ジャーナル: J.Biol.Chem. / 年: 2013 タイトル: Gentamicin binds to the megalin receptor as a competitive inhibitor using the common ligand binding motif of complement type repeats: insight from the nmr structure of the 10th ...タイトル: Gentamicin binds to the megalin receptor as a competitive inhibitor using the common ligand binding motif of complement type repeats: insight from the nmr structure of the 10th complement type repeat domain alone and in complex with gentamicin. 著者: Dagil, R. / O'Shea, C. / Nykjar, A. / Bonvin, A.M. / Kragelund, B.B.
0.6 mM [U-100% 13C; U-100% 15N] CR10, 100 mM sodium chloride, 50 mM calcium chloride, 50 mM TRIS, 0.1 mM DSS, 0.1 % sodium azide, 90% H2O/10% D2O
90% H2O/10% D2O
2
0.6 mM [U-100% 13C; U-100% 15N] CR10, 50 mM calcium chloride, 100 mM sodium chloride, 50 mM TRIS, 0.1 mM DSS, 0.1 % sodium azide, 100% D2O
100% D2O
試料
濃度 (mg/ml)
構成要素
Isotopic labeling
Solution-ID
0.6mM
CR10-1
[U-100% 13C; U-100% 15N]
1
100mM
sodium chloride-2
1
50mM
calcium chloride-3
1
50mM
TRIS-4
1
0.1mM
DSS-5
1
0.1 %
sodium azide-6
1
0.6mM
CR10-7
[U-100% 13C; U-100% 15N]
2
50mM
calcium chloride-8
2
100mM
sodium chloride-9
2
50mM
TRIS-10
2
0.1mM
DSS-11
2
0.1 %
sodium azide-12
2
試料状態
イオン強度: 0.2 / pH: 6.5 / 圧: ambient / 温度: 298 K
-
NMR測定
NMRスペクトロメーター
タイプ
製造業者
モデル
磁場強度 (MHz)
Spectrometer-ID
Varian INOVA
Varian
INOVA
750
1
Varian INOVA
Varian
INOVA
800
2
Bruker Avance
Bruker
AVANCE
800
3
-
解析
NMR software
名称
バージョン
開発者
分類
Analysis
2.2
CCPN
chemicalshiftassignment
Analysis
2.2
CCPN
peakpicking
ARIA
Linge, O'DonoghueandNilges
構造決定
ARIA
Linge, O'DonoghueandNilges
精密化
NMRDraw
Delaglio, Grzesiek, Vuister, Zhu, PfeiferandBax
解析
精密化
手法: simulated annealing / ソフトェア番号: 1
NMR constraints
NOE constraints total: 555 / NOE intraresidue total count: 273 / NOE long range total count: 101 / NOE medium range total count: 87 / NOE sequential total count: 94 / Disulfide bond constraints total count: 3 / Hydrogen bond constraints total count: 15 / Protein phi angle constraints total count: 21 / Protein psi angle constraints total count: 17
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: 200 / 登録したコンフォーマーの数: 20