- PDB-7nmo: Crystal structure of beta-2-microglobulin D76A mutant -
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基本情報
登録情報
データベース: PDB / ID: 7nmo
タイトル
Crystal structure of beta-2-microglobulin D76A mutant
要素
Beta-2-microglobulin
キーワード
IMMUNE SYSTEM / major histocompatibility complex class 1 / beta-2-microglobulin / mutant / D76A
機能・相同性
機能・相同性情報
positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol 類似検索 - 分子機能
解像度: 1.2→44.41 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.834 / SU ML: 0.018 / 交差検証法: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.037 / 詳細: Hydrogens have been added in their riding positions
Rfactor
反射数
%反射
Rfree
0.1586
1506
5.017 %
Rwork
0.13
28514
-
all
0.131
-
-
obs
-
30020
97.234 %
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 BULK SOLVENT
原子変位パラメータ
Biso mean: 16.658 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.22 Å2
0 Å2
0.12 Å2
2-
-
0.418 Å2
0 Å2
3-
-
-
-0.223 Å2
精密化ステップ
サイクル: LAST / 解像度: 1.2→44.41 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
834
0
0
153
987
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.021
0.013
867
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.017
768
X-RAY DIFFRACTION
r_angle_refined_deg
2.188
1.652
1176
X-RAY DIFFRACTION
r_angle_other_deg
1.556
1.581
1792
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.696
5
101
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.892
22.6
50
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.06
15
151
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
13.452
15
5
X-RAY DIFFRACTION
r_chiral_restr
0.155
0.2
108
X-RAY DIFFRACTION
r_gen_planes_refined
0.013
0.02
969
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
190
X-RAY DIFFRACTION
r_nbd_refined
0.228
0.2
148
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.209
0.2
712
X-RAY DIFFRACTION
r_nbtor_refined
0.18
0.2
398
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.091
0.2
479
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.237
0.2
88
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.188
0.2
7
X-RAY DIFFRACTION
r_nbd_other
0.152
0.2
40
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.325
0.2
30
X-RAY DIFFRACTION
r_xyhbond_nbd_other
0.185
0.2
1
X-RAY DIFFRACTION
r_mcbond_it
1.592
1.189
404
X-RAY DIFFRACTION
r_mcbond_other
1.582
1.188
403
X-RAY DIFFRACTION
r_mcangle_it
2.144
1.8
505
X-RAY DIFFRACTION
r_mcangle_other
2.145
1.801
506
X-RAY DIFFRACTION
r_scbond_it
7.644
1.828
463
X-RAY DIFFRACTION
r_scbond_other
7.643
1.831
463
X-RAY DIFFRACTION
r_scangle_it
5.289
2.502
671
X-RAY DIFFRACTION
r_scangle_other
5.289
2.505
671
X-RAY DIFFRACTION
r_lrange_it
7.04
18.547
993
X-RAY DIFFRACTION
r_lrange_other
6.986
17.326
952
X-RAY DIFFRACTION
r_rigid_bond_restr
10.286
3
1635
LS精密化 シェル
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20