+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2ljw | ||||||
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タイトル | Solution NMR structure of Alr2454 protein from Nostoc sp. strain PCC 7120, Northeast Structural Genomics Consortium Target NsR264 | ||||||
要素 | Alr2454 protein | ||||||
キーワード | Structural Genomics (構造ゲノミクス) / Unknown Function / novel fold / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / PSI-BIOLOGY / Protein Structure Initiative | ||||||
機能・相同性 | Protein of unknown function DUF3067 / Protein of unknown function DUF3067 / Domain of unknown function (DUF3067) / HIT family, subunit A / 2-Layer Sandwich / Alpha Beta / Alr2454 protein 機能・相同性情報 | ||||||
生物種 | Nostoc sp. (バクテリア) | ||||||
手法 | 溶液NMR / simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
データ登録者 | Aramini, J.M. / Lee, D. / Ciccosanti, C. / Janjua, H. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) | ||||||
引用 | ジャーナル: J.Struct.Funct.Genom. / 年: 2012 タイトル: Solution NMR structure of Alr2454 from Nostoc sp. PCC 7120, the first structural representative of Pfam domain family PF11267. 著者: Aramini, J.M. / Petrey, D. / Lee, D.Y. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. | ||||||
履歴 |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED |
-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 | 2ljw.cif.gz | 763.1 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2ljw.ent.gz | 652.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2ljw.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/lj/2ljw ftp://data.pdbj.org/pub/pdb/validation_reports/lj/2ljw | HTTPS FTP |
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-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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NMR アンサンブル |
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-要素
#1: タンパク質 | 分子量: 12992.762 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Nostoc sp. (バクテリア) / 株: PCC 7120 / 遺伝子: alr2454 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3)pMgK / 参照: UniProt: Q8YUA0 |
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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 PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY, STATIC LIGHT SCATTERING AND 15N T1/T2 RELAXATION. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. SPECTRA FOR ...Text: THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY, STATIC LIGHT SCATTERING AND 15N T1/T2 RELAXATION. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. SPECTRA FOR BACKBONE AND SIDE CHAIN ASSIGNMENTS WERE OBTAINED ON A 1.7-MM MICROCRYOPROBE AT 600 MHZ. ALL NOESY DATA WERE ACQUIRED AT 800 MHZ USING A 5-MM CRYOPROBE. BACKBONE ASSIGNMENTS WERE MADE USING PINE, AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS WERE DETERMINED USING CYANA 3.0. BACKBONE (PHI/PSI) DIHEDRAL ANGLE CONSTRAINTS WERE OBTAINED FROM TALOSplus. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HIS6): BACKBONE, 99.4%, SIDE CHAIN, 98.3%, AROMATICS, 96.6%, STEREOSPECIFIC METHYL, 100%, STEREOSPECIFIC SIDE CHAIN NH2: 100.0%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 TO 104, PSVS 1.4), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 1-100: (A) RMSD (ORDERED RESIDUES): BB, 0.6, HEAVY ATOM, 0.9. (B) MOLPROBITY RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 96.8%, ADDITIONALLY ALLOWED, 3.1%, DISALLOWED, 0.1%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.15/-0.28, ALL, -0.03/-0.18. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 12.51/-0.62 (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 1 TO 104): RECALL, 0.976, PRECISION, 0.934, F-MEASURE, 0.955, DP-SCORE, 0.817. (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 2. THE FINAL SIX HISTIDINE RESIDUES IN THE C-TERMINAL AFFINITY TAG WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS AND HAVE BEEN OMITTED FROM THIS DEPOSITION. |
-試料調製
詳細 |
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試料 |
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試料状態 | pH: 4.5 / 圧: ambient / 温度: 298 K |
-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: simulated annealing / ソフトェア番号: 1 詳細: THE FINAL STRUCTURES ARE BASED ON A TOTAL OF 2478 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS AND 162 DIHEDRAL ANGLE CONSTRAINTS; 0 HYDROGEN BOND CONSTRAINTS (25.4 ...詳細: THE FINAL STRUCTURES ARE BASED ON A TOTAL OF 2478 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS AND 162 DIHEDRAL ANGLE CONSTRAINTS; 0 HYDROGEN BOND CONSTRAINTS (25.4 CONSTRAINTS PER RESIDUE, 6.8 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 104 BY PSVS 1.4). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA 3.0. THE 20 STRUCTURES OUT OF 100 WITH THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) WITH PARAM19. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 2478 / NOE intraresidue total count: 688 / NOE long range total count: 709 / NOE medium range total count: 462 / NOE sequential total count: 619 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 |