PDB-8qw0: Human NDPK-C in complex with GDP

基本情報

• 登録情報: データベース: PDB / ID: 8qw0
• タイトル: Human NDPK-C in complex with GDP
• 要素: Nucleoside diphosphate kinase 3
• キーワード: TRANSFERASE / Kinase

機能・相同性

分子機能:

nucleoside triphosphate biosynthetic process / nucleoside-diphosphate kinase / Interconversion of nucleotide di- and triphosphates / UTP biosynthetic process / CTP biosynthetic process / mitochondrial fusion / GTP biosynthetic process / nucleoside diphosphate kinase activity / ciliary basal body / mitochondrial outer membrane / DNA repair / apoptotic process / ATP binding / metal ion binding / cytosol / cytoplasm

ドメイン・相同性:

Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily

構成要素:

GUANOSINE-5'-DIPHOSPHATE / Nucleoside diphosphate kinase 3

• 生物種: Homo sapiens (ヒト)
• 手法: X線回折 / シンクロトロン / 分子置換 / 解像度: 2.175 Å
• データ登録者: Werten, S. / Amjadi, R. / Scheffzek, K.

資金援助

1件

組織	認可番号	国
Not funded

• 引用: ジャーナル: Int J Mol Sci / 年: 2024; タイトル: Mechanistic Insights into Substrate Recognition of Human Nucleoside Diphosphate Kinase C Based on Nucleotide-Induced Structural Changes.; 著者: Amjadi, R. / Werten, S. / Lomada, S.K. / Baldin, C. / Scheffzek, K. / Dunzendorfer-Matt, T. / Wieland, T.

履歴

登録	2023年10月18日	登録サイト: PDBE / 処理サイト: PDBE
改定 1.0	2024年9月18日	Provider: repository / タイプ: Initial release
改定 1.1	2024年10月9日	Group: Database references / Structure summary / カテゴリ: citation / pdbx_entry_details Item: _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_entry_details.has_protein_modification

集合体

登録構造単位

A: Nucleoside diphosphate kinase 3

B: Nucleoside diphosphate kinase 3

C: Nucleoside diphosphate kinase 3

D: Nucleoside diphosphate kinase 3

E: Nucleoside diphosphate kinase 3

F: Nucleoside diphosphate kinase 3

G: Nucleoside diphosphate kinase 3

H: Nucleoside diphosphate kinase 3

I: Nucleoside diphosphate kinase 3

J: Nucleoside diphosphate kinase 3

K: Nucleoside diphosphate kinase 3

L: Nucleoside diphosphate kinase 3

ヘテロ分子

概要:

• 216 kDa, 12 ポリマー

構成要素の詳細:

	分子量 (理論値)	分子数
合計 (水以外)	216,052	26
ポリマ－	210,542	12
非ポリマー	5,511	14
水	5,459	303

1

A: Nucleoside diphosphate kinase 3

B: Nucleoside diphosphate kinase 3

C: Nucleoside diphosphate kinase 3

D: Nucleoside diphosphate kinase 3

E: Nucleoside diphosphate kinase 3

F: Nucleoside diphosphate kinase 3

ヘテロ分子

概要:

• 登録者・ソフトウェアが定義した集合体
• 根拠: gel filtration
• 108 kDa, 6 ポリマー

構成要素の詳細:

	分子量 (理論値)	分子数
合計 (水以外)	108,122	14
ポリマ－	105,271	6
非ポリマー	2,851	8
水	108	6

対称操作:

タイプ	名称	対称操作	数
identity operation	1_555	x,y,z	1

計算値:

Buried area	22850 Å2
ΔGint	-125 kcal/mol
Surface area	32740 Å2
手法	PISA

2

G: Nucleoside diphosphate kinase 3

H: Nucleoside diphosphate kinase 3

I: Nucleoside diphosphate kinase 3

J: Nucleoside diphosphate kinase 3

K: Nucleoside diphosphate kinase 3

L: Nucleoside diphosphate kinase 3

ヘテロ分子

概要:

• 登録者・ソフトウェアが定義した集合体
• 根拠: gel filtration
• 108 kDa, 6 ポリマー

構成要素の詳細:

	分子量 (理論値)	分子数
合計 (水以外)	107,930	12
ポリマ－	105,271	6
非ポリマー	2,659	6
水	108	6

対称操作:

タイプ	名称	対称操作	数
identity operation	1_555	x,y,z	1

計算値:

Buried area	22380 Å2
ΔGint	-108 kcal/mol
Surface area	32840 Å2
手法	PISA

単位格子

Length a, b, c (Å)	104.340, 78.640, 112.370
Angle α, β, γ (deg.)	90.000, 97.561, 90.000
Int Tables number	4
Space group name H-M	P1211

