dipeptidyl-peptidase I / peptidase activator activity involved in apoptotic process / positive regulation of proteolysis involved in protein catabolic process / negative regulation of myelination / positive regulation of microglial cell activation / Cargo concentration in the ER / dipeptidyl-peptidase activity / COPII-mediated vesicle transport / chloride ion binding / COPII-coated ER to Golgi transport vesicle ...dipeptidyl-peptidase I / peptidase activator activity involved in apoptotic process / positive regulation of proteolysis involved in protein catabolic process / negative regulation of myelination / positive regulation of microglial cell activation / Cargo concentration in the ER / dipeptidyl-peptidase activity / COPII-mediated vesicle transport / chloride ion binding / COPII-coated ER to Golgi transport vesicle / phosphatase binding / cysteine-type peptidase activity / MHC class II antigen presentation / endoplasmic reticulum-Golgi intermediate compartment membrane / : / proteolysis involved in protein catabolic process / positive regulation of apoptotic signaling pathway / T cell mediated cytotoxicity / azurophil granule lumen / protein-folding chaperone binding / collagen-containing extracellular matrix / lysosome / immune response / endoplasmic reticulum lumen / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / serine-type endopeptidase activity / centrosome / Neutrophil degranulation / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane 類似検索 - 分子機能
Cathepsin C, exclusion domain / Cysteine proteinases. Chain C / Cathepsin C exclusion / Cathepsin C, exclusion domain superfamily / Cathepsin C / Cathepsin C exclusion domain / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site ...Cathepsin C, exclusion domain / Cysteine proteinases. Chain C / Cathepsin C exclusion / Cathepsin C, exclusion domain superfamily / Cathepsin C / Cathepsin C exclusion domain / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Lipocalin / Papain-like cysteine peptidase superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta 類似検索 - ドメイン・相同性
タイプ: Bruker Platinum 135 / 検出器: CCD / 日付: 2010年12月1日
放射
モノクロメーター: Si(111) / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長
波長: 1.5418 Å / 相対比: 1
反射
解像度: 2→27.9 Å / Num. obs: 29396 / % possible obs: 94 % / 冗長度: 11.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 29.8
反射 シェル
解像度: 2→2.1 Å / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 6.9 / % possible all: 61.2
-
解析
ソフトウェア
名称
バージョン
分類
REFMAC
5.8.02382018/15/10
精密化
PROTEUM2
データ削減
SCALA
データスケーリング
REFMAC
位相決定
精密化
解像度: 2→27.505 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.367 / SU ML: 0.081 / 交差検証法: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.143 / 詳細: Hydrogens have been added in their riding positions
Rfactor
反射数
%反射
Rfree
0.1983
1429
-
Rwork
0.1519
-
-
all
0.154
-
-
obs
-
28534
93.97 %
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
原子変位パラメータ
Biso mean: 17.937 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.053 Å2
0 Å2
0 Å2
2-
-
0.146 Å2
0 Å2
3-
-
-
-0.093 Å2
精密化ステップ
サイクル: LAST / 解像度: 2→27.505 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
2759
0
128
372
3259
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.013
0.013
3008
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.018
2578
X-RAY DIFFRACTION
r_angle_refined_deg
1.838
1.709
4106
X-RAY DIFFRACTION
r_angle_other_deg
1.451
1.631
6008
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.914
5
351
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.526
22.886
149
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.701
15
439
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
23.52
15
11
X-RAY DIFFRACTION
r_chiral_restr
0.086
0.2
391
X-RAY DIFFRACTION
r_gen_planes_refined
0.011
0.02
3339
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
675
X-RAY DIFFRACTION
r_nbd_refined
0.208
0.2
617
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.187
0.2
2547
X-RAY DIFFRACTION
r_nbtor_refined
0.183
0.2
1463
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.086
0.2
1374
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.209
0.2
319
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_other
0.004
0.2
2
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.234
0.2
17
X-RAY DIFFRACTION
r_nbd_other
0.216
0.2
62
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.312
0.2
28
X-RAY DIFFRACTION
r_mcbond_it
1.031
1.071
1398
X-RAY DIFFRACTION
r_mcbond_other
1.031
1.071
1397
X-RAY DIFFRACTION
r_mcangle_it
1.737
1.597
1745
X-RAY DIFFRACTION
r_mcangle_other
1.737
1.597
1746
X-RAY DIFFRACTION
r_scbond_it
1.248
1.332
1609
X-RAY DIFFRACTION
r_scbond_other
1.248
1.334
1610
X-RAY DIFFRACTION
r_scangle_it
2.069
1.963
2356
X-RAY DIFFRACTION
r_scangle_other
2.069
1.965
2357
X-RAY DIFFRACTION
r_lrange_it
5.718
14.955
3617
X-RAY DIFFRACTION
r_lrange_other
5.719
14.969
3618
LS精密化 シェル
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20