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基本情報
登録情報 | データベース: PDB / ID: 1d8b | ||||||
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タイトル | NMR STRUCTURE OF THE HRDC DOMAIN FROM SACCHAROMYCES CEREVISIAE RECQ HELICASE | ||||||
![]() | SGS1 RECQ HELICASE | ||||||
![]() | DNA BINDING PROTEIN / FIVE HELICES / THREE-HELICAL BUNDLE FLANKED BY TWO HELICES | ||||||
機能・相同性 | ![]() negative regulation of meiotic joint molecule formation / gene conversion at mating-type locus => GO:0007534 / regulation of reciprocal meiotic recombination / : / meiotic DNA double-strand break processing / telomeric 3' overhang formation / RecQ family helicase-topoisomerase III complex / meiotic chromosome segregation / four-way junction helicase activity / DNA double-strand break processing ...negative regulation of meiotic joint molecule formation / gene conversion at mating-type locus => GO:0007534 / regulation of reciprocal meiotic recombination / : / meiotic DNA double-strand break processing / telomeric 3' overhang formation / RecQ family helicase-topoisomerase III complex / meiotic chromosome segregation / four-way junction helicase activity / DNA double-strand break processing / telomere maintenance via recombination / mitotic G2/M transition checkpoint / mitotic intra-S DNA damage checkpoint signaling / DNA duplex unwinding / DNA unwinding involved in DNA replication / mitotic sister chromatid segregation / 3'-5' DNA helicase activity / DNA topological change / chromosome organization / DNA helicase activity / telomere maintenance / double-strand break repair via homologous recombination / chromosome / DNA recombination / DNA helicase / nucleic acid binding / DNA repair / nucleolus / ATP binding / nucleus / cytoplasm 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() | ||||||
手法 | 溶液NMR / ARIA (AMBIGUOUS RESTRAINTS IN ITERATIVE ASSIGNMENTS) AMBIGUOUS DISTANCE RESTRAINTS SIMULATED ANNEALING WITH TORSION ANGLE DYNAMICS | ||||||
![]() | Liu, Z. / Macias, M.J. / Bottomley, M.J. / Stier, G. / Linge, J.P. / Nilges, M. / Bork, P. / Sattler, M. | ||||||
![]() | ![]() タイトル: The three-dimensional structure of the HRDC domain and implications for the Werner and Bloom syndrome proteins. 著者: Liu, Z. / Macias, M.J. / Bottomley, M.J. / Stier, G. / Linge, J.P. / Nilges, M. / Bork, P. / Sattler, M. | ||||||
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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その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 348 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 446.8 KB | 表示 | |
XML形式データ | ![]() | 20.2 KB | 表示 | |
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-関連構造データ
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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: 9385.962 Da / 分子数: 1 / 断片: HRDC DOMAIN / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 発現宿主: ![]() ![]() |
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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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試料調製
詳細 |
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試料状態 | イオン強度: 20 mM SODIUM PHOSPHATE / pH: 6.5 / 圧: 1 bar / 温度: 295 K | |||||||||
結晶化 | *PLUS 手法: other / 詳細: NMR |
-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: ARIA (AMBIGUOUS RESTRAINTS IN ITERATIVE ASSIGNMENTS) AMBIGUOUS DISTANCE RESTRAINTS SIMULATED ANNEALING WITH TORSION ANGLE DYNAMICS ソフトェア番号: 1 詳細: STARTING WITH AN ALMOST COMPLETE LIST OF CHEMICAL SHIFTS, THE PROGRAM ARIA ( AMBIGUOUS RESTRAINTS IN ITERATIVE ASSIGNMENT) CALIBRATES NOES, MERGES THE OBTAINED AMBIGUOUS DISTANCE RESTRAINTS ...詳細: STARTING WITH AN ALMOST COMPLETE LIST OF CHEMICAL SHIFTS, THE PROGRAM ARIA ( AMBIGUOUS RESTRAINTS IN ITERATIVE ASSIGNMENT) CALIBRATES NOES, MERGES THE OBTAINED AMBIGUOUS DISTANCE RESTRAINTS FROM DIFFERENT NOE SPECTRA AND ASSIGNS THE NOE PEAKS IN AN ITERATIVE MANNER. FROM A TOTAL OF 1890 NOES ABOUT 85% WERE MANUALLY ASSIGNED, THE REMAINDER WAS ASSIGNED BY ARIA. FLOATING POINT CHIRALITY ASSIGNMENT WAS USED DURING THE STRUCTURE CALCULATION IN ORDER TO OBTAIN STEREOSPECIFIC ASSIGNMENTS FOR METHYL AND METHYLENE GROUPS. THEREFORE, SOME METHYL AND METHYLENE CARBON/PROTON ATOM NAMES IN THE RESTRAINT FILES MIGHT BE INCONSISTENT COMPARED TO THOSE IN THE COORIDINATE FILES. THE DEPOSITED STRUCTURES HAVE BEEN WATER-REFINED AS DESCRIBED IN THE PUBLICATION. PSI REFINEMENT: THE STRUCTURES HAVE BEEN DIRECTLY REFINED AGAINST CROSS- CORRELATED RELAXATION RATES (C-ALPHA-H-ALPHA DIPOLE, CO CSA) AND THE THREE- BOND H/D ISOTOPE EFFECT ON THE C-ALPHA CHEMICAL SHIFT. "REFINEMENT OF THE PROTEIN BACKBONE ANGLE PSI IN NMR STRUCTURE CALCULATIONS." SPRANGERS, BOTTOMLEY, LINGE, SCHULTZ, NILGES, SATTLER. | ||||||||||||||||||||||||||||
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 ACCEPTABLE COVALENT GEOMETRY, STRUCTURES WITH FAVORABLE NON- BOND 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: 15 |