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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: 1cb6 | ||||||
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タイトル | STRUCTURE OF HUMAN APOLACTOFERRIN AT 2.0 A RESOLUTION. | ||||||
![]() | Lactotransferrin | ||||||
![]() | IRON TRANSPORT / APOLACTOFERRIN / CONFORMATIONAL CHANGE | ||||||
機能・相同性 | ![]() host-mediated suppression of viral proces / membrane destabilizing activity / Mtb iron assimilation by chelation / phagocytic vesicle lumen / Metal sequestration by antimicrobial proteins / negative regulation of viral process / positive regulation of toll-like receptor 4 signaling pathway / negative regulation of tumor necrosis factor (ligand) superfamily member 11 production / negative regulation of single-species biofilm formation in or on host organism / positive regulation of bone mineralization involved in bone maturation ...host-mediated suppression of viral proces / membrane destabilizing activity / Mtb iron assimilation by chelation / phagocytic vesicle lumen / Metal sequestration by antimicrobial proteins / negative regulation of viral process / positive regulation of toll-like receptor 4 signaling pathway / negative regulation of tumor necrosis factor (ligand) superfamily member 11 production / negative regulation of single-species biofilm formation in or on host organism / positive regulation of bone mineralization involved in bone maturation / negative regulation of osteoclast development / antifungal humoral response / specific granule / negative regulation of lipopolysaccharide-mediated signaling pathway / positive regulation of chondrocyte proliferation / negative regulation of ATP-dependent activity / regulation of tumor necrosis factor production / bone morphogenesis / Antimicrobial peptides / negative regulation of viral genome replication / positive regulation of osteoblast proliferation / humoral immune response / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; セリンエンドペプチターゼ / cysteine-type endopeptidase inhibitor activity / positive regulation of protein serine/threonine kinase activity / positive regulation of osteoblast differentiation / regulation of cytokine production / ossification / secretory granule / protein serine/threonine kinase activator activity / innate immune response in mucosa / lipopolysaccharide binding / positive regulation of NF-kappaB transcription factor activity / recycling endosome / specific granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / tertiary granule lumen / heparin binding / iron ion transport / defense response to Gram-negative bacterium / killing of cells of another organism / early endosome / positive regulation of canonical NF-kappaB signal transduction / iron ion binding / Amyloid fiber formation / serine-type endopeptidase activity / Neutrophil degranulation / negative regulation of apoptotic process / cell surface / protein-containing complex / proteolysis / DNA binding / extracellular space / extracellular exosome / extracellular region / nucleus / plasma membrane / cytoplasm 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Jameson, G.B. / Anderson, B.F. / Norris, G.E. / Thomas, D.H. / Baker, E.N. | ||||||
![]() | ![]() タイトル: Structure of human apolactoferrin at 2.0 A resolution. Refinement and analysis of ligand-induced conformational change. 著者: Jameson, G.B. / Anderson, B.F. / Norris, G.E. / Thomas, D.H. / Baker, E.N. #1: ジャーナル: Nature / 年: 1990 タイトル: Apolactoferrin structure demonstrates ligand-induced conformational change in transferrins. 著者: Anderson, B.F. / Baker, H.M. / Norris, G.E. / Rumball, S.V. / Baker, E.N. #2: ジャーナル: J.Mol.Biol. / 年: 1989 タイトル: Structure of human lactoferrin: crystallographic structure analysis and refinement at 2.8 A resolution. 著者: Anderson, B.F. / Baker, H.M. / Norris, G.E. / Rice, D.W. / Baker, E.N. #3: ![]() タイトル: Transferrins: Insights Into Structure and Function from Studies on Lactoferrin 著者: Baker, E.N. / Rumball, S.V. / Anderson, B.F. #4: ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 1987 タイトル: Structure of human lactoferrin at 3.2-A resolution. 著者: Anderson, B.F. / Baker, H.M. / Dodson, E.J. / Norris, G.E. / Rumball, S.V. / Waters, J.M. / Baker, E.N. | ||||||
