+
データを開く
-
基本情報
登録情報 | データベース: PDB / ID: 2jqn | ||||||
---|---|---|---|---|---|---|---|
タイトル | Solution NMR structure of CC0527 from Caulobacter crescentus. Northeast Structural Genomics Target CCR55 | ||||||
![]() | Hypothetical protein | ||||||
![]() | STRUCTURAL GENOMICS / solution NMR structure / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
機能・相同性 | Protein of unknown function DUF952 / Protein of unknown function DUF952 / Protein of unknown function (DUF952) / ADP-ribosylation fold / Alpha-Beta Barrel / Alpha Beta / DUF952 domain-containing protein![]() | ||||||
生物種 | ![]() | ||||||
手法 | 溶液NMR / simulated annealing | ||||||
![]() | Aramini, J.M. / Rossi, P. / Moseley, H.N.B. / Wang, D. / Nwosu, C. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J. / Baran, M.C. ...Aramini, J.M. / Rossi, P. / Moseley, H.N.B. / Wang, D. / Nwosu, C. / Cunningham, K. / Ma, L. / 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 CC0527 from Caulobacter crescentus 著者: Aramini, J.M. / Rossi, P. / Moseley, H.N.B. / Wang, D. / Nwosu, C. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. | ||||||
履歴 |
|
-
構造の表示
構造ビューア | 分子: ![]() ![]() |
---|
-
ダウンロードとリンク
-
ダウンロード
PDBx/mmCIF形式 | ![]() | 691.6 KB | 表示 | ![]() |
---|---|---|---|---|
PDB形式 | ![]() | 577.2 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 509.5 KB | 表示 | ![]() |
---|---|---|---|---|
文書・詳細版 | ![]() | 639.4 KB | 表示 | |
XML形式データ | ![]() | 37.9 KB | 表示 | |
CIF形式データ | ![]() | 62.2 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | |
---|---|
類似構造データ | |
その他のデータベース |
-
リンク
-
集合体
登録構造単位 | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR アンサンブル |
|
-
要素
#1: タンパク質 | 分子量: 13529.084 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) ![]() 遺伝子: CC0527 / 発現宿主: ![]() ![]() |
---|
-実験情報
-実験
実験 | 手法: 溶液NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR実験 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR実験の詳細 | Text: THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE AND GFT NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN, AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. ...Text: THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE AND GFT NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN, AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE, DIHEDRAL ANGLE (HYPER) AND HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING AUTOSTRUCTURE. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HHHHHH): BACKBONE, 97.6%, SIDE CHAIN, 96.5%, AROMATICS, 89.1%, STEREOSPECIFIC METHYL, 91.3%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 TO 116, PSVS 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 3-22,26-31,34-35,40-49,56-62,69-73,80-96,109-112: (A) RMSD (ORDERED RESIDUES): BB, 0.9, HEAVY ATOM, 1.3. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 91.3%, ADDITIONALLY ALLOWED, 8.7%, GENEROUSLY ALLOWED, 0.0%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.25/-0.67, ALL, -0.15/-0.89. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 19.99/-1.90. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 1-116): RECALL, 0.985, PRECISION, 0.900, F-MEASURE, 0.941, DP-SCORE, 0.755. THE C-TERMINAL HIS TAG RESIDUES OF THE PROTEIN (HHHHHH) WERE INCLUDED IN ALL STRUCTURE CALCULATIONS BUT HAVE BEEN OMITTED FROM THIS DEPOSITION. COORDINATES FOR THE FOLLOWING RESIDUES ARE NOT WELL DETERMINED (S(PHI) + S(PSI) < 1.8): 1-2,23-25,32-33,36-39,50-55,63-68,74-79,97-108,113-116. |
-
試料調製
詳細 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
試料 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
試料状態 | イオン強度: 100 / pH: 6.5 / 圧: ambient / 温度: 293 K |
-NMR測定
NMRスペクトロメーター |
|
---|
-
解析
NMR software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
精密化 | 手法: simulated annealing / ソフトェア番号: 1 詳細: THE STRUCTURES ARE BASED ON A TOTAL OF 1164 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 108 DIHEDRAL ANGLE CONSTRAINTS, AND 66 HYDROGEN BOND CONSTRAINTS (11.7 CONSTRAINTS ...詳細: THE STRUCTURES ARE BASED ON A TOTAL OF 1164 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 108 DIHEDRAL ANGLE CONSTRAINTS, AND 66 HYDROGEN BOND CONSTRAINTS (11.7 CONSTRAINTS PER RESIDUE, 3.6 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 116 BY PSVS 1.3). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING AUTOSTRUCTURE (XPLOR-NIH). AFTER A FINAL XPLOR CALCULATION USING THE CONSTRAINTS DERIVED FROM AUTOSTRUCTURE, THE 20 LOWEST ENERGY STRUCTURES OUT OF 100 WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYANMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 1164 / NOE intraresidue total count: 221 / NOE long range total count: 375 / NOE medium range total count: 244 / NOE sequential total count: 324 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 torsion angle constraint violation: 2.1 ° / Maximum upper distance constraint violation: 0.17 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.01 Å |