+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1j5d | |||||||||
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タイトル | SOLUTION STRUCTURE OF OXIDIZED PARAMAGNETIC CU(II) PLASTOCYANIN FROM SYNECHOCYSTIS PCC6803-MINIMIZED AVERAGE STRUCTURE | |||||||||
要素 | PLASTOCYANINプラストシアニン | |||||||||
キーワード | ELECTRON TRANSPORT (電子伝達系) / copper protein beta barrel electron transfer (銅) | |||||||||
機能・相同性 | 機能・相同性情報 plasma membrane-derived thylakoid membrane / electron transfer activity / copper ion binding 類似検索 - 分子機能 | |||||||||
生物種 | Synechocystis sp. PCC 6803 (バクテリア) | |||||||||
手法 | 溶液NMR / energy minimization | |||||||||
データ登録者 | Bertini, I. / Ciurli, S. / Dikiy, A. / Fernandez, C.O. / Luchinat, C. / Safarov, N. / Shumilin, S. / Vila, A.J. | |||||||||
引用 | ジャーナル: J.Am.Chem.Soc. / 年: 2001 タイトル: The first solution structure of a paramagnetic copper(II) protein: the case of oxidized plastocyanin from the cyanobacterium Synechocystis PCC6803. 著者: Bertini, I. / Ciurli, S. / Dikiy, A. / Fernandez, C.O. / Luchinat, C. / Safarov, N. / Shumilin, S. / Vila, A.J. | |||||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 1j5d.cif.gz | 41.1 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1j5d.ent.gz | 28.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1j5d.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/j5/1j5d ftp://data.pdbj.org/pub/pdb/validation_reports/j5/1j5d | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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NMR アンサンブル |
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-要素
#1: タンパク質 | 分子量: 10249.430 Da / 分子数: 1 / 変異: D98E / 由来タイプ: 組換発現 由来: (組換発現) Synechocystis sp. PCC 6803 (バクテリア) 株: PCC6803 / プラスミド: PET3D / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BLR(DE3) / 参照: UniProt: P21697 |
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#2: 化合物 | ChemComp-CU / |
-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: 3 mM plastocyanin U-15N 50 mM phosphate buffer / 溶媒系: 90% H2O/10% D2O |
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試料状態 | イオン強度: 50 mM phosphate / pH: 5.2 / 圧: ambient / 温度: 295 K |
結晶化 | *PLUS 手法: その他 / 詳細: NMR |
-NMR測定
放射 | プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M | |||||||||||||||
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放射波長 | 相対比: 1 | |||||||||||||||
NMRスペクトロメーター |
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-解析
NMR software |
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精密化 | 手法: energy minimization / ソフトェア番号: 1 詳細: The protein contains paramagnetic copper(II), whose electronic relaxation times are quite unfavorable for NMR solution studies. The structure has been solved on the basis of 1041 meaningful ...詳細: The protein contains paramagnetic copper(II), whose electronic relaxation times are quite unfavorable for NMR solution studies. The structure has been solved on the basis of 1041 meaningful NOESY cross peaks, 18 1D NOEs, 26 T1 values, 96 dihedral angle constraints and 18 H-bonds. The detection of broad hyperfine shifted signals and their full assignment allowed the identification of the copper(II) ligands and the determination of the Cu-S-C-H dihedral angle for the coordinated cysteine. The global root mean square deviation from the mean structure for the solution structure family is 0.72 and 1.16 for backbone and heavy atoms, respectively. The mean structure from the DYANA family was calculated using MOLMOL and subjected to restrained energy minimization (REM) using the SANDER module of the AMBER 5.0 program package. The force field parameters for all residues, excluded those for the copper-coordinated ligands, were the standard AMBER "all-atoms" parameters. The calculations were performed in vacuo with the distance-dependent dielectric constant option. The non-bonded interactions were evaluated with a cut-off of 10 A. The mixed linear-harmonic flat-bottomed potential implemented in SANDER was applied to all structural constraints. This potential involves a null force constant for structural constraints within the allowed limits, a non-zero harmonic force constant in a small interval outside the allowed limits, and a linearly dependent potential beyond that limit. NOE-derived distance constraints were restricted below the upper distance limit (ri), using a force constant of 32 kcal mol-1 A-2 for the interval ri+0.5 A. Distance constraints involving the same H-bonds used for DYANA calculations were included in the REM calculation, restricting the NH...O and N...O distances to the same upper (ri) values used in DYANA, with a force constant of 32 kcal mol-1 A-2 for the range ri + 0.5 A. The Cu-H distances derived from the analysis of the non-selective longitudinal relaxation rates were also restrained to the same upper (ri) limits used in DYANA, with a force constant of 32 kcal mol-1 A-2 for ri + 0.5 A. The Cu-NHis and Cu-SCys distances were constrained at 2.1+/-0.1 A and 2.2+/-0.1 A, respectively, using a linear-harmonic flat-bottomed potential with force constants of 50 kcal mol-1 A-2 in the 0.3-A distance ranges below and above these limits. The Cu-SMet distance was analogously constrained within the 2.75+/-0.05 A range, using a force constant of 40 kcal mol-1 A-2. The Cu-N(His)-Cg, Cu-N(His)-Ce, Cu-S(Cys)-Cb, Cu-S(Met)-Cg, and Cu-S(Met)-Ce angles were restrained around 127+/-0, 127+/-0, 105+/-5, 130+/-10, 110+/-10, respectively, using a linear-harmonic flat-bottomed potential with force constants of 50 kcal mol-1 deg-2 in the 50 ranges below and above the given values. Analogously, the (His)N-Cu-N(His), (His)N-Cu-S(Cys), (His)N-Cu-S(Met), and (Met)S-Cu-S(Cys) angles were restrained in the 110+/-10, 125+/-15, 95+/-15, and 100+/-10 range with a force constant of 20 kcal mol-1 deg-2 in the 50 angle ranges below and above these limits. | ||||||||||||||||||||||||
NMRアンサンブル | 登録したコンフォーマーの数: 1 |