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基本情報
登録情報 | データベース: PDB / ID: 1yh5 | ||||||
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タイトル | Solution NMR Structure of Protein yggU from Escherichia coli. Northeast Structural Genomics Consortium Target ER14. | ||||||
![]() | ORF, HYPOTHETICAL PROTEIN | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / ALPHA+BETA / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / PSI / Protein Structure Initiative / NESG | ||||||
機能・相同性 | ![]() | ||||||
生物種 | ![]() ![]() | ||||||
手法 | 溶液NMR / TORSION ANGLE DYNAMICS SIMULATED ANNEALING | ||||||
![]() | Aramini, J.M. / Xiao, R. / Huang, Y.J. / Acton, T.B. / Wu, M.J. / Mills, J.L. / Tejero, R.T. / Szyperski, T. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() タイトル: Solution Structure of the Hypothetical Protein Yggu from E. Coli. Northeast Structural Genomics Consortium Target Er14. 著者: Aramini, J.M. / Xiao, R. / Huang, Y.J. / Acton, T.B. / Wu, M.J. / Mills, J.L. / Tejero, R.T. / Szyperski, T. / Montelione, G.T. #1: ![]() タイトル: Protein NMR Recall, Precision, and F-measure scores (RFP Scores): Structure Quality Assessment Measures Based on Information Retrieval Statistics 著者: Huang, Y.J. / Powers, R. / Montelione, G.T. | ||||||
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 | ![]() | 336.9 KB | 表示 | ![]() |
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PDB形式 | ![]() | 276.6 KB | 表示 | ![]() |
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-検証レポート
文書・要旨 | ![]() | 347.2 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 426.6 KB | 表示 | |
XML形式データ | ![]() | 21.3 KB | 表示 | |
CIF形式データ | ![]() | 33.3 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | |
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類似構造データ | |
その他のデータベース |
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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 | 分子量: 11903.733 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() |
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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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NMR実験の詳細 | Text: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY. AUTOMATIC BACKBONE RESONANCE ASSIGNMENTS WERE MADE USING AUTOASSIGN. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE AND ...Text: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY. AUTOMATIC BACKBONE RESONANCE ASSIGNMENTS WERE MADE USING AUTOASSIGN. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE AND HYDROGEN BOND RESTRAINTS WERE DETERMINED USING THE AUTOSTRUCTURE PROGRAM. DIHEDRAL ANGLE RESTRAINTS WERE DETERMINED USING HYPER AND TALOS.FINAL STRUCTURE QUALITY FACTORS FOR THE ENSEMBLE, WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE 8-23,28-29,31-34,37-41,44-65,67-77,80-87: (A) RMSD FOR ORDERED RESIDUES: BB, 0.7 ANG; HEAVY ATOM, 1.2 ANG. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED: 75.9%; ADDITIONALLY ALLOWED: 23.0%; GENEROUSLY ALLOWED, 1.0%; DISALLOWED, 0.2% (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z): BB, -1.14/-2.23; ALL, -1.0/-4.17. (D) MAGE MOLPROBITY CLASH SCORE (RAW/Z): 33.22/-4.18 (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA: F-MEASURE, 0.944; RECALL, 0.977; PRECISION, 0.802; DP-SCORE, 0.726. |
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試料調製
詳細 | 内容: 1.0 MM ER14 U-15N,13C IN 20MM MES, 50MM NACL, 5MM DTT, PH 6.5; 1.0 MM ER14 U-15N,13C IN 20MM MES, 50MM NACL, 5MM DTT, PH 6.5 |
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試料状態 | イオン強度: 50 mM NACL / pH: 6.5 / 圧: AMBIENT / 温度: 293 K |
-NMR測定
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: TORSION ANGLE DYNAMICS SIMULATED ANNEALING / ソフトェア番号: 1 詳細: THE STRUCTURE IS BASED ON A TOTAL OF 1031 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 207 DIHEDRAL ANGLE CONSTRAINTS, AND 56 HYDROGEN BOND CONSTRAINTS (12.6 CONSTRAINTS PER ...詳細: THE STRUCTURE IS BASED ON A TOTAL OF 1031 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 207 DIHEDRAL ANGLE CONSTRAINTS, AND 56 HYDROGEN BOND CONSTRAINTS (12.6 CONSTRAINTS PER RESIDUE; 4.1 LONG-RANGE CONTRAINTS PER RESIDUE). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING AUTOSTRUCTURE WITH XPLOR. | ||||||||||||||||||||||||||||||||||||||||||||
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: 56 / 登録したコンフォーマーの数: 10 |