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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: 6ynd | |||||||||
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タイトル | GAPDH purified from the supernatant of HEK293F cells: crystal form 1 of 4. | |||||||||
![]() | Glyceraldehyde-3-phosphate dehydrogenase | |||||||||
![]() | BIOSYNTHETIC PROTEIN / HEK293F / kifunensine / Cysteine-S-Sulfonic acid | |||||||||
機能・相同性 | ![]() peptidyl-cysteine S-trans-nitrosylation / 転移酵素; 含窒素の基を移すもの; その他の含窒素の基を移すもの / peptidyl-cysteine S-nitrosylase activity / killing by host of symbiont cells / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / aspartic-type endopeptidase inhibitor activity / negative regulation of endopeptidase activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / Gluconeogenesis / GAIT complex ...peptidyl-cysteine S-trans-nitrosylation / 転移酵素; 含窒素の基を移すもの; その他の含窒素の基を移すもの / peptidyl-cysteine S-nitrosylase activity / killing by host of symbiont cells / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / aspartic-type endopeptidase inhibitor activity / negative regulation of endopeptidase activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / Gluconeogenesis / GAIT complex / Glycolysis / positive regulation of type I interferon production / regulation of macroautophagy / defense response to fungus / lipid droplet / positive regulation of cytokine production / glycolytic process / cellular response to type II interferon / microtubule cytoskeleton organization / glucose metabolic process / NAD binding / microtubule cytoskeleton / disordered domain specific binding / antimicrobial humoral immune response mediated by antimicrobial peptide / NADP binding / microtubule binding / nuclear membrane / neuron apoptotic process / positive regulation of canonical NF-kappaB signal transduction / vesicle / killing of cells of another organism / protein stabilization / negative regulation of translation / ribonucleoprotein complex / intracellular membrane-bounded organelle / perinuclear region of cytoplasm / extracellular exosome / identical protein binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | ![]() | |||||||||
手法 | ![]() ![]() ![]() | |||||||||
![]() | Roversi, P. / Lia, A. | |||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Partial catalytic Cys oxidation of human GAPDH to Cys-sulfonic acid. 著者: Lia, A. / Dowle, A. / Taylor, C. / Santino, A. / Roversi, P. | |||||||||
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 | ![]() | 989.9 KB | 表示 | ![]() |
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PDB形式 | ![]() | 835.5 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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2 | ![]()
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単位格子 |
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要素
#1: タンパク質 | 分子量: 36179.230 Da / 分子数: 8 / 変異: C152X / 由来タイプ: 天然 詳細: GAPDH with catalytic Cys partially oxidised to Cys-S-Sulfonic Acid 由来: (天然) ![]() 参照: UniProt: P04406, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating), 転移酵素; 含窒素の基を移すもの; その他の含窒素の基を移すもの #2: 化合物 | ChemComp-XPE / #3: 水 | ChemComp-HOH / | 研究の焦点であるリガンドがあるか | Y | |
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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: 2.48 Å3/Da / 溶媒含有率: 50.34 % / 解説: Prism |
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結晶化 | 温度: 291 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8.5 詳細: 0.1M MORPHEUS Amino acids solution (DL-Glutamic acid; DL-Alanine; Glycine; DL-Lysine; DL-Serine), 0.1M MORPHEUS Buffer System 3 (Tris (base); BICINE), 30% v/v MORPHEUS Precipitant Mix 1 (40% ...詳細: 0.1M MORPHEUS Amino acids solution (DL-Glutamic acid; DL-Alanine; Glycine; DL-Lysine; DL-Serine), 0.1M MORPHEUS Buffer System 3 (Tris (base); BICINE), 30% v/v MORPHEUS Precipitant Mix 1 (40% v/v PEG 500* MME; 20 % w/v PEG 20000) |
-データ収集
回折 | 平均測定温度: 100 K / Serial crystal experiment: N |
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放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: DECTRIS EIGER2 XE 16M / 検出器: PIXEL / 日付: 2019年7月22日 |
放射 | モノクロメーター: Double crystal monochromator / 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: 0.97622 Å / 相対比: 1 |
反射 | 解像度: 1.52→140.09 Å / Num. obs: 295271 / % possible obs: 69.4 % / 冗長度: 6.9 % / Biso Wilson estimate: 23.93 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.03 / Rrim(I) all: 0.09 / Net I/σ(I): 11.7 |
反射 シェル | 解像度: 1.52→1.71 Å / 冗長度: 6.8 % / Rmerge(I) obs: 1.071 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 14763 / CC1/2: 0.608 / Rpim(I) all: 0.444 / Rrim(I) all: 1.161 / % possible all: 12.2 |
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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: 1U8F 解像度: 1.525→140.09 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.948 / SU R Cruickshank DPI: 0.135 / 交差検証法: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.104 / SU Rfree Blow DPI: 0.095 / SU Rfree Cruickshank DPI: 0.095 詳細: Initial automated water addition and positional and individual B-factor refinement were carried out in autoBUSTER. Automated non-crystallographic restraints were used throughtout, including ...詳細: Initial automated water addition and positional and individual B-factor refinement were carried out in autoBUSTER. Automated non-crystallographic restraints were used throughtout, including water molecules (assigned to each chain using CCP4-Sortwater). At each catalytic Cys152 site, a 0.5:0.5 occupancy ratio mixture of Cys and Cys S-Sulfonic acid was initially modelled in Fo-Fc residual density. At each Cys152 site, occupancies for Cys and Cys S-Sulfonic acid were refined and constrained so that they sum up to 1.000 plus or minus 0.005.
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原子変位パラメータ | Biso mean: 27.48 Å2
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Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.525→140.09 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.525→1.63 Å
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