- PDB-4g7p: Rat Heme Oxygenase-1 in complex with Heme and CO with 1 hr Illumi... -
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基本情報
登録情報
データベース: PDB / ID: 4g7p
タイトル
Rat Heme Oxygenase-1 in complex with Heme and CO with 1 hr Illumination at 100 K: Laser off
要素
Heme oxygenase 1HMOX1
キーワード
OXIDOREDUCTASE (酸化還元酵素) / ALL ALPHA PROTEIN / OXYGENASE (酸素添加酵素)
機能・相同性
機能・相同性情報
Regulation of HMOX1 expression and activity / arachidonic acid omega-hydroxylase activity / Iron uptake and transport / response to 3-methylcholanthrene / Heme degradation / Cytoprotection by HMOX1 / negative regulation of mast cell degranulation / heme metabolic process / response to arachidonic acid / phospholipase D activity ...Regulation of HMOX1 expression and activity / arachidonic acid omega-hydroxylase activity / Iron uptake and transport / response to 3-methylcholanthrene / Heme degradation / Cytoprotection by HMOX1 / negative regulation of mast cell degranulation / heme metabolic process / response to arachidonic acid / phospholipase D activity / heme oxygenase (biliverdin-producing) / cellular response to cisplatin / heme oxidation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / heme oxygenase (decyclizing) activity / wound healing involved in inflammatory response / negative regulation of muscle cell apoptotic process / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of mast cell cytokine production / heme catabolic process / cellular response to nutrient / cellular response to arsenic-containing substance / negative regulation of epithelial cell apoptotic process / positive regulation of epithelial cell apoptotic process / erythrocyte homeostasis / epithelial cell apoptotic process / negative regulation of macroautophagy / small GTPase-mediated signal transduction / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of vascular associated smooth muscle cell proliferation / positive regulation of macroautophagy / phospholipid metabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / cellular response to cadmium ion / カベオラ / liver regeneration / negative regulation of smooth muscle cell proliferation / オートファジー / positive regulation of smooth muscle cell proliferation / response to nicotine / response to hydrogen peroxide / 血圧 / multicellular organismal-level iron ion homeostasis / response to estrogen / positive regulation of angiogenesis / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to heat / cellular response to hypoxia / 血管新生 / intracellular iron ion homeostasis / response to oxidative stress / negative regulation of neuron apoptotic process / response to hypoxia / intracellular signal transduction / response to xenobiotic stimulus / negative regulation of cell population proliferation / heme binding / endoplasmic reticulum membrane / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / structural molecule activity / enzyme binding / 小胞体 / protein homodimerization activity / identical protein binding / metal ion binding / 細胞核 類似検索 - 分子機能
解像度: 1.9→32.8 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.063 / SU ML: 0.075 / 交差検証法: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.12 / 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
0.20135
1175
5.2 %
RANDOM
Rwork
0.16636
-
-
-
all
0.16812
21519
-
-
obs
0.16812
21519
92.84 %
-
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: 1.2 Å / 溶媒モデル: MASK
原子変位パラメータ
Biso mean: 28.321 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.01 Å2
0 Å2
0 Å2
2-
-
0.01 Å2
0 Å2
3-
-
-
-0.01 Å2
精密化ステップ
サイクル: LAST / 解像度: 1.9→32.8 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
1728
0
48
134
1910
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.022
0.02
1848
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1242
X-RAY DIFFRACTION
r_angle_refined_deg
2.938
1.993
2513
X-RAY DIFFRACTION
r_angle_other_deg
2.105
3
3025
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.709
5
215
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.767
24.13
92
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.309
15
313
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
18.629
15
11
X-RAY DIFFRACTION
r_chiral_restr
0.138
0.2
260
X-RAY DIFFRACTION
r_gen_planes_refined
0.012
0.021
2058
X-RAY DIFFRACTION
r_gen_planes_other
0.004
0.02
394
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
X-RAY DIFFRACTION
r_scbond_it
X-RAY DIFFRACTION
r_scangle_it
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: 1.9→1.95 Å / Total num. of bins used: 20
Rfactor
反射数
%反射
Rfree
0.263
89
-
Rwork
0.221
1470
-
obs
-
-
95.12 %
精密化 TLS
手法: refined / Origin x: -31.099 Å / Origin y: 11.713 Å / Origin z: -23.714 Å