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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: 1dvg | ||||||
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タイトル | CRYSTAL STRUCTURE OF RAT HEME OXYGENASE-1 IN COMPLEX WITH HEME; SELELENO-METHIONINE DERIVATIVE, MUTATED AT M51T,M93L,M155L,M191L. | ||||||
![]() | HEME OXYGENASE-1 | ||||||
![]() | OXIDOREDUCTASE / ALL ALPHA / PROTEIN-SUBSTRATE COMPLEX | ||||||
機能・相同性 | ![]() Regulation of HMOX1 expression and activity / arachidonic acid omega-hydroxylase activity / Iron uptake and transport / response to 3-methylcholanthrene / Heme degradation / Cytoprotection by HMOX1 / negative regulation of mast cell degranulation / response to arachidonic acid / heme metabolic process / phospholipase D activity ...Regulation of HMOX1 expression and activity / arachidonic acid omega-hydroxylase activity / Iron uptake and transport / response to 3-methylcholanthrene / Heme degradation / Cytoprotection by HMOX1 / negative regulation of mast cell degranulation / response to arachidonic acid / heme metabolic process / phospholipase D activity / heme oxygenase (biliverdin-producing) / cellular response to cisplatin / heme oxidation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / heme oxygenase (decyclizing) activity / wound healing involved in inflammatory response / negative regulation of muscle cell apoptotic process / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of mast cell cytokine production / heme catabolic process / cellular response to arsenic-containing substance / cellular response to nutrient / negative regulation of epithelial cell apoptotic process / positive regulation of epithelial cell apoptotic process / erythrocyte homeostasis / epithelial cell apoptotic process / positive regulation of cell migration involved in sprouting angiogenesis / small GTPase-mediated signal transduction / negative regulation of macroautophagy / negative regulation of vascular associated smooth muscle cell proliferation / positive regulation of macroautophagy / phospholipid metabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / cellular response to cadmium ion / caveola / liver regeneration / macroautophagy / negative regulation of smooth muscle cell proliferation / positive regulation of smooth muscle cell proliferation / response to nicotine / response to hydrogen peroxide / regulation of blood pressure / multicellular organismal-level iron ion homeostasis / response to estrogen / positive regulation of angiogenesis / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to heat / cellular response to hypoxia / angiogenesis / intracellular iron ion homeostasis / response to oxidative stress / negative regulation of neuron apoptotic process / response to hypoxia / intracellular signal transduction / response to xenobiotic stimulus / negative regulation of cell population proliferation / heme binding / endoplasmic reticulum membrane / regulation of transcription by RNA polymerase II / structural molecule activity / perinuclear region of cytoplasm / enzyme binding / endoplasmic reticulum / protein homodimerization activity / identical protein binding / nucleus / metal ion binding 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() | ||||||
手法 | ![]() ![]() | ||||||
![]() | Sugishima, M. / Omata, Y. / Kakuta, Y. / Sakamoto, H. / Noguchi, M. / Fukuyama, K. | ||||||
![]() | ![]() タイトル: Crystal structure of rat heme oxygenase-1 in complex with heme. 著者: Sugishima, M. / Omata, Y. / Kakuta, Y. / Sakamoto, H. / Noguchi, M. / Fukuyama, K. | ||||||
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
PDBx/mmCIF形式 | ![]() | 98.8 KB | 表示 | ![]() |
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PDB形式 | ![]() | 80.9 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 | ![]() | 1 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1 MB | 表示 | |
XML形式データ | ![]() | 19.4 KB | 表示 | |
CIF形式データ | ![]() | 26.6 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-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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2 | ![]()
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単位格子 |
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要素
#1: タンパク質 | 分子量: 30655.773 Da / 分子数: 2 変異: M1(MSE), M9(MSE), M34(MSE), M51T, M93L, M155L, M186(MSE), M191L 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() 参照: UniProt: P06762, heme oxygenase (biliverdin-producing) #2: 化合物 | #3: 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: 2.3 Å3/Da / 溶媒含有率: 46.52 % | ||||||||||||||||||||||||||||||
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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 / pH: 8.5 詳細: PEG4000, TRIS-HCL, SODIUM ACETATE, CRYO:ADD GLYCEROL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K | ||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 293 K / pH: 7 詳細: Omata, Y., (1998) Acta Crystallogr., Sect.D, 54, 1017. | ||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 100 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: 1999年5月2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: 0.9793 Å / 相対比: 1 |
反射 | 解像度: 2.2→19.48 Å / Num. all: 27994 / Num. obs: 26622 / % possible obs: 95.1 % / Observed criterion σ(I): 1 / 冗長度: 2.62 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 7.3 |
反射 シェル | 解像度: 2.2→2.28 Å / 冗長度: 2.28 % / Rmerge(I) obs: 0.227 / Num. unique all: 2492 / % possible all: 89.8 |
反射 | *PLUS Num. measured all: 69625 |
反射 シェル | *PLUS % possible obs: 89.8 % |
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解析
ソフトウェア |
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精密化 | 解像度: 2.2→19.48 Å / σ(F): 0 / σ(I): 1
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精密化ステップ | サイクル: LAST / 解像度: 2.2→19.48 Å
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拘束条件 |
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ソフトウェア | *PLUS 名称: CNS / バージョン: 0.9 / 分類: refinement | |||||||||||||||||||||||||
精密化 | *PLUS σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.212 | |||||||||||||||||||||||||
溶媒の処理 | *PLUS | |||||||||||||||||||||||||
原子変位パラメータ | *PLUS | |||||||||||||||||||||||||
拘束条件 | *PLUS
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