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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: 3dji | ||||||
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タイトル | Crystal Structure of Macrophage Migration Inhibitory Factor Bound to an Acetaminophen Dimer Derived from NAPQI | ||||||
![]() | Macrophage migration inhibitory factor | ||||||
![]() | ISOMERASE / homotrimer / acetaminophen dimer / Cytokine / Inflammatory response / Phosphoprotein | ||||||
機能・相同性 | ![]() positive regulation of prostaglandin secretion involved in immune response / positive regulation of myeloid leukocyte cytokine production involved in immune response / phenylpyruvate tautomerase / L-dopachrome isomerase / dopachrome isomerase activity / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonate secretion / negative regulation of myeloid cell apoptotic process ...positive regulation of prostaglandin secretion involved in immune response / positive regulation of myeloid leukocyte cytokine production involved in immune response / phenylpyruvate tautomerase / L-dopachrome isomerase / dopachrome isomerase activity / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonate secretion / negative regulation of myeloid cell apoptotic process / negative regulation of macrophage chemotaxis / negative regulation of mature B cell apoptotic process / carboxylic acid metabolic process / positive regulation of chemokine (C-X-C motif) ligand 2 production / negative regulation of protein metabolic process / prostaglandin biosynthetic process / regulation of macrophage activation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / chemoattractant activity / positive regulation of protein kinase A signaling / protein homotrimerization / negative regulation of cellular senescence / negative regulation of DNA damage response, signal transduction by p53 class mediator / DNA damage response, signal transduction by p53 class mediator / positive regulation of B cell proliferation / positive regulation of phosphorylation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / negative regulation of cell migration / positive regulation of cytokine production / cytokine activity / Cell surface interactions at the vascular wall / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of tumor necrosis factor production / cellular senescence / positive regulation of fibroblast proliferation / positive regulation of peptidyl-serine phosphorylation / protease binding / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / inflammatory response / negative regulation of gene expression / innate immune response / positive regulation of cell population proliferation / Neutrophil degranulation / negative regulation of apoptotic process / cell surface / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / plasma membrane / cytosol / cytoplasm 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() | ||||||
![]() | Crichlow, G.V. / Lolis, E. | ||||||
![]() | ![]() タイトル: Structural and kinetic analyses of macrophage migration inhibitory factor active site interactions. 著者: Crichlow, G.V. / Lubetsky, J.B. / Leng, L. / Bucala, R. / Lolis, E.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 | ![]() | 146.7 KB | 表示 | ![]() |
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PDB形式 | ![]() | 114.7 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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詳細 | The biological unit is possibly a trimer. There are two trimers per asymmetric unit. |
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要素
#1: タンパク質 | 分子量: 12355.056 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #2: 化合物 | ChemComp-CL / #3: 化合物 | ChemComp-3E1 / | #4: 水 | ChemComp-HOH / | |
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-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: 2.23 Å3/Da / 溶媒含有率: 44.91 % |
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結晶化 | 温度: 295 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5 詳細: 2 M Ammonium sulfate, 3% Isopropanol, 0.1 M Tris(hydroxymethyl)aminomethane, mixed with protein-inhibitor complex in a 1:1 ratio, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-データ収集
回折 | 平均測定温度: 94 K |
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放射光源 | 由来: ![]() |
検出器 | タイプ: RIGAKU RAXIS IV / 検出器: IMAGE PLATE / 日付: 2008年5月2日 / 詳細: Mirrors |
放射 | モノクロメーター: graphite / 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: 1.5418 Å / 相対比: 1 |
反射 | 解像度: 1.95→90 Å / Num. obs: 47844 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / 冗長度: 3.6 % / Rmerge(I) obs: 0.07 / Χ2: 1.307 / Net I/σ(I): 15.5 |
反射 シェル | 解像度: 1.95→2.02 Å / 冗長度: 3.6 % / Rmerge(I) obs: 0.443 / Num. unique all: 4773 / Χ2: 0.926 / % possible all: 100 |
-位相決定
位相決定 | 手法: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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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: PDB entry 3DJH 解像度: 1.95→77.68 Å / Occupancy max: 1 / Occupancy min: 0.34 / FOM work R set: 0.832 / Isotropic thermal model: isotropic / 交差検証法: THROUGHOUT / σ(F): 0 / 立体化学のターゲット値: Engh & Huber
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溶媒の処理 | Bsol: 51.808 Å2 | ||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 65.65 Å2 / Biso mean: 32.06 Å2 / Biso min: 15.42 Å2
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Refine analyze |
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精密化ステップ | サイクル: LAST / 解像度: 1.95→77.68 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.95→2.02 Å / Rfactor Rfree error: 0.021
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Xplor file |
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