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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: 7rv5 | ||||||
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タイトル | Crystal structure of the BCL6 BTB domain in complex with OICR-9287 | ||||||
![]() | Isoform 2 of B-cell lymphoma 6 protein | ||||||
![]() | TRANSCRIPTION / immunity / inflammatory response / transcription repressor | ||||||
機能・相同性 | ![]() regulation of memory T cell differentiation / negative regulation of mitotic cell cycle DNA replication / intronic transcription regulatory region sequence-specific DNA binding / negative regulation of isotype switching to IgE isotypes / negative regulation of plasma cell differentiation / negative regulation of T-helper 2 cell differentiation / isotype switching to IgE isotypes / negative regulation of mast cell cytokine production / regulation of germinal center formation / negative regulation of mononuclear cell proliferation ...regulation of memory T cell differentiation / negative regulation of mitotic cell cycle DNA replication / intronic transcription regulatory region sequence-specific DNA binding / negative regulation of isotype switching to IgE isotypes / negative regulation of plasma cell differentiation / negative regulation of T-helper 2 cell differentiation / isotype switching to IgE isotypes / negative regulation of mast cell cytokine production / regulation of germinal center formation / negative regulation of mononuclear cell proliferation / plasma cell differentiation / paraspeckles / germinal center formation / regulation of immune system process / pyramidal neuron differentiation / type 2 immune response / T-helper 2 cell differentiation / positive regulation of regulatory T cell differentiation / negative regulation of B cell apoptotic process / positive regulation of cell motility / negative regulation of Rho protein signal transduction / FOXO-mediated transcription of cell death genes / negative regulation of cell-matrix adhesion / regulation of T cell proliferation / negative regulation of Notch signaling pathway / B cell proliferation / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / regulation of cell differentiation / negative regulation of cellular senescence / Rho protein signal transduction / regulation of immune response / erythrocyte development / positive regulation of B cell proliferation / regulation of cytokine production / positive regulation of neuron differentiation / cell-matrix adhesion / transcription corepressor binding / cell motility / heterochromatin formation / cell morphogenesis / negative regulation of cell growth / chromatin DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / protein localization / regulation of cell population proliferation / regulation of inflammatory response / actin cytoskeleton organization / spermatogenesis / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / inflammatory response / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / nucleolus / Golgi apparatus / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / metal ion binding 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Kuntz, D.A. / Prive, G.G. | ||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Structure of the BCL6 BTB domain 著者: Watson, I. / Isaac, M. | ||||||
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 | ![]() | 69.1 KB | 表示 | ![]() |
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PDB形式 | ![]() | 46.3 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 |
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-関連構造データ
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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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Components on special symmetry positions |
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要素
#1: タンパク質 | 分子量: 14559.823 Da / 分子数: 1 / 変異: C8Q,C67R,C84N / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
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#2: 化合物 | ChemComp-7RB / |
#3: 水 | ChemComp-HOH / |
研究の焦点であるリガンドがあるか | Y |
-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: 2.01 Å3/Da / 溶媒含有率: 38.81 % |
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結晶化 | 温度: 292 K / 手法: マイクロバッチ法 / pH: 6.5 詳細: Precipitant solution was 16-20% PEG 8K in 0.1M pH 6.5 Hepes buffer, 50 mM CaCl2 with microseeding. Crystals were soaked in 0.1M Hepes 7.4, 20% PEG 8K, 25% glycerol 0.5 mM ligand prior to ...詳細: Precipitant solution was 16-20% PEG 8K in 0.1M pH 6.5 Hepes buffer, 50 mM CaCl2 with microseeding. Crystals were soaked in 0.1M Hepes 7.4, 20% PEG 8K, 25% glycerol 0.5 mM ligand prior to passage through paratone and freezing. Crystals grew as large doubly birefringent rods which were gently crushed. Singly birefringent pieces were selected for data collection. |
-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 PILATUS 6M / 検出器: PIXEL / 日付: 2013年8月10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: 1 Å / 相対比: 1 |
反射 | 解像度: 2.21→52.95 Å / Num. obs: 5769 / % possible obs: 99.6 % / 冗長度: 3.3 % / Biso Wilson estimate: 28.32 Å2 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.09 / Rrim(I) all: 0.131 / Net I/σ(I): 9 |
反射 シェル | 解像度: 2.21→2.37 Å / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1019 / Rpim(I) all: 0.456 / Rrim(I) all: 0.665 |
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解析
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精密化 | 構造決定の手法: ![]() 開始モデル: 1R29 解像度: 2.21→36.1 Å / SU ML: 0.2615 / 交差検証法: FREE R-VALUE / σ(F): 0 / 位相誤差: 21.9824 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: 33.37 Å2 | |||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.21→36.1 Å
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拘束条件 |
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LS精密化 シェル |
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