+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1a4t | ||||||
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タイトル | SOLUTION STRUCTURE OF PHAGE P22 N PEPTIDE-BOX B RNA COMPLEX, NMR, 20 STRUCTURES | ||||||
要素 |
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キーワード | TRANSCRIPTION/RNA / BACTERIOPHAGE TRANSCRIPTIONAL ANTITERMINATION / PEPTIDE-RNA RECOGNITION / GNRA LOOP / BENT ALPHA-HELICAL PEPTIDE / TRANSCRIPTION REGULATION / TRANSCRIPTION-RNA COMPLEX | ||||||
機能・相同性 | DNA-templated transcription termination / リボ核酸 / RNA (> 10) / Probable regulatory protein N 機能・相同性情報 | ||||||
生物種 | Enterobacteria phage P22 (ファージ) | ||||||
手法 | 溶液NMR / distance geometry | ||||||
データ登録者 | Cai, Z. / Gorin, A.A. / Frederick, R. / Ye, X. / Hu, W. / Majumdar, A. / Kettani, A. / Patel, D.J. | ||||||
引用 | ジャーナル: Nat.Struct.Biol. / 年: 1998 タイトル: Solution structure of P22 transcriptional antitermination N peptide-boxB RNA complex. 著者: Cai, Z. / Gorin, A. / Frederick, R. / Ye, X. / Hu, W. / Majumdar, A. / Kettani, A. / Patel, D.J. | ||||||
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 | 1a4t.cif.gz | 331.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1a4t.ent.gz | 272.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1a4t.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/a4/1a4t ftp://data.pdbj.org/pub/pdb/validation_reports/a4/1a4t | HTTPS FTP |
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-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: RNA鎖 | 分子量: 4829.969 Da / 分子数: 1 / 由来タイプ: 合成 |
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#2: タンパク質・ペプチド | 分子量: 2415.781 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) Enterobacteria phage P22 (ファージ) 属: P22-like viruses / 参照: UniProt: P04891 |
-実験情報
-実験
実験 | 手法: 溶液NMR |
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NMR実験 | タイプ: SEE BELOW |
-試料調製
試料状態 | pH: 5.7 / 温度: 297 K |
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-NMR測定
NMRスペクトロメーター |
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-解析
ソフトウェア |
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NMR software |
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精密化 | 手法: distance geometry / ソフトェア番号: 1 詳細: A TOTAL OF 100 INITIAL STRUCTURES OF THE COMPLEX WERE GENERATED USING THE X-PLOR METRIC MATRIX DISTANCE GEOMETRY PROTOCOL GUIDED BY THE NOE DISTANCE RESTRAINTS. ALL THE DISTANCE WERE ...詳細: A TOTAL OF 100 INITIAL STRUCTURES OF THE COMPLEX WERE GENERATED USING THE X-PLOR METRIC MATRIX DISTANCE GEOMETRY PROTOCOL GUIDED BY THE NOE DISTANCE RESTRAINTS. ALL THE DISTANCE WERE SUBJECTED TO TWO ROUNDS OF MOLECULAR DYNAMICS REFINEMENT WITH THE NONBO NDED INTERACTIONS SUBJECTED TO A REPULSIVE FORCE FIELD IN THE INITIAL ROUND AND A CHARMM-22 FORCE FIELD CONTAINING VAN DER WAALS AND HYDROGEN BOND (WITH WELL DEPTH OF 3 KCAL/MOL) ENERGY TERM IN THE SUBSEQUENT ROUND. THE ELECTROSTATIC ENERGY TERM WAS TURNE D OFF DURING BOTH ROUNDS OF THE COMPUTATIONS. THE MOLECULAR DYNAMICS PROTOCOL DURING EACH ROUND OF THE COMPUTATIONS WAS AS FOLLOWS. THE STRUCTURES WERE HEATED TO 1000K AND EQUILIBRATED AT THIS TEMPERATURE FOR 0.8 PS, FOLLOWED BY GRADUAL COOLING TO 300 K O VER 48 PS AND SUBSEQUENT EQUILIBRATION AT THIS TEMPERATURE FOR 6 PS. THE RESULTING STRUCTURES WERE SUBJECTED TO 2,000 CYCLES OF ENERGY MINIMIZATION. THE FORCE CONSTANTS FOR NOE DISTANCE RESTRAINTS AND COUPLING CONSTANT BASED DIHEDRAL ANGLE RESTRAINTS WERE MAINTAINED AT VALUES 50 KCAL/MOL A A AND 25 KCAL/MOL RAD RAD, RESPECTIVELY THROUGHOUT THE CALCULATIONS. A FORCE CONSTANT OF 60 KCAL/MOL A A WAS APPLIED TO MAINTAIN HYDROGEN BONDING DISTANCE RESTRAINTS FOR WATSON-CRICK BASE PAIRS IN THE RNA STEM OF THE CO MPLEX. A SUBSET OF 27 REFINED STRUCTURES WERE SELECTED BASED ON THEIR LOWER VALUES OF TOTAL ENERGY, VAN DER WAALS ENERGY AND NOE VIOLATIONS ENERGY. THESE 27 REFINED STRUCTURES DEFINED A NOTICEABLE CONVERGED SUBSET (~10 KCAL/MOL VARIATION OF TOTAL ENERGY W ITHIN SUBSET) AND WERE SEPARATED BY A GAP OF ~120 KCAL/MOL OF TOTAL ENERGY FROM THE REST OF THE ENSEMBLE OF REFINED STRUCTURES. THE 20 STRUCTURES OF THE COMPLEX WITH THE LOWEST NUMBER OF NOE VIOLATIONS EXHIBITED PAIRWISE R.M.S.D. VALUE FOR ALL HEAVY ATOMS OF 1.27 A. | ||||||||||||||||||||||||||||
NMRアンサンブル | コンフォーマー選択の基準: DESCRIBED BELOW / 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 |