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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 7ymf | ||||||
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タイトル | Crystal Structure of DDX3X449_450ET>DP | ||||||
![]() | (ATP-dependent RNA helicase DDX3X) x 2 | ||||||
![]() | HYDROLASE / DDX3X / NUCLEAR PROTEIN | ||||||
機能・相同性 | ![]() CTPase activity / positive regulation of toll-like receptor 8 signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / positive regulation of translation in response to endoplasmic reticulum stress / protein localization to cytoplasmic stress granule / eukaryotic initiation factor 4E binding / RNA strand annealing activity / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of mitochondrial translation / gamete generation ...CTPase activity / positive regulation of toll-like receptor 8 signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / positive regulation of translation in response to endoplasmic reticulum stress / protein localization to cytoplasmic stress granule / eukaryotic initiation factor 4E binding / RNA strand annealing activity / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of mitochondrial translation / gamete generation / positive regulation of protein K63-linked ubiquitination / NLRP3 inflammasome complex / cellular response to arsenic-containing substance / poly(A) binding / gamma-tubulin binding / P granule / cellular response to osmotic stress / negative regulation of non-canonical NF-kappaB signal transduction / cytoplasmic pattern recognition receptor signaling pathway / transcription factor binding / positive regulation of NLRP3 inflammasome complex assembly / lipid homeostasis / cell leading edge / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of interferon-alpha production / positive regulation of translational initiation / ribosomal small subunit binding / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of type I interferon production / positive regulation of G1/S transition of mitotic cell cycle / negative regulation of protein-containing complex assembly / positive regulation of viral genome replication / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / translation initiation factor binding / signaling adaptor activity / stress granule assembly / DNA helicase activity / intrinsic apoptotic signaling pathway / positive regulation of interferon-beta production / ribonucleoside triphosphate phosphatase activity / positive regulation of translation / protein serine/threonine kinase activator activity / cytosolic ribosome assembly / chromosome segregation / translational initiation / positive regulation of non-canonical NF-kappaB signal transduction / negative regulation of cell growth / mRNA 5'-UTR binding / cellular response to virus / response to virus / Wnt signaling pathway / RNA stem-loop binding / cytoplasmic stress granule / positive regulation of canonical Wnt signaling pathway / lamellipodium / positive regulation of cell growth / secretory granule lumen / ficolin-1-rich granule lumen / cell differentiation / RNA helicase activity / negative regulation of translation / intracellular signal transduction / RNA helicase / positive regulation of apoptotic process / cadherin binding / negative regulation of gene expression / innate immune response / mRNA binding / GTPase activity / centrosome / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / DNA binding / RNA binding / extracellular exosome / extracellular region / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Xiong, J. | ||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Crystal Structure of DDX3X449_450ET>DP 著者: Xiong, J. | ||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 110 KB | 表示 | ![]() |
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PDB形式 | ![]() | 75.6 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 444 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 450 KB | 表示 | |
XML形式データ | ![]() | 19.1 KB | 表示 | |
CIF形式データ | ![]() | 27 KB | 表示 | |
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 | ![]() 4pxaS S: 精密化の開始モデル |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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リンク
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集合体
登録構造単位 | ![]()
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単位格子 |
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要素
#1: タンパク質 | 分子量: 34187.074 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
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#2: タンパク質 | 分子量: 20255.672 Da / 分子数: 1 / Mutation: E449D, T450P / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
#3: 水 | ChemComp-HOH / |
-実験情報
-実験
実験 | 手法: ![]() |
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試料調製
結晶 | マシュー密度: 2.34 Å3/Da / 溶媒含有率: 47.51 % |
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結晶化 | 温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 詳細: 0.1 M MES pH 6.5, 1.5 M Sodium Formate , 50 mM Magnesium chloride |
-データ収集
回折 | 平均測定温度: 100 K / Serial crystal experiment: N |
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放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2020年7月23日 |
放射 | 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: 0.9791 Å / 相対比: 1 |
反射 | 解像度: 2.3→50 Å / Num. obs: 21930 / % possible obs: 100 % / 冗長度: 9.2 % / Biso Wilson estimate: 27.52 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.039 / Net I/σ(I): 24.5 |
反射 シェル | 解像度: 2.3→2.34 Å / 冗長度: 7.6 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 2050 / CC1/2: 0.92 / Rpim(I) all: 0.264 / % possible all: 99.9 |
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解析
ソフトウェア |
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精密化 | 構造決定の手法: ![]() 開始モデル: 4PXA 解像度: 2.3→49.32 Å / SU ML: 0.2455 / 交差検証法: FREE R-VALUE / σ(F): 2.01 / 位相誤差: 25.378 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 34.01 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.3→49.32 Å
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拘束条件 |
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LS精密化 シェル |
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