP*CP*GP*CP*TP*GP*CP*CP*CP*GP*CP*CP*T)-3') E: RNA (5'-R(*AP*GP*GP*CP*GP*GP*GP*CP*AP*G)-3') D: DNA (5'-D(*TP*TP*TP*TP*CP*GP*CP*TP*GP*CP*CP*CP*GP*CP*CP*T)-3') F: RNA (5'-R(*AP*GP*GP*CP*GP*GP*GP*CP*AP*G)-3')
A: DNA polymerase alpha catalytic subunit A C: DNA (5'-D(*TP*TP*TP*TP*CP*GP*CP*TP*GP*CP*CP*CP*GP*CP*CP*T)-3') E: RNA (5'-R(*AP*GP*GP*CP*GP*GP*GP*CP*AP*G)-3')
B: DNA polymerase alpha catalytic subunit A D: DNA (5'-D(*TP*TP*TP*TP*CP*GP*CP*TP*GP*CP*CP*CP*GP*CP*CP*T)-3') F: RNA (5'-R(*AP*GP*GP*CP*GP*GP*GP*CP*AP*G)-3')
解像度: 3→55.526 Å / SU ML: 0.52 / 交差検証法: THROUGHOUT / σ(F): 0 / 位相誤差: 34.05 / 立体化学のターゲット値: ML 詳細: FOR REFINEMENT, REFMAC, BUSTER AND PHENIX WERE USED. THE STRUCTURE WAS REFINED WITH RIDING HYDROGENS. THE HYDROGENS OF THE LAST REFINEMENT RUN ARE INCLUDED.
Rfactor
反射数
%反射
Selection details
Rfree
0.2848
2264
5.03 %
Random
Rwork
0.2539
-
-
-
obs
0.2555
45009
97.79 %
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all
-
45009
-
-
溶媒の処理
減衰半径: 0.8 Å / VDWプローブ半径: 1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL.