+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2lp6 | ||||||
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タイトル | Refined Solution NMR Structure of the 50S ribosomal protein L35Ae from Pyrococcus furiosus, Northeast Structural Genomics Consortium Target (NESG) PfR48 | ||||||
要素 | 50S ribosomal protein L35Ae | ||||||
キーワード | RIBOSOMAL PROTEIN / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-Biology / Protein Structure Initiative | ||||||
機能・相同性 | 機能・相同性情報 ribosomal large subunit biogenesis / cytosolic large ribosomal subunit / cytoplasmic translation / structural constituent of ribosome 類似検索 - 分子機能 | ||||||
生物種 | Pyrococcus furiosus (古細菌) | ||||||
手法 | 溶液NMR / simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
データ登録者 | Snyder, D.A. / Aramini, J.M. / Yu, B. / Huang, Y.J. / Xiao, R. / Cort, J.R. / Shastry, R. / Ma, L. / Liu, J. / Rost, B. ...Snyder, D.A. / Aramini, J.M. / Yu, B. / Huang, Y.J. / Xiao, R. / Cort, J.R. / Shastry, R. / Ma, L. / Liu, J. / Rost, B. / Acton, T.B. / Kennedy, M.A. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) | ||||||
引用 | ジャーナル: Proteins / 年: 2012 タイトル: Solution NMR structure of the ribosomal protein RP-L35Ae from Pyrococcus furiosus. 著者: Snyder, D.A. / Aramini, J.M. / Yu, B. / Huang, Y.J. / Xiao, R. / Cort, J.R. / Shastry, R. / Ma, L.C. / Liu, J. / Rost, B. / Acton, T.B. / Kennedy, M.A. / Montelione, G.T. | ||||||
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 | 2lp6.cif.gz | 671.7 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2lp6.ent.gz | 571.6 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2lp6.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
文書・要旨 | 2lp6_validation.pdf.gz | 544.2 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 2lp6_full_validation.pdf.gz | 712 KB | 表示 | |
XML形式データ | 2lp6_validation.xml.gz | 44.1 KB | 表示 | |
CIF形式データ | 2lp6_validation.cif.gz | 57.8 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/lp/2lp6 ftp://data.pdbj.org/pub/pdb/validation_reports/lp/2lp6 | HTTPS FTP |
-関連構造データ
関連構造データ | |
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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 |
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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: 10826.713 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Pyrococcus furiosus (古細菌) / 株: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / 遺伝子: PF1872, rpl35Ae / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3)pMgK / 参照: UniProt: Q8TZV6 |
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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 WITH STATIC LIGHT SCATTERING AND 15N T1/T2 RELAXATION. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATIC ...Text: THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING AND 15N T1/T2 RELAXATION. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATIC BACKBONE RESONANCE ASSIGNMENTS WERE MADE USING AUTOASSIGN, FOLLOWED BY MANUAL SIDE CHAIN ASSIGNMENT. AUTOMATIC NOESY ASSIGNMENTS WERE DETERMINED USING CYANA 3.0. BACKBONE (PHI/PSI) DIHEDRAL ANGLE CONSTRAINTS WERE OBTAINED FROM TALOSplus, AND HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING AUTOSTRUCTURE. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING THE C-TERMINAL HIS6): BACKBONE, 98.2%, SIDE CHAIN, 90.9%, AROMATICS, 100%, STEREOSPECIFIC METHYL, 84.2%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 TO 91, PSVS 1.4), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 2-12,21-76,79-87: (A) RMSD (ORDERED RESIDUES): BB, 0.5, HEAVY ATOM, 1.0. (B) MOLPROBITY RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 97.0%, ADDITIONALLY ALLOWED, 3.0%, DISALLOWED, 0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.56/-1.89, ALL, -0.26/-1.54. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 15.13/-1.07 (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 1 TO 91): RECALL, 0.965, PRECISION, 0.878, F-MEASURE, 0.920, DP-SCORE, 0.784. (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 5. THE FINAL FOUR UNASSIGNED HISTIDINE RESIDUES IN THE C-TERMINAL AFFINITY TAG 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]: 1,13-20,77-78,88-91. |
-試料調製
詳細 |
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試料 |
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試料状態 | pH: 6.5 / 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 REFINED STRUCTURES ARE BASED ON A TOTAL OF 1402 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 153 DIHEDRAL ANGLE CONSTRAINTS, AND 56 HYDROGEN BOND CONSTRAINTS (18.3 ...詳細: THE FINAL REFINED STRUCTURES ARE BASED ON A TOTAL OF 1402 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 153 DIHEDRAL ANGLE CONSTRAINTS, AND 56 HYDROGEN BOND CONSTRAINTS (18.3 CONSTRAINTS PER RESIDUE, 7.0 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 91 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 1.3) WITH PARAM19. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 1402 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 |