+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2hep | ||||||
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タイトル | Solution NMR structure of the UPF0291 protein ynzC from Bacillus subtilis. Northeast Structural Genomics target SR384. | ||||||
要素 | UPF0291 protein ynzC | ||||||
キーワード | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / SR384 / AUTOSTRUCTURE / Northeast Structural Genomics Consortium / PSI-1 / Protein Structure Initiative / NESG | ||||||
機能・相同性 | Protein of unknown function DUF896 / Bacterial protein of unknown function (DUF896) / Helix hairpin bin / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / cytoplasm / UPF0291 protein YnzC 機能・相同性情報 | ||||||
生物種 | Bacillus subtilis (枯草菌) | ||||||
手法 | 溶液NMR / simulated annealing | ||||||
データ登録者 | Aramini, J.M. / Swapna, G.V.T. / Ho, C.K. / Shetty, K. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M. / Acton, T.B. ...Aramini, J.M. / Swapna, G.V.T. / Ho, C.K. / Shetty, K. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M. / Acton, T.B. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) | ||||||
引用 | ジャーナル: Proteins / 年: 2008 タイトル: Solution NMR structure of the SOS response protein YnzC from Bacillus subtilis 著者: Aramini, J.M. / Sharma, S. / Huang, Y.J. / Swapna, G.V. / Ho, C.K. / Shetty, K. / Cunningham, K. / Ma, L.C. / Zhao, L. / Owens, L.A. / Jiang, M. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T. ...著者: Aramini, J.M. / Sharma, S. / Huang, Y.J. / Swapna, G.V. / Ho, C.K. / Shetty, K. / Cunningham, K. / Ma, L.C. / Zhao, L. / Owens, L.A. / Jiang, M. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. | ||||||
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 | 2hep.cif.gz | 277.6 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2hep.ent.gz | 227.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2hep.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
文書・要旨 | 2hep_validation.pdf.gz | 342.8 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 2hep_full_validation.pdf.gz | 457.7 KB | 表示 | |
XML形式データ | 2hep_validation.xml.gz | 13.9 KB | 表示 | |
CIF形式データ | 2hep_validation.cif.gz | 22.3 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/he/2hep ftp://data.pdbj.org/pub/pdb/validation_reports/he/2hep | HTTPS FTP |
-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: 9895.350 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Bacillus subtilis (枯草菌) / 遺伝子: ynzC / プラスミド: PET21, SR384-21.4 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3)MGK / 参照: UniProt: O31818 |
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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. AUTOASSIGN was used to obtain automatic backbone assignments from GFT peak lists. Side chain assignments were completed ...Text: The structure was determined using triple resonance NMR spectroscopy. AUTOASSIGN was used to obtain automatic backbone assignments from GFT peak lists. Side chain assignments were completed manually. Automatic NOESY assignment, as well as distance and hydrogen bond constraints were determined using AutoStructure. Dihedral angle constraints were determined using HYPER. Completeness of NMR assignments (excluding C-terminal LEHHHHHH tag): Backbone: 91.9%; Side chain: 78.3%; Aromatics, 100%: Stereospecific methyl, 87.5%. Final structure quality factors (for residues 1 to 42 only; PSVS 1.2), where ordered residues [S(PHI)+ S(PSI) > 1.8] comprise 5-20 and 23-40: (A) RMSD (ordered residues): BB, 0.9; heavy atom, 1.5. (B) Ramachandran statistics for ordered residues: Most favored, 96.4%, Additionally allowed, 3.6%, generously allowed, 0.0%, disallowed, 0.0%. (C) Procheck scores for ordered residues (Raw/Z-): PHI-PSI, 0.11/0.75; All, -0.12/-0.71. (D) Molprobity clash score (Raw/Z-): 14.69/-1.00. (E) RPF scores for goodness of fit to NOESY data (all residues): Recall, 0.952, Precision, 0.839, F-measure, 0.892, DP-score, 0.628 |
-試料調製
詳細 |
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試料状態 | イオン強度: 100 mM NaCl / pH: 6.5 / 圧: ambient / 温度: 293 K |
-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: simulated annealing / ソフトェア番号: 1 詳細: The structures are based on a total of 403 conformationally restricting NOE-derived distance constraints, 67 dihedral angle constraints, 42 hydrogen bond constraints, and 29 J(HN-Halpha) ...詳細: The structures are based on a total of 403 conformationally restricting NOE-derived distance constraints, 67 dihedral angle constraints, 42 hydrogen bond constraints, and 29 J(HN-Halpha) coupling constants (12.5 constraints per residue; 1.1 long range constraints per residue; computed for residues 1 to 42 by PSVS 1.2). Structure determination was performed iteratively using AutoStructure (XPLOR-NIH). A final XPLOR calculation using the final constraints derived from AutoStructure was performed to yield the final structures. The unstructured C-terminal half of the molecule was included in all structural calculations but has been omitted from this deposition. Heteronuclear 15N,1H NOE experiments corroborate the presence of significant disorder in the C-terminal half of the protein (residues 43 to C-terminus). | ||||||||||||||||||||||||||||||||||||||||
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 lowest conformational 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: 20 |