+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3fj9 | ||||||
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タイトル | Crystal structure of F85W mutant of Human acidic fibroblast growth factor | ||||||
要素 | Heparin-binding growth factor 1 | ||||||
キーワード | HORMONE / beta-trefoil / Acetylation / Angiogenesis / Developmental protein / Differentiation / Growth factor / Heparin-binding / Mitogen / Polymorphism | ||||||
機能・相同性 | 機能・相同性情報 mesonephric epithelium development / branch elongation involved in ureteric bud branching / regulation of endothelial tube morphogenesis / FGFR3b ligand binding and activation / regulation of endothelial cell chemotaxis to fibroblast growth factor / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / FGFR2b ligand binding and activation / positive regulation of cholesterol biosynthetic process ...mesonephric epithelium development / branch elongation involved in ureteric bud branching / regulation of endothelial tube morphogenesis / FGFR3b ligand binding and activation / regulation of endothelial cell chemotaxis to fibroblast growth factor / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / FGFR2b ligand binding and activation / positive regulation of cholesterol biosynthetic process / fibroblast growth factor receptor binding / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / Phospholipase C-mediated cascade; FGFR2 / FGFR4 ligand binding and activation / FGFR1b ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / positive regulation of hepatocyte proliferation / S100 protein binding / positive regulation of intracellular signal transduction / Signaling by FGFR2 IIIa TM / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR2 / positive regulation of sprouting angiogenesis / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / positive regulation of cell division / PI3K Cascade / fibroblast growth factor receptor signaling pathway / anatomical structure morphogenesis / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / Hsp70 protein binding / Signaling by FGFR1 in disease / activation of protein kinase B activity / positive regulation of endothelial cell migration / extracellular matrix / epithelial cell proliferation / positive regulation of epithelial cell proliferation / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / animal organ morphogenesis / Negative regulation of FGFR1 signaling / growth factor activity / positive regulation of MAP kinase activity / lung development / wound healing / positive regulation of angiogenesis / Constitutive Signaling by Aberrant PI3K in Cancer / integrin binding / PIP3 activates AKT signaling / heparin binding / cellular response to heat / cell cortex / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / angiogenesis / positive regulation of ERK1 and ERK2 cascade / cell differentiation / positive regulation of cell migration / positive regulation of cell population proliferation / positive regulation of gene expression / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / nucleoplasm / nucleus / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / 分子置換 / 解像度: 1.9 Å | ||||||
データ登録者 | Blaber, M. / Lee, J. | ||||||
引用 | ジャーナル: J.Mol.Biol. / 年: 2009 タイトル: The interaction between thermodynamic stability and buried free cysteines in regulating the functional half-life of fibroblast growth factor-1. 著者: Lee, J. / Blaber, M. | ||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 3fj9.cif.gz | 73.7 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3fj9.ent.gz | 55.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3fj9.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 3fj9_validation.pdf.gz | 441.1 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 3fj9_full_validation.pdf.gz | 443.6 KB | 表示 | |
XML形式データ | 3fj9_validation.xml.gz | 15.4 KB | 表示 | |
CIF形式データ | 3fj9_validation.cif.gz | 21.7 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/fj/3fj9 ftp://data.pdbj.org/pub/pdb/validation_reports/fj/3fj9 | HTTPS FTP |
-関連構造データ
-リンク
-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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詳細 | monomer |
-要素
#1: タンパク質 | 分子量: 16725.783 Da / 分子数: 2 / 変異: F85W / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: FGF1, FGFA / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P05230 #2: 化合物 | ChemComp-FMT / #3: 水 | ChemComp-HOH / | |
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-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 1 |
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-試料調製
結晶 | マシュー密度: 2.91 Å3/Da / 溶媒含有率: 57.74 % |
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結晶化 | 温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5 詳細: 3M Na-formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-データ収集
回折 | 平均測定温度: 103 K |
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放射光源 | 由来: 回転陽極 / タイプ: RIGAKU RUH2R / 波長: 1.5481 Å |
検出器 | タイプ: RIGAKU RAXIS IIC / 検出器: IMAGE PLATE / 日付: 2007年2月23日 / 詳細: OSMIC BLUE CONFOCAL MIRROR |
放射 | モノクロメーター: OSMIC MIRROR / 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: 1.5481 Å / 相対比: 1 |
反射 | 解像度: 1.9→25.86 Å / Num. all: 30761 / Num. obs: 27769 / % possible obs: 90.3 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / 冗長度: 7 % / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.079 |
反射 シェル | 解像度: 1.9→1.97 Å / 冗長度: 3.8 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 3.64 / Num. unique all: 2716 / % possible all: 89.2 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 1JQZ 解像度: 1.9→25.86 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 316647.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 2
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 42.974 Å2 / ksol: 0.389503 e/Å3 | |||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 21.6 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: 1.9→25.86 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.9→2.02 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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