+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1dxa | ||||||
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タイトル | BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA IN DUPLEX DNA | ||||||
要素 |
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キーワード | DNA / DOUBLE HELIX / BENZO[A]PYRENE DIOL EPOXIDE ADDUCT / DUPLEX DNA / NON-WATSON-CRICK BASE PAIR | ||||||
機能・相同性 | 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE / DNA 機能・相同性情報 | ||||||
手法 | 溶液NMR / ENERGY MINIMIZATION, MOLECULAR DYNAMICS | ||||||
データ登録者 | Yeh, H.J.C. / Sayer, J.M. / Liu, X. / Altieri, A.S. / Byrd, R.A. / Lakshman, M.K. / Yagi, H. / Schurter, E.J. / Gorenstein, D.G. / Jerina, D.M. | ||||||
引用 | ジャーナル: Biochemistry / 年: 1995 タイトル: NMR solution structure of a nonanucleotide duplex with a dG mismatch opposite a 10S adduct derived from trans addition of a deoxyadenosine N6-amino group to (+)-(7R,8S,9S,10R)-7,8- ...タイトル: NMR solution structure of a nonanucleotide duplex with a dG mismatch opposite a 10S adduct derived from trans addition of a deoxyadenosine N6-amino group to (+)-(7R,8S,9S,10R)-7,8-dihydroxy-9,10-epoxy-7,8,9,10- tetrahydrobenzo[a]pyrene: an unusual syn glycosidic torsion angle at the modified dA 著者: Yeh, H.J. / Sayer, J.M. / Liu, X. / Altieri, A.S. / Byrd, R.A. / Lakshman, M.K. / Yagi, H. / Schurter, E.J. / Gorenstein, D.G. / Jerina, D.M. | ||||||
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 | 1dxa.cif.gz | 22.1 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1dxa.ent.gz | 14 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1dxa.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 | 1dxa_validation.pdf.gz | 385.4 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 1dxa_full_validation.pdf.gz | 384.5 KB | 表示 | |
XML形式データ | 1dxa_validation.xml.gz | 1.8 KB | 表示 | |
CIF形式データ | 1dxa_validation.cif.gz | 2 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/dx/1dxa ftp://data.pdbj.org/pub/pdb/validation_reports/dx/1dxa | 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: DNA鎖 | 分子量: 2780.836 Da / 分子数: 1 / 由来タイプ: 合成 / 詳細: chemically synthesized / キーワード: DEOXYRIBONUCLEIC ACID |
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#2: DNA鎖 | 分子量: 2716.787 Da / 分子数: 1 / 由来タイプ: 合成 / 詳細: chemically synthesized / キーワード: DEOXYRIBONUCLEIC ACID |
#3: 化合物 | ChemComp-BAP / |
-実験情報
-実験
実験 | 手法: 溶液NMR |
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NMR実験の詳細 | Text: (+)-(7R,8S,9S,10R)-7,8-DIHYDROXY-9,10-EPOXY-7,8,9,10- TETRAHYDROBENZO[A]PYRENE IS COVALENTLY BONDED TO THE EXOCYCLIC N6 AMINO GROUP OF DEOXYADENOSINE IN THE CENTER OF THE DUPLEX THROUGH TRANS ...Text: (+)-(7R,8S,9S,10R)-7,8-DIHYDROXY-9,10-EPOXY-7,8,9,10- TETRAHYDROBENZO[A]PYRENE IS COVALENTLY BONDED TO THE EXOCYCLIC N6 AMINO GROUP OF DEOXYADENOSINE IN THE CENTER OF THE DUPLEX THROUGH TRANS ADDITION AT THE C10 OF THE EPOXIDE. |
-試料調製
結晶化 | *PLUS 手法: other |
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-解析
NMR software | 名称: NMRCHITECT / 開発者: BIOSYM / 分類: 精密化 |
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精密化 | 手法: ENERGY MINIMIZATION, MOLECULAR DYNAMICS / ソフトェア番号: 1 詳細: TWO STARTING STRUCTURES WITH BENZO[A]PYRENE MOIETY INSIDE THE DUPLEX AND OUTSIDE THE DUPLEX, RESPECTIVELY, WERE GENERATED BY CONNECTING A STANDARD B-TYPE DNA FRAGMENT WITH A MANUALLY BUILD (+) ...詳細: TWO STARTING STRUCTURES WITH BENZO[A]PYRENE MOIETY INSIDE THE DUPLEX AND OUTSIDE THE DUPLEX, RESPECTIVELY, WERE GENERATED BY CONNECTING A STANDARD B-TYPE DNA FRAGMENT WITH A MANUALLY BUILD (+)-DE2-[BAP] FRAGMENT. SOLUTION STRUCTURES FOR THE DUPLEX WERE GENERATED BY RESTRAINTED MOLECULAR DYNAMICS AND RESTRAINTED ENERGY MINIMIZATION USING A SET OF INTER-PROTON DISTANCE RESTRAINTS AND DIHEDRAL ANGLE RESTRAINTS WHICH WERE DERIVED FROM NMR EXPERIMENTS. SOME OF STRUCTURES WITH MINIMUM RESTRAINT VIOLATIONS WERE FURTHER REFINED BY THE ITERATIVE RELAXATION MATRIX ANALYSIS (IRMA) METHOD OVER 111 WELL-SEPARATED CROSS PEAKS IN NOESY SPECTRA RECORDED IN D2O AND MIXING TIMES OF 50, 80, 120, 160 AND 200 MS. THE STRUCTURE PRESENTED HERE WAS ONE OF THE FIVE REFINED AND MINIMIZED STRUCTURES. THE FOLLOWING RESTRAINTS WERE APPLIED IN THE MOLECULAR DYNAMICS/ENERGY MINIMIZATION CALCULATIONS. THESE WERE; (1) INTER-PROTON DISTANCE RESTRAINTS DIRECTLY DERIVED FROM NOE DATA; (2) BACKBONE DIHEDRAL ANGLE RESTRAINTS FOR A STANDARD B-DNA EXCEPT THOSE IMMEDIATELY ADJACENT TO THE MODIFIED RESIDUE; (3) DIHEDRAL ANGLE RESTRAINTS FOR ALL GLYCOSIDIC BONDS, EXCEPT MODIFIED DA RESIDUE IN THE CENTER; (4) HYDROGEN BOND RESTRAINTS (BOTH DISTANCE AND PLANARITY ) FOR ALL BASE-PAIRS EXCEPT CENTRAL DA-DG MISMATCH PAIR. THESE RESTRAINTS WERE JUSTIFIED BY THE FACT THAT THE MODIFIED DUPLEX DISPLAYED CHARACTERISTIC NMR SPECTRA OF A B-DNA EXCEPT NEAR LESION SITE, WHERE THE BAP MOIETY WAS INTERCALATED. THE MODIFIED DA RESIDUE DISPLAYED C3'-ENDO SUGAR RING AND A SYN GLYCOSIDIC BOND. IT ALSO FORMED A NON-WATSON-CRICK BASE PAIR WITH THE OPPOSITE DG. |
NMRアンサンブル | 登録したコンフォーマーの数: 1 |