非結晶学的対称性 (NCS)

NCSドメイン:

ID	Ens-ID	詳細
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A
7	4	A
8	4	A
9	5	A
10	5	A
11	6	A
12	6	A
13	7	A
14	7	A
15	8	A
16	8	A
17	9	A
18	9	A
19	10	A
20	10	A
21	11	A
22	11	A
23	12	A
24	12	A
25	13	A
26	13	A
27	14	A
28	14	A
29	15	A
30	15	A
31	16	A
32	16	A
33	17	A
34	17	A
35	18	A
36	18	A
37	19	A
38	19	A
39	20	A
40	20	A
41	21	A
42	21	A
43	22	A
44	22	A
45	23	A
46	23	A
47	24	A
48	24	A
49	25	A
50	25	A
51	26	A
52	26	A
53	27	A
54	27	A
55	28	A
56	28	A
57	29	A
58	29	A
59	30	A
60	30	A
61	31	A
62	31	A
63	32	A
64	32	A
65	33	A
66	33	A
67	34	A
68	34	A
69	35	A
70	35	A
71	36	A
72	36	A
73	37	A
74	37	A
75	38	A
76	38	A
77	39	A
78	39	A
79	40	A
80	40	A
81	41	A
82	41	A
83	42	A
84	42	A
85	43	A
86	43	A
87	44	A
88	44	A
89	45	A
90	45	A
91	46	A
92	46	A
93	47	A
94	47	A
95	48	A
96	48	A
97	49	A
98	49	A
99	50	A
100	50	A
101	51	A
102	51	A
103	52	A
104	52	A
105	53	A
106	53	A
107	54	A
108	54	A
109	55	A
110	55	A
111	56	A
112	56	A
113	57	A
114	57	A
115	58	A
116	58	A
117	59	A
118	59	A
119	60	A
120	60	A
121	61	A
122	61	A
123	62	A
124	62	A
125	63	A
126	63	A
127	64	A
128	64	A
129	65	A
130	65	A
131	66	A
132	66	A

NCSドメイン領域:

Dom-ID	Component-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	1	A	19 - 169
2	1	1	A	19 - 169
3	2	2	A	19 - 169
4	2	2	A	19 - 169
5	3	3	A	19 - 169
6	3	3	A	19 - 169
7	4	4	A	19 - 168
8	4	4	A	19 - 168
9	5	5	A	19 - 169
10	5	5	A	19 - 169
11	6	6	A	19 - 169
12	6	6	A	19 - 169
13	7	7	A	19 - 169
14	7	7	A	19 - 169
15	8	8	A	19 - 169
16	8	8	A	19 - 169
17	9	9	A	19 - 168
18	9	9	A	19 - 168
19	10	10	A	19 - 168
20	10	10	A	19 - 168
21	11	11	A	19 - 169
22	11	11	A	19 - 169
23	12	12	A	19 - 169
24	12	12	A	19 - 169
25	13	13	A	19 - 169
26	13	13	A	19 - 169
27	14	14	A	19 - 168
28	14	14	A	19 - 168
29	15	15	A	19 - 169
30	15	15	A	19 - 169
31	16	16	A	19 - 169
32	16	16	A	19 - 169
33	17	17	A	19 - 169
34	17	17	A	19 - 169
35	18	18	A	19 - 169
36	18	18	A	19 - 169
37	19	19	A	19 - 168
38	19	19	A	19 - 168
39	20	20	A	19 - 168
40	20	20	A	19 - 168
41	21	21	A	19 - 169
42	21	21	A	19 - 169
43	22	22	A	19 - 169
44	22	22	A	19 - 169
45	23	23	A	19 - 168
46	23	23	A	19 - 168
47	24	24	A	19 - 169
48	24	24	A	19 - 169
49	25	25	A	19 - 169
50	25	25	A	19 - 169
51	26	26	A	19 - 169
52	26	26	A	19 - 169
53	27	27	A	19 - 169
54	27	27	A	19 - 169
55	28	28	A	19 - 168
56	28	28	A	19 - 168
57	29	29	A	19 - 168
58	29	29	A	19 - 168
59	30	30	A	19 - 169
60	30	30	A	19 - 169
61	31	31	A	19 - 168
62	31	31	A	19 - 168
63	32	32	A	19 - 169
64	32	32	A	19 - 169
65	33	33	A	19 - 169
66	33	33	A	19 - 169
67	34	34	A	19 - 169
68	34	34	A	19 - 169
69	35	35	A	19 - 169
70	35	35	A	19 - 169
71	36	36	A	19 - 168
72	36	36	A	19 - 168
73	37	37	A	19 - 168
74	37	37	A	19 - 168
75	38	38	A	19 - 169
76	38	38	A	19 - 169
77	39	39	A	19 - 168
78	39	39	A	19 - 168
79	40	40	A	19 - 168
80	40	40	A	19 - 168
81	41	41	A	19 - 168
82	41	41	A	19 - 168
83	42	42	A	19 - 168
84	42	42	A	19 - 168
85	43	43	A	18 - 168
86	43	43	A	18 - 168
87	44	44	A	18 - 169
88	44	44	A	18 - 169
89	45	45	A	19 - 168
90	45	45	A	19 - 168
91	46	46	A	19 - 169
92	46	46	A	19 - 169
93	47	47	A	19 - 169
94	47	47	A	19 - 169
95	48	48	A	19 - 169
96	48	48	A	19 - 169
97	49	49	A	19 - 168
98	49	49	A	19 - 168
99	50	50	A	19 - 168
100	50	50	A	19 - 168
101	51	51	A	19 - 169
102	51	51	A	19 - 169
103	52	52	A	19 - 169
104	52	52	A	19 - 169
105	53	53	A	19 - 169
106	53	53	A	19 - 169
107	54	54	A	19 - 168
108	54	54	A	19 - 168
109	55	55	A	19 - 168
110	55	55	A	19 - 168
111	56	56	A	19 - 169
112	56	56	A	19 - 169
113	57	57	A	19 - 169
114	57	57	A	19 - 169
115	58	58	A	19 - 168
116	58	58	A	19 - 168
117	59	59	A	19 - 168
118	59	59	A	19 - 168
119	60	60	A	19 - 169
120	60	60	A	19 - 169
121	61	61	A	19 - 168
122	61	61	A	19 - 168
123	62	62	A	19 - 168
124	62	62	A	19 - 168
125	63	63	A	19 - 169
126	63	63	A	19 - 169
127	64	64	A	18 - 168
128	64	64	A	18 - 168
129	65	65	A	19 - 168
130	65	65	A	19 - 168
131	66	66	A	19 - 168
132	66	66	A	19 - 168

