- PDB-1xhg: Crystal structure of a 40 kDa signalling protein from Porcine (SP... -
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IDまたはキーワード:
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基本情報
登録情報
データベース: PDB / ID: 1xhg
タイトル
Crystal structure of a 40 kDa signalling protein from Porcine (SPP-40) at 2.89A resolution
要素
SPP-40
キーワード
SIGNALING PROTEIN / Signalling Protein / Porcine
機能・相同性
機能・相同性情報
response to interleukin-6 / activation of NF-kappaB-inducing kinase activity / chitin catabolic process / chitin binding / response to tumor necrosis factor / response to mechanical stimulus / response to interleukin-1 / positive regulation of peptidyl-threonine phosphorylation / positive regulation of interleukin-8 production / lung development ...response to interleukin-6 / activation of NF-kappaB-inducing kinase activity / chitin catabolic process / chitin binding / response to tumor necrosis factor / response to mechanical stimulus / response to interleukin-1 / positive regulation of peptidyl-threonine phosphorylation / positive regulation of interleukin-8 production / lung development / positive regulation of angiogenesis / cellular response to tumor necrosis factor / carbohydrate binding / carbohydrate metabolic process / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / inflammatory response / apoptotic process / perinuclear region of cytoplasm / endoplasmic reticulum / extracellular space / extracellular region / cytoplasm 類似検索 - 分子機能
解像度: 2.9→56 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.91 / SU B: 21.59 / SU ML: 0.401 / 交差検証法: THROUGHOUT / ESU R Free: 0.381 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
反射数
%反射
Selection details
Rfree
0.21765
450
4.7 %
RANDOM
Rwork
0.17723
-
-
-
all
0.18
9476
-
-
obs
0.17911
9026
90.22 %
-
溶媒の処理
イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.4 Å / 溶媒モデル: BABINET MODEL WITH MASK
原子変位パラメータ
Biso mean: 28.47 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.91 Å2
0 Å2
0 Å2
2-
-
-0.97 Å2
0 Å2
3-
-
-
1.88 Å2
Refine analyze
Luzzati coordinate error obs: 0.32 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.49 Å
精密化ステップ
サイクル: LAST / 解像度: 2.9→56 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
2875
0
28
79
2982
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.023
0.021
2981
X-RAY DIFFRACTION
r_bond_other_d
0.003
0.02
2630
X-RAY DIFFRACTION
r_angle_refined_deg
2.015
1.945
4044
X-RAY DIFFRACTION
r_angle_other_deg
1.486
3
6095
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
3.142
3
359
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
21.681
15
498
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
X-RAY DIFFRACTION
r_chiral_restr
0.117
0.2
436
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
3317
X-RAY DIFFRACTION
r_gen_planes_other
0.005
0.02
657
X-RAY DIFFRACTION
r_nbd_refined
0.281
0.3
770
X-RAY DIFFRACTION
r_nbd_other
0.259
0.3
2869
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
0.393
0.5
4
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.164
0.5
187
X-RAY DIFFRACTION
r_xyhbond_nbd_other
0.086
0.5
5
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.356
0.3
13
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.461
0.3
30
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.228
0.5
5
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_mcbond_it
1.355
1.5
1792
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
2.528
2
2875
X-RAY DIFFRACTION
r_scbond_it
3.058
3
1189
X-RAY DIFFRACTION
r_scangle_it
5.032
4.5
1169
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS精密化 シェル
解像度: 2.896→2.971 Å / Total num. of bins used: 20 /