- PDB-1e1t: LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM COMPLEXED WITH THE LY... -
+
データを開く
IDまたはキーワード:
読み込み中...
-
基本情報
登録情報
データベース: PDB / ID: 1e1t
タイトル
LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM COMPLEXED WITH THE LYSYL_ADENYLATE INTERMEDIATE
要素
LYSYL-TRNA SYNTHETASE, HEAT INDUCIBLE
キーワード
LIGASE / AMINOACYL-TRNA SYNTHETASE / PROTEIN BIOSYNTHESIS
機能・相同性
機能・相同性情報
RNA capping / ATP:ADP adenylyltransferase activity / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / aminoacyl-tRNA synthetase multienzyme complex / tRNA aminoacylation for protein translation / positive regulation of macrophage activation / ligase activity ...RNA capping / ATP:ADP adenylyltransferase activity / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / aminoacyl-tRNA synthetase multienzyme complex / tRNA aminoacylation for protein translation / positive regulation of macrophage activation / ligase activity / cellular response to heat / nucleic acid binding / tRNA binding / magnesium ion binding / protein homodimerization activity / extracellular space / ATP binding / membrane / cytosol / cytoplasm 類似検索 - 分子機能
Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysine-tRNA ligase, class II / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 ...Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysine-tRNA ligase, class II / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta 類似検索 - ドメイン・相同性
WHEN CRYSTALS GROWN IN THE PRESENCE OF LYSINE WERE SOAKED OVERNIGHT IN A SOLUTION CONTAINING ATP ...WHEN CRYSTALS GROWN IN THE PRESENCE OF LYSINE WERE SOAKED OVERNIGHT IN A SOLUTION CONTAINING ATP AND MG2+, THE ELECTRON DENSITY IN THE ACTIVE SITE CLEARLY SHOWED THAT THE FIRST STEP OF THE REACTION HAD OCCURRED WITHIN THE CRYSTAL WITH THE FORMATION OF THE LYSYL-ADENYLATE INTERMEDIATE. AN ADDITIONAL ELECTRON DENSITY PEAK COULD BE MODELLED AS A PARTIALLY OCCUPIED PYROPHOSPHATE MOLECULE.
-
実験情報
-
実験
実験
手法: X線回折 / 使用した結晶の数: 1
-
試料調製
結晶
マシュー密度: 4.8 Å3/Da / 溶媒含有率: 74 % 解説: STRUCTURE WAS SOLVED BY DIFFERENCE FOURIER METHODS USING PHASES FROM 1E1O
結晶化
pH: 6.8 詳細: THE PROTEIN WAS CONCENTRATED TO 12 MG/ML IN THE PRESENCE OF 5MM LYSINE AND WAS CRYSTALLISED FROM 0.1 M PIPES PH 6.8, 0.5 M LICL, 20% PEG 4K, 17% GLYCEROL; THEN, A SMALL AMOUNT OF A SOLUTION ...詳細: THE PROTEIN WAS CONCENTRATED TO 12 MG/ML IN THE PRESENCE OF 5MM LYSINE AND WAS CRYSTALLISED FROM 0.1 M PIPES PH 6.8, 0.5 M LICL, 20% PEG 4K, 17% GLYCEROL; THEN, A SMALL AMOUNT OF A SOLUTION CONTAINING ATP AND MGCL2 WAS ADDED TO THE DROP TO GET A FINAL CONCENTRATION OF ABOUT 5 MM.
解像度: 2.4→15 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0 詳細: WHEN CRYSTALS GROWN IN THE PRESENCE OF LYSINE WERE SOAKED OVERNIGHT IN A SOLUTION CONTAINING ATP AND MG2+, THE ELECTRON DENSITY IN THE ACTIVE SITE CLEARLY SHOWED THAT THE FIRST STEP OF THE ...詳細: WHEN CRYSTALS GROWN IN THE PRESENCE OF LYSINE WERE SOAKED OVERNIGHT IN A SOLUTION CONTAINING ATP AND MG2+, THE ELECTRON DENSITY IN THE ACTIVE SITE CLEARLY SHOWED THAT THE FIRST STEP OF THE REACTION HAD OCCURRED WITHIN THE CRYSTAL WITH THE FORMATION OF THE LYSYL-ADENYLATE INTERMEDIATE. AN ADDITIONAL ELECTRON DENSITY PEAK COULD BE MODELLED AS A PARTIALLY OCCUPIED PYROPHOSPHATE MOLECULE. THE ASSIGNMENT OF THE ELECTRON DENSITY PEAKS AS MG2+ IONS IS BASED ON THE POSITIONS OBSERVED FOR METAL IONS WHEN THE ELECTRON- DENSE MN2+ IONS WERE USED.
Rfactor
反射数
%反射
Selection details
Rfree
0.267
1639
4 %
RANDOM
Rwork
0.186
-
-
-
obs
0.186
40860
98 %
-
Refine analyze
Luzzati d res low obs: 20 Å
精密化ステップ
サイクル: LAST / 解像度: 2.4→15 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
3834
0
85
337
4256
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
X-RAY DIFFRACTION
x_bond_d
0.007
X-RAY DIFFRACTION
x_bond_d_na
X-RAY DIFFRACTION
x_bond_d_prot
X-RAY DIFFRACTION
x_angle_d
X-RAY DIFFRACTION
x_angle_d_na
X-RAY DIFFRACTION
x_angle_d_prot
X-RAY DIFFRACTION
x_angle_deg
1.6
X-RAY DIFFRACTION
x_angle_deg_na
X-RAY DIFFRACTION
x_angle_deg_prot
X-RAY DIFFRACTION
x_dihedral_angle_d
17
X-RAY DIFFRACTION
x_dihedral_angle_d_na
X-RAY DIFFRACTION
x_dihedral_angle_d_prot
X-RAY DIFFRACTION
x_improper_angle_d
1.66
X-RAY DIFFRACTION
x_improper_angle_d_na
X-RAY DIFFRACTION
x_improper_angle_d_prot
X-RAY DIFFRACTION
x_mcbond_it
2.26
1.5
X-RAY DIFFRACTION
x_mcangle_it
3.4
2
X-RAY DIFFRACTION
x_scbond_it
4.2
2
X-RAY DIFFRACTION
x_scangle_it
6.3
2.5
LS精密化 シェル
解像度: 2.4→2.51 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8