履歴 |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR-MODIFIED KABSCH & SANDER | ||||||
Remark 700 | SHEET THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. THESE ARE REPRESENTED BY TWO SHEETS ...SHEET THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. THESE ARE REPRESENTED BY TWO SHEETS WHICH HAVE ONE OR MORE IDENTICAL STRANDS. SHEETS *N2A* AND *N2B* REPRESENT ONE BIFURCATED SHEET AND STRAND FOUR OF SHEET BN1 IS ALSO PART OF THIS SHEET. SHEETS *C2A* AND *C2B* REPRESENT ONE BIFURCATED SHEET AND STRAND FOUR OF SHEET BC1 IS ALSO PART OF THIS SHEET. THE RESIDUES LISTED IN REMARK 500, TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS, ARE IN WELL DEFINED GAMMA-TURNS AT POSITIONALLY HOMOLOGOUS SITES ON BOTH LOBES. THE PEPTIDE BOND IN REMARK 500 AND ITS POSITIONAL HOMOLOG ARE ALSO SUBSTANTIALLY NON-PLANAR IN LACTOFERRIN |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 432.4 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 450 KB | 表示 | |
XML形式データ | ![]() | 30.7 KB | 表示 | |
CIF形式データ | ![]() | 44.1 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 1lgfS S: 精密化の開始モデル |
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類似構造データ |
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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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要素
#1: タンパク質 | 分子量: 76263.266 Da / 分子数: 1 / 断片: UNP residues 20-710 / 由来タイプ: 天然 / 由来: (天然) ![]() 参照: UniProt: P02788, 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; セリンエンドペプチターゼ | ||||||||
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#2: 化合物 | #3: 水 | ChemComp-HOH / | 構成要素の詳細 | THERE IS A TWO FOLD INTERNAL SEQUENCE HOMOLOGY (~40% IDENTITY). | Has protein modification | Y | 配列の詳細 | THE SEQUENCE USED IN THE X-RAY STRUCTURE FOR RESIDUES 1001-1005 (GRRRS) IS AT VARIANCE WITH THE ...THE SEQUENCE USED IN THE X-RAY STRUCTURE FOR RESIDUES 1001-1005 (GRRRS) IS AT VARIANCE WITH THE MOST RECENT SEQUENCE (SWS P02788, TRFL_H: GRRRRS). IN THIS REGION ELECTRON DENSITY IS POORLY DEFINED AND THE DIFFERENCE | |
-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: 2.61 Å3/Da / 溶媒含有率: 53 % 解説: SYNCHROTRON OSCILLATION DATA TO 1.9 A MERGED WITH ENRAF-NONIUS CAD4 DATA TO 2.8 A; DATA TO 2.0 A RETAINED | |||||||||||||||||||||||||
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結晶化 | pH: 7.8 / 詳細: pH 7.8 | |||||||||||||||||||||||||
結晶化 | *PLUS 手法: microdialysis | |||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 295 K |
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放射光源 | 由来: ![]() ![]() ![]() ![]() ![]() |
検出器 | 検出器: FILM / 詳細: MIRRORS |
放射 | モノクロメーター: NI MIRRORS / 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: 0.87 Å / 相対比: 1 |
反射 | 解像度: 2→17 Å / Num. obs: 53450 / % possible obs: 92 % / 冗長度: 3.3 % / Biso Wilson estimate: 42.3 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 30.3 |
反射 シェル | 解像度: 2→2.12 Å / 冗長度: 3 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.7 / % possible all: 91 |
反射 シェル | *PLUS % possible obs: 91 % |
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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: 1LGF (LACTOFERRIN) 解像度: 2→10 Å / Num. parameters: 22947 / Num. restraintsaints: 22209 / 交差検証法: THROUGHOUT / σ(F): 0 詳細: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56. PROLSQ WAS USED FOR INITIAL REFINEMENTS. SHELXL97 WAS USED FOR FINAL REFINEMENTS. THERE IS POOR ...詳細: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56. PROLSQ WAS USED FOR INITIAL REFINEMENTS. SHELXL97 WAS USED FOR FINAL REFINEMENTS. THERE IS POOR DENSITY FOR RESIDUES 1-3. DENSITY FOR RESIDUES 418 - 424 IS POORLY DEFINED.
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溶媒の処理 | 溶媒モデル: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 53.5 Å2 | |||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2→10 Å
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拘束条件 |
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ソフトウェア | *PLUS 名称: SHELXL-97 / 分類: refinement | |||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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