BMRB: 34869Solution NMR structure of the peptidyl carrier domain TomAPCP from the Tomaymycin non-ribosomal peptide synthetase in its substrate-loaded state
分子量: 10483.499 Da / 分子数: 1 / 由来タイプ: 組換発現 詳細: First four residues (GPMA) in the protein are from cloning artifacts. Therefore, the appropriate residue numbering has the first residue (G) designated as residue-number '-3', so that the ...詳細: First four residues (GPMA) in the protein are from cloning artifacts. Therefore, the appropriate residue numbering has the first residue (G) designated as residue-number '-3', so that the fifth residue has residue-number '1'. A special modified residue SPA is designated for the serine residue covalently linked to a 4'-phosphopantetheine-anthranilate prosthetic group. 由来: (組換発現) Streptomyces regensis (バクテリア) Variant: FH6421 / 発現宿主: Escherichia coli (大腸菌)
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
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実験
実験
手法: 溶液NMR
NMR実験
Conditions-ID
Experiment-ID
Solution-ID
Sample state
Spectrometer-ID
タイプ
1
1
1
isotropic
1
2D 1H-15N HSQC
1
2
3
isotropic
2
2D 1H-13C HSQC
1
3
2
isotropic
2
2D 1H-13C HSQC
1
4
1
isotropic
1
3D 1H-15N NOESY
1
5
2
isotropic
2
3D 1H-13C NOESY
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試料調製
詳細
タイプ
Solution-ID
内容
Label
溶媒系
solution
1
350 uM [U-13C; U-15N] TomAPCP substrate-loaded, 50 mM sodium phosphate, 150 mM sodium chloride, 0.02 w/v sodium azide, 10 v/v [U-2H] D2O, 90% H2O/10% D2O
13C15N_sample
90% H2O/10% D2O
solution
3
100 uM [U-13C; U-15N] TomAPCP substrate-loaded, 50 mM sodium phosphate, 150 mM sodium chloride, 0.02 w/v sodium azide, 10 v/v [U-2H] D2O, 90% H2O/10% D2O
13C15N_sample_2
90% H2O/10% D2O
solution
2
500 uM [U-13C; U-15N] TomAPCP substrate-loaded, 50 mM sodium phosphate, 150 mM sodium chloride, 0.02 % w/v sodium azide, 100 v/v [U-2H] D2O, 100% D2O
13C15N_D2O_sample
100% D2O
試料
濃度 (mg/ml)
構成要素
Isotopic labeling
Solution-ID
350uM
TomAPCP substrate-loaded
[U-13C; U-15N]
1
50mM
sodiumphosphate
naturalabundance
1
150mM
sodiumchloride
naturalabundance
1
0.02w/v
sodiumazide
naturalabundance
1
10v/v
D2O
[U-2H]
1
100uM
TomAPCP substrate-loaded
[U-13C; U-15N]
3
50mM
sodiumphosphate
naturalabundance
3
150mM
sodiumchloride
naturalabundance
3
0.02w/v
sodiumazide
naturalabundance
3
10v/v
D2O
[U-2H]
3
500uM
TomAPCP substrate-loaded
[U-13C; U-15N]
2
50mM
sodiumphosphate
naturalabundance
2
150mM
sodiumchloride
naturalabundance
2
0.02 % w/v
sodiumazide
naturalabundance
2
100v/v
D2O
[U-2H]
2
試料状態
イオン強度: 265 mM / Label: conditions_1 / pH: 7 / 圧: 1 atm / 温度: 298 K
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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
Bruker AVANCE III
Bruker
AVANCEIII
600
1
Bruker AVANCE III HD
Bruker
AVANCEIIIHD
850
2
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解析
NMR software
名称
バージョン
開発者
分類
TopSpin
3.2
BrukerBiospin
collection
NMRPipe
10.2
Delaglio, Grzesiek, Vuister, Zhu, PfeiferandBax
解析
CcpNmr Analysis
2.4
CCPN
peakpicking
CcpNmr Analysis
2.4
CCPN
chemicalshiftassignment
CcpNmr Analysis
2.4
CCPN
データ解析
ARIA
2.3
Linge, O'DonoghueandNilges
structurecalculation
CNS
1.21
Brunger, Adams, Clore, Gros, NilgesandRead
structurecalculation
CNS
1.21
Brunger, Adams, Clore, Gros, NilgesandRead
structurecalculation
CNS
1.21
Brunger, Adams, Clore, Gros, NilgesandRead
structurecalculation
精密化
手法
ソフトェア番号
simulated annealing
7
torsion angle dynamics
8
molecular dynamics
9
代表構造
選択基準: closest to the average
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: 100 / 登録したコンフォーマーの数: 10