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基本情報
登録情報 | データベース: PDB / ID: 9g1c | ||||||||||||||||||
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タイトル | Fragment screening of FosAKP, room-temperature structure in complex with fragment F2X-entry A12 | ||||||||||||||||||
![]() | Fosfomycin resistance protein | ||||||||||||||||||
![]() | TRANSFERASE / antibiotic resistance / fosfomycin / fragment screening | ||||||||||||||||||
機能・相同性 | ![]() | ||||||||||||||||||
生物種 | ![]() | ||||||||||||||||||
手法 | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Guenther, S. / Galchenkova, M. / Fischer, P. / Reinke, P.Y.A. / Falke, S. / Thekku Veedu, S. / Rodrigues, A.C. / Senst, J. / Meents, A. | ||||||||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Room temperature X-ray fragment screening with serial crystallography 著者: Guenther, S. / Meents, A. | ||||||||||||||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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-検証レポート
文書・要旨 | ![]() | 774.8 KB | 表示 | ![]() |
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-関連構造データ
関連構造データ | ![]() 9g1aC ![]() 9g1bC ![]() 9g1dC ![]() 9g1eC ![]() 9g1fC ![]() 9g1gC ![]() 9g1hC ![]() 9g1iC ![]() 9g1jC ![]() 9g1kC ![]() 9g1lC ![]() 9g1mC ![]() 9g1nC ![]() 9g1oC ![]() 9g1pC ![]() 9g1qC ![]() 9g1rC ![]() 9g1sC C: 同じ文献を引用 ( |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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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: 16309.347 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #2: 化合物 | ChemComp-TJ1 / | #3: 化合物 | #4: 水 | ChemComp-HOH / | 研究の焦点であるリガンドがあるか | Y | Has protein modification | N | |
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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: 2.45 Å3/Da / 溶媒含有率: 49.75 % |
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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: 5.5 詳細: 25 mg/mL FosAKP in 10 mM Hepes, pH 7.5, 75 mM NaCl was supplemented with 6 mM MnCl2 and mixed with an equal volume of 16% (w/v) PEG3350, 0.25 M MgCl2, 0.2 M KBr, 0.1 M BisTris, pH 5.5 and ...詳細: 25 mg/mL FosAKP in 10 mM Hepes, pH 7.5, 75 mM NaCl was supplemented with 6 mM MnCl2 and mixed with an equal volume of 16% (w/v) PEG3350, 0.25 M MgCl2, 0.2 M KBr, 0.1 M BisTris, pH 5.5 and 1/10 volume of seed stock in 26% (w/v) PEG3350, 0.25 M MgCl2, 0.2 M KBr, 0.1 M BisTris, pH 5.5. Approximately of this solution 14 uL were added per window of the fixed-target chip. The sample holder was then inserted for into a 3D-printed crystal growth chamber with 3 mL of precipitant solution in the bottom for vapor-diffusion crystallization and incubated at 20C. For fragment application sample holders were removed from the crystal growth chamber and excess precipitant was removed by blotting through the micropores of the membranes, before 10 uL of fragment solution at a concentration of 25 mM in 5% DMSO were pipetted to the crystals in the individual compartments. Sample holders were then placed back into the growths vessel and incubated for 24h. Before data collection sample holder was removed from the crystal growth chamber and excess precipitant was removed by blotting through the micropores of the membranes, before 10 uL of crystallization solution with 5% DMSO were pipetted to the crystals in the individual compartments. Sample holders were then placed back into the growths vessel and incubated for 24h. Before data collection blotting was repeated for removal of excess liquid in order to minimize background scattering. Sample holders were then equipped with a protective cover to prevent them from drying-out and stored in a humid atmosphere. Compound addition and liquid removal were conducted in a glove box with >95% rel. humidity. |
-データ収集
回折 | 平均測定温度: 296.15 K Ambient temp details: Temperature and relative humidity was controlled during experiment using a custom-build setup. Serial crystal experiment: Y |
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放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2023年7月15日 / 詳細: CRL |
放射 | モノクロメーター: Si111 DCM / 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: 0.7749 Å / 相対比: 1 |
反射 | 解像度: 1.4→91.7 Å / Num. obs: 59629 / % possible obs: 99.956 % / 冗長度: 127.58 % / Biso Wilson estimate: 16.05 Å2 / CC1/2: 0.989 / CC star: 0.9972 / R split: 0.1053 / Net I/σ(I): 6.1605 |
反射 シェル | 解像度: 1.4→1.45 Å / 冗長度: 20.7 % / Mean I/σ(I) obs: 0.84 / Num. unique obs: 5846 / CC1/2: 0.346 / CC star: 0.717 / R split: 1.2012 / % possible all: 99.63 |
Serial crystallography sample delivery | 解説: fixed target using Kapton chip / 手法: fixed target |
Serial crystallography sample delivery fixed target | 解説: Crystals were directly grown on the chip surface. Excess liquid was removed by blotting in an glove box to maintain rel. humidity levels >95%. Motion control: Roadrunner Goniometer Sample dehydration prevention: Temperature and rel. humdity levels around sample were tightly controlled with custom setup. Furthermore crystals were protected from dehyration using a mylar cover for the chip. Sample holding: micro-perforated kapton / Sample unit size: 25 µm / Support base: kinematic mount |
Serial crystallography data reduction | Frame hits: 19567 / Frames indexed: 17836 / Frames total: 27740 / Lattices indexed: 24381 |
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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: ![]() 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
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溶媒の処理 | 減衰半径: 0.7 Å / VDWプローブ半径: 0.9 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 20.83 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.4→45.85 Å
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拘束条件 |
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LS精密化 シェル |
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