+
データを開く
-
基本情報
登録情報 | データベース: PDB / ID: 8icq | ||||||
---|---|---|---|---|---|---|---|
タイトル | DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF OF DATP (0.1 MILLIMOLAR) AND MNCL2 (0.5 MILLIMOLAR) | ||||||
![]() |
| ||||||
![]() | TRANSFERASE/DNA / DNA-DIRECTED DNA POLYMERASE / DNA REPLICATION / DNA REPAIR / NUCLEOTIDYLTRANSFERASE / COMPLEX (NUCLEOTIDYLTRANSFERASE-DNA / TRANSFERASE-DNA complex | ||||||
機能・相同性 | ![]() Resolution of AP sites via the single-nucleotide replacement pathway / immunoglobulin heavy chain V-D-J recombination / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / 付加脱離酵素(リアーゼ); 炭素-酸素リアーゼ類; その他の炭素-酸素リアーゼ / homeostasis of number of cells / POLB-Dependent Long Patch Base Excision Repair / 5'-deoxyribose-5-phosphate lyase activity / PCNA-Dependent Long Patch Base Excision Repair ...Resolution of AP sites via the single-nucleotide replacement pathway / immunoglobulin heavy chain V-D-J recombination / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / 付加脱離酵素(リアーゼ); 炭素-酸素リアーゼ類; その他の炭素-酸素リアーゼ / homeostasis of number of cells / POLB-Dependent Long Patch Base Excision Repair / 5'-deoxyribose-5-phosphate lyase activity / PCNA-Dependent Long Patch Base Excision Repair / pyrimidine dimer repair / response to hyperoxia / somatic hypermutation of immunoglobulin genes / lymph node development / salivary gland morphogenesis / spleen development / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair, gap-filling / spindle microtubule / response to gamma radiation / base-excision repair / DNA-templated DNA replication / double-strand break repair via nonhomologous end joining / intrinsic apoptotic signaling pathway in response to DNA damage / microtubule binding / neuron apoptotic process / response to ethanol / in utero embryonic development / microtubule / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / lyase activity / Ub-specific processing proteases / inflammatory response / DNA repair / DNA damage response / enzyme binding / protein-containing complex / nucleoplasm / nucleus / metal ion binding / cytoplasm 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() | ||||||
![]() | Pelletier, H. / Sawaya, M.R. | ||||||
![]() | ![]() タイトル: A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta. 著者: Pelletier, H. / Sawaya, M.R. / Wolfle, W. / Wilson, S.H. / Kraut, J. #1: ![]() タイトル: Crystal Structures of Human DNA Polymerase Beta Complexed with Nicked and Gapped DNA Substrates 著者: Sawaya, M.R. / Rawson, T. / Wilson, S.H. / Kraut, J. / Pelletier, H. #2: ![]() タイトル: The Role of Thumb Movement and Template Bending in Polymerase Fidelity 著者: Pelletier, H. #3: ![]() タイトル: Crystal Structures of Human DNA Polymerase Beta Complexed with DNA; Implications for Catalytic Mechanism, Processivity, and Fidelity 著者: Pelletier, H. / Sawaya, M.R. / Wolfle, W. / Wilson, S.H. / Kraut, J. #4: ![]() タイトル: Characterization of the Metal Ion-Binding HHH Motifs in Human DNA Polymerase Beta by X-Ray Structural Analysis 著者: Pelletier, H. / Sawaya, M.R. #6: ![]() タイトル: Structures of Ternary Complexes of Rat DNA Polymerase Beta, a DNA Template- Primer, and ddCTP 著者: Pelletier, H. / Sawaya, M.R. / Kumar, A. / Wilson, S.H. / Kraut, J. #7: ![]() タイトル: Crystal Structure of Rat DNA Polymerase Beta: Evidence for a Common Polymerase Mechanism 著者: Sawaya, M.R. / Pelletier, H. / Kumar, A. / Wilson, S.H. / Kraut, J. | ||||||
履歴 |
|
-
構造の表示
構造ビューア | 分子: ![]() ![]() |
---|
-
ダウンロードとリンク
-
ダウンロード
PDBx/mmCIF形式 | ![]() | 90.5 KB | 表示 | ![]() |
---|---|---|---|---|
PDB形式 | ![]() | 70 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
---|
-関連構造データ
関連構造データ | ![]() 1zqtC ![]() 7iceC ![]() 7icfC ![]() 7icgC ![]() 7ichC ![]() 7iciC ![]() 7icjC ![]() 7ickC ![]() 7iclC ![]() 7icmC ![]() 7icnC ![]() 7icoC ![]() 7icpC ![]() 7icqC ![]() 7icrC ![]() 7icsC ![]() 7ictC ![]() 7icuC ![]() 7icvC ![]() 8icjC ![]() 8ickC ![]() 8iclC ![]() 8icmC ![]() 8icnC ![]() 8icoC ![]() 8icpC ![]() 8icrC ![]() 8icsC ![]() 8ictC ![]() 8icuC ![]() 8icvC ![]() 8icwC ![]() 8icxC ![]() 8icyC ![]() 9icfC ![]() 9ickC ![]() 9icnC ![]() 9icoC ![]() 9icpC ![]() 9icqC ![]() 9icrC ![]() 9icsC ![]() 9ictC ![]() 9icuC ![]() 9icvC ![]() 8icbS C: 同じ文献を引用 ( S: 精密化の開始モデル |
---|---|
類似構造データ |
-
リンク
-
集合体
登録構造単位 | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
単位格子 |
|
-
要素
#1: DNA鎖 | 分子量: 2434.643 Da / 分子数: 1 / 由来タイプ: 合成 | ||||
---|---|---|---|---|---|
#2: DNA鎖 | 分子量: 2112.422 Da / 分子数: 1 / 由来タイプ: 合成 | ||||
#3: タンパク質 | 分子量: 38241.672 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() | ||||
#4: 化合物 | #5: 水 | ChemComp-HOH / | 構成要素の詳細 | A POSSIBLE PHYSIOLOGICAL SUBSTRATE FOR POL BETA IS A DNA GAP, WHERE THE LENGTH OF THE GAP CAN RANGE ...A POSSIBLE PHYSIOLOGI | |
-実験情報
-実験
実験 | 手法: ![]() |
---|
-
試料調製
結晶 | マシュー密度: 3 Å3/Da / 溶媒含有率: 58.4 % |
---|---|
結晶化 | pH: 6.5 詳細: THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE ...詳細: THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DATP, 0.1 MILLIMOLAR MNCL2, 0.5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE. |
-データ収集
回折 | 平均測定温度: 298 K |
---|---|
放射光源 | 由来: ![]() |
検出器 | タイプ: SDMS / 検出器: AREA DETECTOR / 日付: 1995年4月29日 |
放射 | モノクロメーター: GRAPHITE / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 相対比: 1 |
反射 | 解像度: 3→20 Å / Num. obs: 9640 / % possible obs: 91 % / Observed criterion σ(I): 0 / 冗長度: 2.2 % / Rsym value: 0.054 |
反射 シェル | 解像度: 3→3.1 Å / 冗長度: 1.6 % / Rsym value: 0.151 / % possible all: 89 |
-
解析
ソフトウェア |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
精密化 | 構造決定の手法: DIFFERENCE FOURIER 開始モデル: 8ICB 解像度: 3→20 Å / σ(F): 0 / 立体化学のターゲット値: STANDARD TNT /
| ||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | 溶媒モデル: MOEWS | ||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 3→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
|