NCSアンサンブル:

ID	詳細
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30
16	Local NCS retraints between domains: 31 32
17	Local NCS retraints between domains: 33 34
18	Local NCS retraints between domains: 35 36
19	Local NCS retraints between domains: 37 38
20	Local NCS retraints between domains: 39 40
21	Local NCS retraints between domains: 41 42
22	Local NCS retraints between domains: 43 44
23	Local NCS retraints between domains: 45 46
24	Local NCS retraints between domains: 47 48
25	Local NCS retraints between domains: 49 50
26	Local NCS retraints between domains: 51 52
27	Local NCS retraints between domains: 53 54
28	Local NCS retraints between domains: 55 56
29	Local NCS retraints between domains: 57 58
30	Local NCS retraints between domains: 59 60
31	Local NCS retraints between domains: 61 62
32	Local NCS retraints between domains: 63 64
33	Local NCS retraints between domains: 65 66
34	Local NCS retraints between domains: 67 68
35	Local NCS retraints between domains: 69 70
36	Local NCS retraints between domains: 71 72
37	Local NCS retraints between domains: 73 74
38	Local NCS retraints between domains: 75 76
39	Local NCS retraints between domains: 77 78
40	Local NCS retraints between domains: 79 80
41	Local NCS retraints between domains: 81 82
42	Local NCS retraints between domains: 83 84
43	Local NCS retraints between domains: 85 86
44	Local NCS retraints between domains: 87 88
45	Local NCS retraints between domains: 89 90
46	Local NCS retraints between domains: 91 92
47	Local NCS retraints between domains: 93 94
48	Local NCS retraints between domains: 95 96
49	Local NCS retraints between domains: 97 98
50	Local NCS retraints between domains: 99 100
51	Local NCS retraints between domains: 101 102
52	Local NCS retraints between domains: 103 104
53	Local NCS retraints between domains: 105 106
54	Local NCS retraints between domains: 107 108
55	Local NCS retraints between domains: 109 110
56	Local NCS retraints between domains: 111 112
57	Local NCS retraints between domains: 113 114
58	Local NCS retraints between domains: 115 116
59	Local NCS retraints between domains: 117 118
60	Local NCS retraints between domains: 119 120
61	Local NCS retraints between domains: 121 122
62	Local NCS retraints between domains: 123 124
63	Local NCS retraints between domains: 125 126
64	Local NCS retraints between domains: 127 128
65	Local NCS retraints between domains: 129 130
66	Local NCS retraints between domains: 131 132

要素

#1: タンパク質

A B C D E F G H I J K L
Nucleoside diphosphate kinase 3

詳細:

分子量: 17545.137 Da / 分子数: 12 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: NME3 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q13232

#2: 化合物

A-201 B-201 C-201 D-201 E-201 F-201 G-201 H-201 I-201 J-201 K-201 L-201
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / GDP

詳細:

タイプ: RNA linking / 分子量: 443.201 Da / 分子数: 12 / 由来タイプ: 合成 / 式: C₁₀H₁₅N₅O₁₁P₂ / タイプ: SUBJECT OF INVESTIGATION / コメント: GDP, エネルギー貯蔵分子*YM

#3: 化合物

C-202 D-202 ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン

詳細:

分子量: 96.063 Da / 分子数: 2 / 由来タイプ: 合成 / 式: SO₄

#4: 水

ChemComp-HOH / water

詳細:

分子量: 18.015 Da / 分子数: 303 / 由来タイプ: 天然 / 式: H₂O

• 研究の焦点であるリガンドがあるか: Y
• Has protein modification: N

実験情報

実験

• 実験: 手法: X線回折 / 使用した結晶の数: 1

試料調製

• 結晶: マシュー密度: 2.17 ų/Da / 溶媒含有率: 43.5 %
• 結晶化: 温度: 291 K / 手法: 蒸気拡散法 / pH: 5.4 ; 詳細: 6% PEG 3350, 150 mM Li2SO4, 100 mM Tri-sodium citrate pH 5.4

データ収集

• 回折: 平均測定温度: 100 K / Serial crystal experiment: N
• 放射光源: 由来: シンクロトロン / サイト: ESRF / ビームライン: MASSIF-3 / 波長: 0.9677 Å
• 検出器: タイプ: DECTRIS EIGER X 4M / 検出器: PIXEL / 日付: 2021年5月7日 / 詳細: Vertical CRL / horizontal eliptical mirror
• 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: 0.9677 Å / 相対比: 1
• 反射: 解像度: 2.17→46.592 Å / Num. obs: 94493 / % possible obs: 99.5 % / 冗長度: 10.3 % / B_iso Wilson estimate: 46.2 Ų / CC_1/2: 0.998 / R_merge(I) obs: 0.152 / R_rim(I) all: 0.16 / Net I/σ(I): 9.64
• 反射 シェル: 解像度: 2.17→2.23 Å / 冗長度: 7.2 % / R_merge(I) obs: 1.388 / Mean I/σ(I) obs: 1.04 / Num. unique obs: 6518 / CC_1/2: 0.549 / R_rim(I) all: 1.495 / % possible all: 94.2

解析

ソフトウェア

名称	バージョン	分類
REFMAC	5.8.0419	精密化
XDS		データ削減
XSCALE		データスケーリング
PHASER		位相決定

精密化

構造決定の手法: 分子置換 / 解像度: 2.175→46.592 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.945 / SU B: 15.974 / SU ML: 0.184 / 交差検証法: FREE R-VALUE / ESU R: 0.285 / ESU R Free: 0.203 / 詳細: Hydrogens have been added in their riding positions

	Rfactor	反射数	%反射
Rfree	0.2289	1996	2.112 %
Rwork	0.1888	92497	-
all	0.19	-	-
obs	-	94493	99.551 %

• 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

B_iso mean: 49.233 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-0.758 Å2	0 Å2	-0.311 Å2
2-	-	1.982 Å2	0 Å2
3-	-	-	-1.103 Å2

精密化ステップ

サイクル: LAST / 解像度: 2.175→46.592 Å

	タンパク質	核酸	リガンド	溶媒	全体
原子数	14463	0	346	303	15112

拘束条件

Refine-ID	タイプ	Dev ideal	Dev ideal target	数
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	15177
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	14343
X-RAY DIFFRACTION	r_angle_refined_deg	1.812	1.655	20606
X-RAY DIFFRACTION	r_angle_other_deg	0.588	1.582	32801
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.454	5	1808
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	12.79	5	188
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.383	5	12
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.227	10	2502
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.36	10	714
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	2219
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	18316
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3780
X-RAY DIFFRACTION	r_nbd_refined	0.219	0.2	2760
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.193	0.2	13157
X-RAY DIFFRACTION	r_nbtor_refined	0.184	0.2	7303
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	8258
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.181	0.2	435
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.171	0.2	10
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.171	0.2	29
X-RAY DIFFRACTION	r_nbd_other	0.223	0.2	94
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.482	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	3.727	3.162	7262
X-RAY DIFFRACTION	r_mcbond_other	3.727	3.162	7262
X-RAY DIFFRACTION	r_mcangle_it	4.818	5.666	9060
X-RAY DIFFRACTION	r_mcangle_other	4.818	5.667	9061
X-RAY DIFFRACTION	r_scbond_it	6.089	3.92	7915
X-RAY DIFFRACTION	r_scbond_other	6.088	3.92	7915
X-RAY DIFFRACTION	r_scangle_it	8.812	6.906	11546
X-RAY DIFFRACTION	r_scangle_other	8.812	6.906	11547
X-RAY DIFFRACTION	r_lrange_it	9.779	32.834	16712
X-RAY DIFFRACTION	r_lrange_other	9.785	32.831	16690
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.076	0.05	4829
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.07	0.05	4785
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.068	0.05	4852
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.083	0.05	4759
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.076	0.05	4826
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.058	0.05	4885
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.072	0.05	4853
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.074	0.05	4755
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.071	0.05	4867
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.08	0.05	4750
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.077	0.05	4843
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.074	0.05	4751
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.073	0.05	4806
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.075	0.05	4732
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.074	0.05	4808
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.078	0.05	4784
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.071	0.05	4842
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.075	0.05	4746
X-RAY DIFFRACTION	r_ncsr_local_group_19	0.075	0.05	4765
X-RAY DIFFRACTION	r_ncsr_local_group_20	0.077	0.05	4707
X-RAY DIFFRACTION	r_ncsr_local_group_21	0.068	0.05	4833
X-RAY DIFFRACTION	r_ncsr_local_group_22	0.08	0.05	4736
X-RAY DIFFRACTION	r_ncsr_local_group_23	0.068	0.05	4751
X-RAY DIFFRACTION	r_ncsr_local_group_24	0.071	0.05	4771
X-RAY DIFFRACTION	r_ncsr_local_group_25	0.077	0.05	4715
X-RAY DIFFRACTION	r_ncsr_local_group_26	0.077	0.05	4759
X-RAY DIFFRACTION	r_ncsr_local_group_27	0.056	0.05	4782
X-RAY DIFFRACTION	r_ncsr_local_group_28	0.084	0.05	4714
X-RAY DIFFRACTION	r_ncsr_local_group_29	0.073	0.05	4778
X-RAY DIFFRACTION	r_ncsr_local_group_30	0.073	0.05	4760
X-RAY DIFFRACTION	r_ncsr_local_group_31	0.079	0.05	4728
X-RAY DIFFRACTION	r_ncsr_local_group_32	0.072	0.05	4792
X-RAY DIFFRACTION	r_ncsr_local_group_33	0.07	0.05	4808
X-RAY DIFFRACTION	r_ncsr_local_group_34	0.078	0.05	4798
X-RAY DIFFRACTION	r_ncsr_local_group_35	0.074	0.05	4722
X-RAY DIFFRACTION	r_ncsr_local_group_36	0.066	0.05	4793
X-RAY DIFFRACTION	r_ncsr_local_group_37	0.075	0.05	4713
X-RAY DIFFRACTION	r_ncsr_local_group_38	0.067	0.05	4823
X-RAY DIFFRACTION	r_ncsr_local_group_39	0.079	0.05	4726
X-RAY DIFFRACTION	r_ncsr_local_group_40	0.084	0.05	4709
X-RAY DIFFRACTION	r_ncsr_local_group_41	0.067	0.05	4759
X-RAY DIFFRACTION	r_ncsr_local_group_42	0.065	0.05	4766
X-RAY DIFFRACTION	r_ncsr_local_group_43	0.092	0.05	4720
X-RAY DIFFRACTION	r_ncsr_local_group_44	0.058	0.05	4819
X-RAY DIFFRACTION	r_ncsr_local_group_45	0.08	0.05	4732
X-RAY DIFFRACTION	r_ncsr_local_group_46	0.079	0.05	4755
X-RAY DIFFRACTION	r_ncsr_local_group_47	0.075	0.05	4818
X-RAY DIFFRACTION	r_ncsr_local_group_48	0.069	0.05	4710
X-RAY DIFFRACTION	r_ncsr_local_group_49	0.079	0.05	4772
X-RAY DIFFRACTION	r_ncsr_local_group_50	0.075	0.05	4724
X-RAY DIFFRACTION	r_ncsr_local_group_51	0.064	0.05	4827
X-RAY DIFFRACTION	r_ncsr_local_group_52	0.077	0.05	4805
X-RAY DIFFRACTION	r_ncsr_local_group_53	0.074	0.05	4723
X-RAY DIFFRACTION	r_ncsr_local_group_54	0.077	0.05	4781
X-RAY DIFFRACTION	r_ncsr_local_group_55	0.08	0.05	4695
X-RAY DIFFRACTION	r_ncsr_local_group_56	0.076	0.05	4795
X-RAY DIFFRACTION	r_ncsr_local_group_57	0.078	0.05	4753
X-RAY DIFFRACTION	r_ncsr_local_group_58	0.077	0.05	4782
X-RAY DIFFRACTION	r_ncsr_local_group_59	0.068	0.05	4737
X-RAY DIFFRACTION	r_ncsr_local_group_60	0.076	0.05	4842
X-RAY DIFFRACTION	r_ncsr_local_group_61	0.082	0.05	4696
X-RAY DIFFRACTION	r_ncsr_local_group_62	0.062	0.05	4760
X-RAY DIFFRACTION	r_ncsr_local_group_63	0.069	0.05	4736
X-RAY DIFFRACTION	r_ncsr_local_group_64	0.091	0.05	4722
X-RAY DIFFRACTION	r_ncsr_local_group_65	0.066	0.05	4810
X-RAY DIFFRACTION	r_ncsr_local_group_66	0.076	0.05	4752

