- PDB-4b08: Yeast DNA polymerase alpha, Selenomethionine protein -
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基本情報
登録情報
データベース: PDB / ID: 4b08
タイトル
Yeast DNA polymerase alpha, Selenomethionine protein
要素
DNA POLYMERASE ALPHA CATALYTIC SUBUNIT A
キーワード
TRANSFERASE / DNA POLYMERASE / DNA REPLICATION
機能・相同性
機能・相同性情報
Inhibition of replication initiation of damaged DNA by RB1/E2F1 / DNA replication initiation / RNA-templated DNA biosynthetic process / 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 / DNA replication initiation / RNA-templated DNA biosynthetic process / 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, alpha/beta motif / 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 / 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, alpha/beta motif / 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 / 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 / Ribonuclease H-like motif / 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 / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta 類似検索 - ドメイン・相同性
DNA polymerase alpha catalytic subunit A 類似検索 - 構成要素
DNAPOLYMERASEALPHACATALYTICSUBUNITA / DNA POLYMERASE I SUBUNIT A / DNA POLYMERASE ALPHA\:PRIMASE COMPLEX P180 SUBUNIT / DNA POLYMERASE- ...DNA POLYMERASE I SUBUNIT A / DNA POLYMERASE ALPHA\:PRIMASE COMPLEX P180 SUBUNIT / DNA POLYMERASE-PRIMASE COMPLEX P180 SUBUNIT / POL ALPHA-PRIMASE COMPLEX P180 SUBUNIT
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: 0.9793 Å / 相対比: 1
反射
解像度: 2.67→73.97 Å / Num. obs: 39626 / % possible obs: 100 % / Observed criterion σ(I): 0 / 冗長度: 19.7 % / Biso Wilson estimate: 45.86 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 17.9
反射 シェル
解像度: 2.67→2.81 Å / 冗長度: 17.2 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 4.6 / % possible all: 99.8
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解析
ソフトウェア
名称
バージョン
分類
PHENIX
(PHENIX.REFINE: DEV_1078)
精密化
MOSFLM
データ削減
SCALA
データスケーリング
PHENIX
位相決定
精密化
構造決定の手法: 単波長異常分散 開始モデル: NONE 解像度: 2.67→65.8 Å / SU ML: 0.28 / σ(F): 1.35 / 位相誤差: 24.75 / 立体化学のターゲット値: ML 詳細: FOR REFINEMENT, REFMAC, BUSTER AND PHENIX WERE USED. RESIDUES 677-679, 816-847, 1056-1062 1176-1185 AND 1129-1258 ARE DISORDERED AND NOT INCLUDED IN THE STRUCTURE. THE STRUCTURE WAS REFINED ...詳細: FOR REFINEMENT, REFMAC, BUSTER AND PHENIX WERE USED. RESIDUES 677-679, 816-847, 1056-1062 1176-1185 AND 1129-1258 ARE DISORDERED AND NOT INCLUDED IN THE STRUCTURE. THE STRUCTURE WAS REFINED WITH RIDING HYDROGEN THE HYDROGENS OF THE LAST REFINEMENT RUN ARE INCLUDED.
Rfactor
反射数
%反射
Rfree
0.234
1986
5 %
Rwork
0.1952
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obs
0.1972
39564
99.86 %
溶媒の処理
減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL