+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2g7j | ||||||
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タイトル | Solution NMR structure of the putative cytoplasmic protein ygaC from Salmonella typhimurium. Northeast Structural Genomics target StR72. | ||||||
要素 | putative cytoplasmic protein | ||||||
キーワード | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / StR72 / AUTOSTRUCTURE / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
機能・相同性 | Protein of unknown function DUF2002 / Protein of unknown function DUF2002 / Protein of unknown function (DUF2002) / Aspartate Aminotransferase, domain 1 / Alpha-Beta Complex / Alpha Beta / : / Putative cytoplasmic protein 機能・相同性情報 | ||||||
生物種 | Salmonella typhimurium (サルモネラ菌) | ||||||
手法 | 溶液NMR / simulated annealing | ||||||
データ登録者 | Aramini, J.M. / Swapna, G.V.T. / Ramelot, T.A. / Ho, C.K. / Cunningham, K. / Ma, L.-C. / Shetty, K. / Xiao, R. / Acton, T.B. / Kennedy, M.A. ...Aramini, J.M. / Swapna, G.V.T. / Ramelot, T.A. / Ho, C.K. / Cunningham, K. / Ma, L.-C. / Shetty, K. / Xiao, R. / Acton, T.B. / Kennedy, M.A. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) | ||||||
引用 | ジャーナル: To be Published タイトル: Solution NMR structure of the putative cytoplasmic protein ygaC from Salmonella typhimurium. Northeast Structural Genomics target StR72. 著者: Aramini, J.M. / Swapna, G.V.T. / Ramelot, T.A. / Ho, C.K. / Cunningham, K. / Ma, L.-C. / Shetty, K. / Xiao, R. / Acton, T.B. / Kennedy, M.A. / 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 | 2g7j.cif.gz | 695 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2g7j.ent.gz | 579 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2g7j.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 | 2g7j_validation.pdf.gz | 348.2 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 2g7j_full_validation.pdf.gz | 491.6 KB | 表示 | |
XML形式データ | 2g7j_validation.xml.gz | 34.8 KB | 表示 | |
CIF形式データ | 2g7j_validation.cif.gz | 58.2 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/g7/2g7j ftp://data.pdbj.org/pub/pdb/validation_reports/g7/2g7j | HTTPS FTP |
-関連構造データ
類似構造データ | |
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その他のデータベース |
-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: 14405.094 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) Salmonella typhimurium (サルモネラ菌) 株: LT2 / 遺伝子: ygaC / プラスミド: StR72-21.1 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3)MGK / 参照: GenBank: 16421350, UniProt: Q8ZML5*PLUS |
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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. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN, AND THE ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ...Text: THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN, AND THE ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE AND HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING AUTOSTRUCTURE. DIHEDRAL ANGLE CONSTRAINTS WERE DETERMINED USING HYPER AND TALOS. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HHHHHH): BACKBONE, 100%, SIDE CHAIN, 94.6%, AROMATICS, 91.1%, STEREOSPECIFIC METHYL, 94.4%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 to 112, PSVS 1.2), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE 3-43,49-50,55-66,69-71,75-76,88-96,98-109: (A) RMSD (ORDERED RESIDUES): BB, 0.6, HEAVY ATOM, 1.1. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 87.4%, ADDITIONALLY ALLOWED, 12.4%, GENEROUSLY ALLOWED, 0.2%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.34/-1.02, ALL, -0.32/-1.89. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 25.21/-2.80. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (ALL RESIDUES): RECALL, 0.971, PRECISION, 0.945, F-MEASURE, 0.958, DP-SCORE, 0.846. |
-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 / 散乱光タイプ: x-ray | ||||||||||||||||||||
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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 1759 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 219 DIHEDRAL ANGLE CONSTRAINTS, AND 58 HYDROGEN BOND CONSTRAINTS (18.2 CONSTRAINTS ...詳細: THE STRUCTURES ARE BASED ON A TOTAL OF 1759 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 219 DIHEDRAL ANGLE CONSTRAINTS, AND 58 HYDROGEN BOND CONSTRAINTS (18.2 CONSTRAINTS PER RESIDUE, 6.7 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 to 112 BY PSVS 1.2). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING AUTOSTRUCTURE (XPLOR-NIH). AFTER A FINAL XPLOR CALCULATION USING THE FINAL CONSTRAINTS DERIVED FROM AUTOSTRUCTURE, THE 20 LOWEST ENERGY STRUCTURES OUT OF 100 WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYANMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS). THE UNSTRUCTURED C-TERMINUS OF THE PROTEIN (EKTD + LEHHHHHH TAG) WERE INCLUDED IN ALL STRUCTURE CALCULATIONS BUT HAVE BEEN OMITTED FROM THIS DEPOSITION. | ||||||||||||||||||||||||||||||||||||||||
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 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: 20 |