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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: 2nn8 | |||||||||
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タイトル | Crystal structure of human galectin-3 carbohydrate-recognition domain with lactose bound, at 1.35 angstrom resolution | |||||||||
![]() | Galectin-3 | |||||||||
![]() | SUGAR BINDING PROTEIN / beta-sandwich | |||||||||
機能・相同性 | ![]() negative regulation of NK T cell activation / negative regulation of immunological synapse formation / disaccharide binding / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / RUNX2 regulates genes involved in differentiation of myeloid cells / regulation of T cell apoptotic process / mononuclear cell migration / receptor ligand inhibitor activity / positive regulation of mononuclear cell migration / negative regulation of endocytosis ...negative regulation of NK T cell activation / negative regulation of immunological synapse formation / disaccharide binding / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / RUNX2 regulates genes involved in differentiation of myeloid cells / regulation of T cell apoptotic process / mononuclear cell migration / receptor ligand inhibitor activity / positive regulation of mononuclear cell migration / negative regulation of endocytosis / IgE binding / eosinophil chemotaxis / regulation of extrinsic apoptotic signaling pathway via death domain receptors / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / signaling receptor inhibitor activity / negative regulation of T cell receptor signaling pathway / protein phosphatase inhibitor activity / positive chemotaxis / positive regulation of calcium ion import / chemoattractant activity / macrophage chemotaxis / monocyte chemotaxis / regulation of T cell proliferation / Advanced glycosylation endproduct receptor signaling / ficolin-1-rich granule membrane / immunological synapse / laminin binding / neutrophil chemotaxis / epithelial cell differentiation / RNA splicing / secretory granule membrane / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein localization to plasma membrane / spliceosomal complex / positive regulation of protein-containing complex assembly / molecular condensate scaffold activity / mRNA processing / carbohydrate binding / : / protein phosphatase binding / mitochondrial inner membrane / innate immune response / Neutrophil degranulation / cell surface / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / plasma membrane / cytosol / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | ![]() | |||||||||
手法 | ![]() ![]() ![]() | |||||||||
![]() | Blanchard, H. / Collins, P.M. | |||||||||
![]() | ![]() タイトル: Slow diffusion of lactose out of galectin-3 crystals monitored by X-ray crystallography: possible implications for ligand-exchange protocols. 著者: Collins, P.M. / Hidari, K.I. / Blanchard, H. | |||||||||
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 | ![]() | 51.7 KB | 表示 | ![]() |
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PDB形式 | ![]() | 34.4 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 | ![]() | 1.1 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.1 MB | 表示 | |
XML形式データ | ![]() | 10.1 KB | 表示 | |
CIF形式データ | ![]() | 14.4 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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単位格子 |
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詳細 | THE BIOLOGICAL MOLECULE(S) IS EXPECTED TO BE FULL-LENGTH GALECTIN-3 WHICH CONSISTS OF N-TERMINAL DOMAIN AND THE CRD DOMAIN. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S) OF CRD DOMAIN. THE BIOLOGICAL UNIT IS A MONOMER OF GALECTIN-3 CARBOHYDRATE -RECOGNITION DOMAIN. THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS ONE MOLECULE OF THE GALECTIN-3 CARBOHYDRATE-RECOGNITION DOMAIN. |
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要素
-タンパク質 , 1種, 1分子 A
#1: タンパク質 | 分子量: 15701.049 Da / 分子数: 1 / 断片: Galectin-3 CRD domain, Residues 113-250 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
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-糖 , 2種, 2分子
#2: 多糖 | beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose |
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#3: 多糖 | beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose / alpha-lactose |
-非ポリマー , 3種, 199分子 




#4: 化合物 | ChemComp-GOL / |
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#5: 化合物 | ChemComp-CL / |
#6: 水 | ChemComp-HOH / |
-詳細
非ポリマーの詳細 | LACTOSE IS MIXTURE OF BOTH ALPHA- AND BETA- FORMS WITH 0.5 OCCUPANCY. THEY ARE LABELED AS LBT FOR ...LACTOSE IS MIXTURE OF BOTH ALPHA- AND BETA- FORMS WITH 0.5 OCCUPANCY. THEY ARE LABELED AS LBT FOR ALPHA AND LAT FOR BETA, RESPECTIVE |
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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: 2.09 Å3/Da / 溶媒含有率: 41.26 % |
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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: 7 詳細: 31% PEG 6000, 100mM MgCL2, 8mM beta mercaptoethanol, 100mM Tris-HCL, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-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: ADSC QUANTUM 4 / 検出器: CCD / 日付: 2005年11月15日 |
放射 | モノクロメーター: SI 111 / 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: 1.1159 Å / 相対比: 1 |
反射 | 解像度: 1.35→42.49 Å / Num. all: 29182 / Num. obs: 29182 / % possible obs: 98.3 % / 冗長度: 3.7 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 11.5 |
反射 シェル | 解像度: 1.35→1.42 Å / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.4 / % possible all: 89.9 |
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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: PDB ENTRY 1A3K 解像度: 1.35→27.62 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.766 / SU ML: 0.033 / 交差検証法: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.055 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.4 Å / 溶媒モデル: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 13.881 Å2
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精密化ステップ | サイクル: LAST / 解像度: 1.35→27.62 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.35→1.385 Å / Total num. of bins used: 20
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