+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1q48 | ||||||
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タイトル | Solution NMR Structure of The Haemophilus Influenzae Iron-Sulfur Cluster Assembly Protein U (IscU) with Zinc Bound at the Active Site. Northeast Structural Genomics Consortium Target IR24. This protein is not apo, it is a model without zinc binding constraints. | ||||||
要素 | NifU-like protein | ||||||
キーワード | STRUCTURAL GENOMICS (構造ゲノミクス) / UNKNOWN FUNCTION / Iron-Sulfur cluster binding (鉄・硫黄クラスター) / Three conserved Cys / 3 beta strands / 4 alpha helixes / NESG / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
機能・相同性 | 機能・相同性情報 iron-sulfur cluster assembly / ferrous iron binding / 2 iron, 2 sulfur cluster binding / intracellular iron ion homeostasis / 細胞質 類似検索 - 分子機能 | ||||||
生物種 | Haemophilus influenzae (インフルエンザ菌) | ||||||
手法 | 溶液NMR / SIMULATED ANNEALING, TORSION ANGLE DYNAMICS, AUTOMATED ANALYSIS OF NOESY DATA, 3D STRUCTURES | ||||||
データ登録者 | Ramelot, T.A. / Cort, J.R. / Xiao, R. / Shastry, R. / Acton, T.B. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG) | ||||||
引用 | ジャーナル: J.Mol.Biol. / 年: 2004 タイトル: Solution NMR structure of the iron-sulfur cluster assembly protein U (IscU) with zinc bound at the active site. 著者: Ramelot, T.A. / Cort, J.R. / Goldsmith-Fischman, S. / Kornhaber, G.J. / Xiao, R. / Shastry, R. / Acton, T.B. / Honig, B. / Montelione, G.T. / Kennedy, M.A. | ||||||
履歴 |
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Remark 400 | COMPOUND THIS PROTEIN HAS STOICHIOMETRIC ZINC BOUND. THIS PDB ENTRY IS A MODEL CALCULATED WITHOUT ...COMPOUND THIS PROTEIN HAS STOICHIOMETRIC ZINC BOUND. THIS PDB ENTRY IS A MODEL CALCULATED WITHOUT THE ZINC-BINDING CONSTRIANTS. PDB ENTRY 1R9P IS THE SAME PROTEIN MODELED WITH ZINC-BINDING CONSTRAINTS OBTAINED BY INDIRECT METHODS. |
-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 | 1q48.cif.gz | 790.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1q48.ent.gz | 659.5 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1q48.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/q4/1q48 ftp://data.pdbj.org/pub/pdb/validation_reports/q4/1q48 | 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: タンパク質 | 分子量: 14486.342 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) Haemophilus influenzae (インフルエンザ菌) 遺伝子: HI0377 / プラスミド: pET21D / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 (LAMDA DE3)PMGK / 参照: UniProt: Q57074 |
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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 ANALYSIS OF 3D STRUCTURE. |
-試料調製
詳細 |
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試料状態 | イオン強度: 20 mM MES, 100 mM NaCl, 5 mM CaCl2 / pH: 6.5 / 圧: ambient / 温度: 293 K | ||||||||||||
結晶化 | *PLUS 手法: その他 / 詳細: NMR |
-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, TORSION ANGLE DYNAMICS, AUTOMATED ANALYSIS OF NOESY DATA, 3D STRUCTURES ソフトェア番号: 1 詳細: THE STRUCTURES ARE BASED ON A TOTAL OF 923 RESTRAINTS. SUMMARY OF EXPERIMENTAL CONSTRAINTS: DISTANCE CONSTRAINTS: TOTAL = 790; INTRA-RESIDUE [I=J] = 12; SEQUENTIAL [(I-J)=1] = 260; MEDIUM ...詳細: THE STRUCTURES ARE BASED ON A TOTAL OF 923 RESTRAINTS. SUMMARY OF EXPERIMENTAL CONSTRAINTS: DISTANCE CONSTRAINTS: TOTAL = 790; INTRA-RESIDUE [I=J] = 12; SEQUENTIAL [(I-J)=1] = 260; MEDIUM RANGE [1<(I-J)<5] = 185; LONG RANGE [(I-J)>=5] = 255; HYDROGEN BOND CONSTRAINTS = 58 (2 PER H-BOND); NUMBER OF DISTANCE CONSTRAINTS PER RESIDUE = 8.0; DIHEDRAL-ANGLE CONSTRAINTS = 133 (66 PHI, 67 PSI); TOTAL NUMBER OF CONSTRAINTS PER RESIDUE = 9.4 (RESIDES 26-123); NUMBER OF LONG RANGE CONSTRAINTS PER RESIDUE = 2.6; NUMBER OF STRUCTURES COMPUTED = 25; NUMBER OF STRUCTURES USED = 20. AVERAGE DISTANCE VIOLATIONS >0.0001 ANG = 24.3; AVERAGE R.M.S. DISTANCE VIOLATION = 0.003 ANG; MAXIMUM NUMBER OF DISTANCE VIOLATIONS 31. AVERAGE DIHEDRAL ANGLE VIOLATIONS: >0.0001 DEG = 1.0; MAX NUMBER OF DIHEDRAL ANGLE VIOLATIONS = 4; AVERAGE R.M.S. ANGLE VIOLATION = 0.01 DEG. RMSD VALUES: BACKBONE ATOMS (N,C,C',O) = 0.80 ANG; ALL HEAVY ATOMS = 1.17 ANG; PROCHECK: MOST FAVORED REGIONS = 77%; ADDITIONAL ALLOWED REGIONS = 20%; GENEROUSLY ALLOWED REGIONS = 3%; DISALLOWED REGIONS = 0%. | ||||||||||||||||||||||||||||
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: 25 / 登録したコンフォーマーの数: 20 |