- PDB-1tkw: The transient complex of poplar plastocyanin with turnip cytochro... -
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基本情報
登録情報
データベース: PDB / ID: 1tkw
タイトル
The transient complex of poplar plastocyanin with turnip cytochrome f determined with paramagnetic NMR
要素
Cytochrome f
Plastocyanin A
キーワード
PHOTOSYNTHESIS / Electron transfer / paramagnetic / rigid body calculations
機能・相同性
機能・相同性情報
electron transporter, transferring electrons from cytochrome b6/f complex of photosystem II activity / chloroplast thylakoid lumen / chloroplast thylakoid membrane / photosynthesis / electron transfer activity / iron ion binding / copper ion binding / heme binding 類似検索 - 分子機能
Cytochrome f large domain / Cytochrome f transmembrane anchor / Cytochrome f / Cytochrome f large domain / Cytochrome f large domain superfamily / Apocytochrome F, C-terminal / Apocytochrome F, N-terminal / Cytochrome f family profile. / Plastocyanin / Blue (type 1) copper protein, plastocyanin-type ...Cytochrome f large domain / Cytochrome f transmembrane anchor / Cytochrome f / Cytochrome f large domain / Cytochrome f large domain superfamily / Apocytochrome F, C-terminal / Apocytochrome F, N-terminal / Cytochrome f family profile. / Plastocyanin / Blue (type 1) copper protein, plastocyanin-type / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Rudiment single hybrid motif / Cupredoxins - blue copper proteins / Cupredoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta 類似検索 - ドメイン・相同性
COPPER (II) ION / HEME C / Plastocyanin A, chloroplastic / Cytochrome f 類似検索 - 構成要素
生物種
Populus nigra (クロヤマナラシ) Brassica rapa subsp. rapa (カブラ)
手法
溶液NMR / Rigid body docking using intermolecular pseudocontact shifts restraints, chemical shift perturbation restraints, electrostatic restraints.
Text: This structure was determined using the XRD structures of plastocyanin and cytochrome f, docked on the basis of intermolecular pseudocontact shifts and chemical shift perturbations due to binding.
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試料調製
詳細
Solution-ID
内容
溶媒系
1
0.5 mM Cd-substituted poplar plastocyanin + 0.35 mM soluble fragment of turnip cytochrome f in oxidized state in 10 mM sodium phosphate pH 6.0
94% H2O, 6% D2O
2
0.5 mM Cd-substituted poplar plastocyanin + 0.35 mM soluble fragment of turnip cytochrome f in reduced state in 10 mM sodium phosphate pH 6.0 + 1 mM sodium ascorbate
94% H2O, 6% D2O
試料状態
Conditions-ID
イオン強度
pH
圧 (kPa)
温度 (K)
1
10mM
6
1atm
303K
2
11mM
6
1atm
303K
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NMR測定
放射
プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M
放射波長
相対比: 1
NMRスペクトロメーター
タイプ: Bruker DMX / 製造業者: Bruker / モデル: DMX / 磁場強度: 600 MHz
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解析
NMR software
名称
バージョン
開発者
分類
Azara
2.7
W. Boucher
解析
ANSIG
Ansig-for-Windows 1.02
P. Kraulis, M. Helgstrand
データ解析
X-PLOR
XPLOR-NIH 2.9.1
構造決定
X-PLOR
XPLOR-NIH 2.9.1
精密化
精密化
手法: Rigid body docking using intermolecular pseudocontact shifts restraints, chemical shift perturbation restraints, electrostatic restraints. ソフトェア番号: 1 詳細: The structures are based on 38 chemical shift perturbation restraints, 42 pseudocontact shifts restraints, 42 pseudocontact angle restraints, 120 minimal distance restraints and 4 ...詳細: The structures are based on 38 chemical shift perturbation restraints, 42 pseudocontact shifts restraints, 42 pseudocontact angle restraints, 120 minimal distance restraints and 4 electrostatic restraints. Backbone RMSD (in Angstrom) with the mean for each model: 1: 1.28, 2: 2.26, 3: 1.29, 4: 3.12, 5: 1.52, 6: 1.49, 7: 3.68, 8: 2.68, 9: 1.58, 10: 3.43, average=2.23+/-0.88
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 least restraint violations 計算したコンフォーマーの数: 104 / 登録したコンフォーマーの数: 10