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	タイプ	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.07565	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.07565	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.07	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.07	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.06836	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.06836	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.08281	0.0501
4	8	A	X-RAY DIFFRACTION	Local ncs	0.08281	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.07608	0.0501
5	10	A	X-RAY DIFFRACTION	Local ncs	0.07608	0.0501
6	11	A	X-RAY DIFFRACTION	Local ncs	0.05776	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.05776	0.0501
7	13	A	X-RAY DIFFRACTION	Local ncs	0.07247	0.0501
7	14	A	X-RAY DIFFRACTION	Local ncs	0.07247	0.0501
8	15	A	X-RAY DIFFRACTION	Local ncs	0.07372	0.0501
8	16	A	X-RAY DIFFRACTION	Local ncs	0.07372	0.0501
9	17	A	X-RAY DIFFRACTION	Local ncs	0.07059	0.0501
9	18	A	X-RAY DIFFRACTION	Local ncs	0.07059	0.0501
10	19	A	X-RAY DIFFRACTION	Local ncs	0.08022	0.0501
10	20	A	X-RAY DIFFRACTION	Local ncs	0.08022	0.0501
11	21	A	X-RAY DIFFRACTION	Local ncs	0.07746	0.0501
11	22	A	X-RAY DIFFRACTION	Local ncs	0.07746	0.0501
12	23	A	X-RAY DIFFRACTION	Local ncs	0.07362	0.0501
12	24	A	X-RAY DIFFRACTION	Local ncs	0.07362	0.0501
13	25	A	X-RAY DIFFRACTION	Local ncs	0.07315	0.0501
13	26	A	X-RAY DIFFRACTION	Local ncs	0.07315	0.0501
14	27	A	X-RAY DIFFRACTION	Local ncs	0.07499	0.0501
14	28	A	X-RAY DIFFRACTION	Local ncs	0.07499	0.0501
15	29	A	X-RAY DIFFRACTION	Local ncs	0.07416	0.0501
15	30	A	X-RAY DIFFRACTION	Local ncs	0.07416	0.0501
16	31	A	X-RAY DIFFRACTION	Local ncs	0.07751	0.0501
16	32	A	X-RAY DIFFRACTION	Local ncs	0.07751	0.0501
17	33	A	X-RAY DIFFRACTION	Local ncs	0.07114	0.0501
17	34	A	X-RAY DIFFRACTION	Local ncs	0.07114	0.0501
18	35	A	X-RAY DIFFRACTION	Local ncs	0.07459	0.0501
18	36	A	X-RAY DIFFRACTION	Local ncs	0.07459	0.0501
19	37	A	X-RAY DIFFRACTION	Local ncs	0.0752	0.0501
19	38	A	X-RAY DIFFRACTION	Local ncs	0.0752	0.0501
20	39	A	X-RAY DIFFRACTION	Local ncs	0.07725	0.0501
20	40	A	X-RAY DIFFRACTION	Local ncs	0.07725	0.0501
21	41	A	X-RAY DIFFRACTION	Local ncs	0.06755	0.0501
21	42	A	X-RAY DIFFRACTION	Local ncs	0.06755	0.0501
22	43	A	X-RAY DIFFRACTION	Local ncs	0.07996	0.0501
22	44	A	X-RAY DIFFRACTION	Local ncs	0.07996	0.0501
23	45	A	X-RAY DIFFRACTION	Local ncs	0.06829	0.0501
23	46	A	X-RAY DIFFRACTION	Local ncs	0.06829	0.0501
24	47	A	X-RAY DIFFRACTION	Local ncs	0.07097	0.0501
24	48	A	X-RAY DIFFRACTION	Local ncs	0.07097	0.0501
25	49	A	X-RAY DIFFRACTION	Local ncs	0.07737	0.0501
25	50	A	X-RAY DIFFRACTION	Local ncs	0.07737	0.0501
26	51	A	X-RAY DIFFRACTION	Local ncs	0.07738	0.0501
26	52	A	X-RAY DIFFRACTION	Local ncs	0.07738	0.0501
27	53	A	X-RAY DIFFRACTION	Local ncs	0.0557	0.0501
27	54	A	X-RAY DIFFRACTION	Local ncs	0.0557	0.0501
28	55	A	X-RAY DIFFRACTION	Local ncs	0.08387	0.0501
28	56	A	X-RAY DIFFRACTION	Local ncs	0.08387	0.0501
29	57	A	X-RAY DIFFRACTION	Local ncs	0.07251	0.0501
29	58	A	X-RAY DIFFRACTION	Local ncs	0.07251	0.0501
30	59	A	X-RAY DIFFRACTION	Local ncs	0.07347	0.0501
30	60	A	X-RAY DIFFRACTION	Local ncs	0.07347	0.0501
31	61	A	X-RAY DIFFRACTION	Local ncs	0.07929	0.0501
31	62	A	X-RAY DIFFRACTION	Local ncs	0.07929	0.0501
32	63	A	X-RAY DIFFRACTION	Local ncs	0.07239	0.0501
32	64	A	X-RAY DIFFRACTION	Local ncs	0.07239	0.0501
33	65	A	X-RAY DIFFRACTION	Local ncs	0.06979	0.0501
