[protein]-arginine 3-hydroxylase / peptidyl-arginine 3-dioxygenase activity / histone H3K36 demethylase activity / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素 / Protein hydroxylation / aminopeptidase activity / methylated histone binding / regulation of signal transduction by p53 class mediator / circadian regulation of gene expression / protein destabilization ...[protein]-arginine 3-hydroxylase / peptidyl-arginine 3-dioxygenase activity / histone H3K36 demethylase activity / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素 / Protein hydroxylation / aminopeptidase activity / methylated histone binding / regulation of signal transduction by p53 class mediator / circadian regulation of gene expression / protein destabilization / G2/M transition of mitotic cell cycle / p53 binding / chromatin organization / chromosome / fibroblast proliferation / endopeptidase activity / in utero embryonic development / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of DNA-templated transcription / proteolysis / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytosol 類似検索 - 分子機能
: / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Cupin-like domain 8 / Cupin-like domain / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Cupin / A domain family that is part of the cupin metalloenzyme superfamily. ...: / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Cupin-like domain 8 / Cupin-like domain / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Cupin / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls / Sandwich / Mainly Beta 類似検索 - ドメイン・相同性
: / N-OXALYLGLYCINE / RCC1 domain-containing protein 1 / Bifunctional peptidase and arginyl-hydroxylase JMJD5 類似検索 - 構成要素
解像度: 1.3→49.84 Å / SU ML: 0.12 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 15.5 / 立体化学のターゲット値: ML 詳細: REFINEMENT TARGET : ML and BULK SOLVENT MODELLING METHOD USED: FLAT MODEL
Rfactor
反射数
%反射
Selection details
Rfree
0.1616
3045
4.91 %
Random
Rwork
0.1427
-
-
-
obs
0.1436
62039
98.89 %
-
溶媒の処理
減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT MODEL / Bsol: 54.2 Å2 / ksol: 0.41 e/Å3
原子変位パラメータ
Biso mean: 24 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.91 Å2
0 Å2
0 Å2
2-
-
-0.52 Å2
0 Å2
3-
-
-
2.43 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.16 Å
0.16 Å
Luzzati d res low
-
5 Å
Luzzati sigma a
-
0.16 Å
精密化ステップ
サイクル: LAST / 解像度: 1.3→49.84 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
1939
0
19
360
2318
拘束条件
Refine-ID
タイプ
Dev ideal
数
X-RAY DIFFRACTION
f_bond_d
0.016
2345
X-RAY DIFFRACTION
f_angle_d
1.401
3232
X-RAY DIFFRACTION
f_dihedral_angle_d
15.683
886
X-RAY DIFFRACTION
f_chiral_restr
0.1
330
X-RAY DIFFRACTION
f_plane_restr
0.011
438
LS精密化 シェル
解像度 (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.2968-1.3171
0.2872
101
0.2715
2005
X-RAY DIFFRACTION
76
1.3171-1.3387
0.3107
131
0.2493
2715
X-RAY DIFFRACTION
100
1.3387-1.3618
0.2626
143
0.2407
2648
X-RAY DIFFRACTION
100
1.3618-1.3865
0.2155
133
0.2307
2676
X-RAY DIFFRACTION
100
1.3865-1.4132
0.2351
139
0.2132
2688
X-RAY DIFFRACTION
100
1.4132-1.4421
0.2169
107
0.2069
2709
X-RAY DIFFRACTION
100
1.4421-1.4734
0.1947
156
0.1847
2650
X-RAY DIFFRACTION
100
1.4734-1.5077
0.204
171
0.1688
2671
X-RAY DIFFRACTION
100
1.5077-1.5454
0.155
160
0.152
2672
X-RAY DIFFRACTION
100
1.5454-1.5872
0.1731
133
0.1482
2685
X-RAY DIFFRACTION
100
1.5872-1.6339
0.16
138
0.1398
2679
X-RAY DIFFRACTION
100
1.6339-1.6866
0.162
123
0.1336
2716
X-RAY DIFFRACTION
100
1.6866-1.7469
0.1225
111
0.1326
2732
X-RAY DIFFRACTION
100
1.7469-1.8169
0.185
131
0.1336
2704
X-RAY DIFFRACTION
100
1.8169-1.8996
0.1472
147
0.1291
2703
X-RAY DIFFRACTION
100
1.8996-1.9997
0.1386
141
0.1175
2705
X-RAY DIFFRACTION
100
1.9997-2.125
0.1217
144
0.1174
2706
X-RAY DIFFRACTION
100
2.125-2.2891
0.1385
125
0.1238
2753
X-RAY DIFFRACTION
100
2.2891-2.5194
0.1497
154
0.1257
2739
X-RAY DIFFRACTION
100
2.5194-2.884
0.146
156
0.1322
2748
X-RAY DIFFRACTION
100
2.884-3.6333
0.1484
147
0.1289
2777
X-RAY DIFFRACTION
100
3.6333-49.8802
0.1778
154
0.1539
2913
X-RAY DIFFRACTION
100
精密化 TLS
手法: refined / Origin x: -39.9383 Å / Origin y: 13.3208 Å / Origin z: 98.6075 Å