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基本情報
登録情報 | データベース: PDB / ID: 2jvw | ||||||
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タイトル | Solution NMR structure of uncharacterized protein Q5E7H1 from Vibrio fischeri. Northeast Structural Genomics target VfR117 | ||||||
![]() | Uncharacterized protein | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / solution NMR structure / alpha helical protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
機能・相同性 | DNA-binding protein VF530-like / DNA-binding protein VF530 / SAP domain / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / SAP domain superfamily / double-stranded DNA binding / Orthogonal Bundle / Mainly Alpha / DNA-binding protein VF_0530![]() | ||||||
生物種 | ![]() | ||||||
手法 | 溶液NMR / simulated annealing | ||||||
![]() | Aramini, J.M. / Rossi, P. / Wang, D. / Nwosu, C. / Owens, L.A. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. ...Aramini, J.M. / Rossi, P. / Wang, D. / Nwosu, C. / Owens, L.A. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() タイトル: Solution NMR structure of VF0530 from Vibrio fischeri reveals a nucleic acid-binding function. 著者: Aramini, J.M. / Rossi, P. / Fischer, M. / Xiao, R. / Acton, T.B. / Montelione, G.T. | ||||||
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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-検証レポート
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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: 10746.398 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
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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 AND STATIC LIGHT SCATTERING. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE ...Text: THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY AND STATIC LIGHT SCATTERING. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN, AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS WERE DETERMINED USING CYANA 2.1. DIHEDRAL ANGLE CONSTRAINTS WERE OBTAINED FROM TALOS. HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING BOTH AUTOSTRUCTURE AND CYANA, AND WERE APPLIED ONLY IN THE FINAL REFINEMENT STAGE (CNS) OF THE STRUCTURE DETERMINATION. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HHHHHH): BACKBONE, 98.8%, SIDE CHAIN, 95.3%, AROMATICS, 100%, STEREOSPECIFIC METHYL, 100%, STEREOSPECIFIC SIDE CHAIN NH2: 100%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 TO 82, PSVS 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 15-37,42-43,46-75: (A) RMSD (ORDERED RESIDUES): BB, 0.5, HEAVY ATOM, 1.1. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 93.9, ADDITIONALLY ALLOWED, 6.1%, GENEROUSLY ALLOWED, 0.0%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, 0.17/0.98, ALL, 0.19/1.12. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 14.65/-0.99. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 1-82): RECALL, 0.989, PRECISION, 0.945, F-MEASURE, 0.967, DP-SCORE, 0.810. (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 2. THE C-TERMINAL HIS TAG RESIDUES OF THE PROTEIN (HHHHHH) WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS AND HAVE BEEN OMITTED FROM THIS DEPOSITION. COORDINATES FOR THE FOLLOWING RESIDUES ARE NOT WELL DETERMINED [S(PHI) + S(PSI) < 1.8]: 1-14,38-41,44-45,76-82. |
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試料調製
詳細 |
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試料状態 | イオン強度: 0.1 / pH: 4.5 / 圧: ambient / 温度: 293 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 1424 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 88 DIHEDRAL ANGLE CONSTRAINTS, AND 46 HYDROGEN BOND CONSTRAINTS (19.2 ...詳細: THE FINAL STRUCTURES ARE BASED ON A TOTAL OF 1424 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 88 DIHEDRAL ANGLE CONSTRAINTS, AND 46 HYDROGEN BOND CONSTRAINTS (19.2 CONSTRAINTS PER RESIDUE, 3.3 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 82 BY PSVS 1.3). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA 2.1. 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: 1424 / NOE intraresidue total count: 489 / NOE long range total count: 270 / NOE medium range total count: 285 / NOE sequential total count: 380 | ||||||||||||||||||||||||||||||||||||||||||||
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 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 1.2 ° / Maximum upper distance constraint violation: 0.32 Å / Torsion angle constraint violation method: PDBStat | ||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.01 Å |