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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: 2jx6 | ||||||
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タイトル | Structure and membrane interactions of the antibiotic peptide dermadistinctin k by solution and oriented 15N and 31P solid-state NMR spectroscopy | ||||||
![]() | Dermadistinctin-K | ||||||
![]() | ANTIMICROBIAL PROTEIN / ALPHA HELIX / AMPHIPATHIC CHARACTER / C-TERMINAL CARBOXYAMIDATION / MEMBRANE PEPTIDE / Amphibian defense peptide / Antibiotic / Antimicrobial / Secreted | ||||||
機能・相同性 | Dermaseptin / Dermaseptin / defense response to bacterium / extracellular region / Dermaseptin-DI1![]() | ||||||
生物種 | Phyllomedusa distincta (カエル) | ||||||
手法 | 溶液NMR / simulated annealing | ||||||
![]() | Mendonca Moraes, C. / Verly, R.M. / Resende, J.M. / Bemquerer, M.P. / Pilo-Veloso, D. / Valente, A. / Almeida, F.C.L. / Bechinger, B. | ||||||
![]() | ![]() タイトル: Structure and membrane interactions of the antibiotic peptide dermadistinctin K by multidimensional solution and oriented 15N and 31P solid-state NMR spectroscopy 著者: Verly, R.M. / de Moraes, C.M. / Resende, J.M. / Aisenbrey, C. / Bemquerer, M.P. / Pilo-Veloso, D. / Valente, A.P. / Almeida, F.C.L. / Bechinger, B. | ||||||
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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PDBx/mmCIF形式 | ![]() | 181.1 KB | 表示 | ![]() |
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PDB形式 | ![]() | 158.5 KB | 表示 | ![]() |
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その他 | ![]() |
-検証レポート
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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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NMR アンサンブル |
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要素
#1: タンパク質・ペプチド | 分子量: 3156.699 Da / 分子数: 1 / 由来タイプ: 合成 詳細: The peptide was synthesized by solid-phase synthesis using fmoc chemistry. The peptide is an antimicrobial peptide that is naturally found from the skin secretion of phyllomedusa distincta, a ...詳細: The peptide was synthesized by solid-phase synthesis using fmoc chemistry. The peptide is an antimicrobial peptide that is naturally found from the skin secretion of phyllomedusa distincta, a frog species found in brazilian forests. 由来: (合成) Phyllomedusa distincta (カエル) / 参照: UniProt: P83638 |
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-実験情報
-実験
実験 | 手法: 溶液NMR | ||||||||||||||||||||
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NMR実験 |
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試料調製
詳細 | 内容: 2.0mM dermadistinctin k; trifluoroethanol; H2O 60%, D2O 40% 溶媒系: trifluoroethanol; H2O 60%, D2O 40% |
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試料 | 濃度: 2.0 mM / 構成要素: dermadistinctin k |
試料状態 | pH: 7 / 圧: ambient / 温度: 293.15 K |
-NMR測定
NMRスペクトロメーター | タイプ: Bruker Avance DRX / 製造業者: Bruker / モデル: AVANCE DRX / 磁場強度: 600 MHz |
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解析
NMR software |
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精密化 | 手法: simulated annealing / ソフトェア番号: 1 詳細: NOE intensities were converted into semi-quantitative distances restrains. The upper limits of the distances thus obtained were 2.8, 3.4 and 5.0A; (for strong, medium, and weak NOEs, ...詳細: NOE intensities were converted into semi-quantitative distances restrains. The upper limits of the distances thus obtained were 2.8, 3.4 and 5.0A; (for strong, medium, and weak NOEs, respectively). Structure calculations were performed using the Xplor-NIH software, version 2.17.0 . Starting with the extended structure, 500 structures were generated using a simulated annealing protocol. This was followed by 20000 steps of simulated annealing at 1000 K and a subsequent decrease in tempera ure in 15000 steps in the first slow-cool annealing stage. | ||||||||||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 294 / NOE intraresidue total count: 178 / NOE long range total count: 0 / NOE medium range total count: 38 / NOE sequential total count: 78 | ||||||||||||||||||||||||||||||||||||||||
代表構造 | 選択基準: lowest energy | ||||||||||||||||||||||||||||||||||||||||
NMRアンサンブル | コンフォーマー選択の基準: structures with the lowest energy 計算したコンフォーマーの数: 500 / 登録したコンフォーマーの数: 20 / 代表コンフォーマー: 19 |