33	66	A	X-RAY DIFFRACTION	Local ncs	0.06979	0.0501
34	67	A	X-RAY DIFFRACTION	Local ncs	0.07841	0.0501
34	68	A	X-RAY DIFFRACTION	Local ncs	0.07841	0.0501
35	69	A	X-RAY DIFFRACTION	Local ncs	0.07403	0.0501
35	70	A	X-RAY DIFFRACTION	Local ncs	0.07403	0.0501
36	71	A	X-RAY DIFFRACTION	Local ncs	0.06603	0.0501
36	72	A	X-RAY DIFFRACTION	Local ncs	0.06603	0.0501
37	73	A	X-RAY DIFFRACTION	Local ncs	0.07483	0.0501
37	74	A	X-RAY DIFFRACTION	Local ncs	0.07483	0.0501
38	75	A	X-RAY DIFFRACTION	Local ncs	0.06744	0.0501
38	76	A	X-RAY DIFFRACTION	Local ncs	0.06744	0.0501
39	77	A	X-RAY DIFFRACTION	Local ncs	0.07878	0.0501
39	78	A	X-RAY DIFFRACTION	Local ncs	0.07878	0.0501
40	79	A	X-RAY DIFFRACTION	Local ncs	0.08392	0.0501
40	80	A	X-RAY DIFFRACTION	Local ncs	0.08392	0.0501
41	81	A	X-RAY DIFFRACTION	Local ncs	0.06702	0.0501
41	82	A	X-RAY DIFFRACTION	Local ncs	0.06702	0.0501
42	83	A	X-RAY DIFFRACTION	Local ncs	0.06503	0.0501
42	84	A	X-RAY DIFFRACTION	Local ncs	0.06503	0.0501
43	85	A	X-RAY DIFFRACTION	Local ncs	0.09152	0.0501
43	86	A	X-RAY DIFFRACTION	Local ncs	0.09152	0.0501
44	87	A	X-RAY DIFFRACTION	Local ncs	0.05822	0.0501
44	88	A	X-RAY DIFFRACTION	Local ncs	0.05822	0.0501
45	89	A	X-RAY DIFFRACTION	Local ncs	0.08013	0.0501
45	90	A	X-RAY DIFFRACTION	Local ncs	0.08013	0.0501
46	91	A	X-RAY DIFFRACTION	Local ncs	0.07851	0.0501
46	92	A	X-RAY DIFFRACTION	Local ncs	0.07851	0.0501
47	93	A	X-RAY DIFFRACTION	Local ncs	0.07492	0.0501
47	94	A	X-RAY DIFFRACTION	Local ncs	0.07492	0.0501
48	95	A	X-RAY DIFFRACTION	Local ncs	0.06877	0.0501
48	96	A	X-RAY DIFFRACTION	Local ncs	0.06877	0.0501
49	97	A	X-RAY DIFFRACTION	Local ncs	0.07876	0.0501
49	98	A	X-RAY DIFFRACTION	Local ncs	0.07876	0.0501
50	99	A	X-RAY DIFFRACTION	Local ncs	0.07451	0.0501
50	100	A	X-RAY DIFFRACTION	Local ncs	0.07451	0.0501
51	101	A	X-RAY DIFFRACTION	Local ncs	0.06399	0.0501
51	102	A	X-RAY DIFFRACTION	Local ncs	0.06399	0.0501
52	103	A	X-RAY DIFFRACTION	Local ncs	0.07676	0.0501
52	104	A	X-RAY DIFFRACTION	Local ncs	0.07676	0.0501
53	105	A	X-RAY DIFFRACTION	Local ncs	0.07439	0.0501
53	106	A	X-RAY DIFFRACTION	Local ncs	0.07439	0.0501
54	107	A	X-RAY DIFFRACTION	Local ncs	0.07733	0.0501
54	108	A	X-RAY DIFFRACTION	Local ncs	0.07733	0.0501
55	109	A	X-RAY DIFFRACTION	Local ncs	0.0799	0.0501
55	110	A	X-RAY DIFFRACTION	Local ncs	0.0799	0.0501
56	111	A	X-RAY DIFFRACTION	Local ncs	0.07581	0.0501
56	112	A	X-RAY DIFFRACTION	Local ncs	0.07581	0.0501
57	113	A	X-RAY DIFFRACTION	Local ncs	0.07795	0.0501
57	114	A	X-RAY DIFFRACTION	Local ncs	0.07795	0.0501
58	115	A	X-RAY DIFFRACTION	Local ncs	0.0774	0.0501
58	116	A	X-RAY DIFFRACTION	Local ncs	0.0774	0.0501
59	117	A	X-RAY DIFFRACTION	Local ncs	0.06796	0.0501
59	118	A	X-RAY DIFFRACTION	Local ncs	0.06796	0.0501
60	119	A	X-RAY DIFFRACTION	Local ncs	0.07598	0.0501
60	120	A	X-RAY DIFFRACTION	Local ncs	0.07598	0.0501
61	121	A	X-RAY DIFFRACTION	Local ncs	0.08189	0.0501
61	122	A	X-RAY DIFFRACTION	Local ncs	0.08189	0.0501
62	123	A	X-RAY DIFFRACTION	Local ncs	0.06191	0.0501
62	124	A	X-RAY DIFFRACTION	Local ncs	0.06191	0.0501
63	125	A	X-RAY DIFFRACTION	Local ncs	0.06919	0.0501
63	126	A	X-RAY DIFFRACTION	Local ncs	0.06919	0.0501
64	127	A	X-RAY DIFFRACTION	Local ncs	0.0909	0.0501
64	128	A	X-RAY DIFFRACTION	Local ncs	0.0909	0.0501
65	129	A	X-RAY DIFFRACTION	Local ncs	0.06621	0.0501
65	130	A	X-RAY DIFFRACTION	Local ncs	0.06621	0.0501
66	131	A	X-RAY DIFFRACTION	Local ncs	0.076	0.0501
66	132	A	X-RAY DIFFRACTION	Local ncs	0.076	0.0501

LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

解像度 (Å)	Rfactor Rfree	Num. reflection Rfree	Rfactor Rwork	Num. reflection Rwork	Rfactor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WRfactor Rwork
2.175-2.231	0.348	139	0.331	6348	0.331	6893	0.909	0.922	94.11	0.326
2.231-2.292	0.288	141	0.273	6689	0.274	6830	0.948	0.952	100	0.262
2.292-2.358	0.283	136	0.26	6463	0.261	6602	0.946	0.959	99.9546	0.244
2.358-2.431	0.319	146	0.251	6260	0.253	6407	0.948	0.963	99.9844	0.233
2.431-2.51	0.286	116	0.237	6129	0.238	6245	0.95	0.968	100	0.217
2.51-2.598	0.268	129	0.225	5874	0.226	6004	0.962	0.972	99.9833	0.203
2.598-2.696	0.247	126	0.207	5719	0.207	5847	0.963	0.975	99.9658	0.185
2.696-2.806	0.306	109	0.201	5497	0.203	5607	0.95	0.976	99.9822	0.179
2.806-2.93	0.248	117	0.199	5251	0.2	5368	0.962	0.977	100	0.178
2.93-3.072	0.234	123	0.187	5010	0.188	5133	0.964	0.98	100	0.17
3.072-3.238	0.25	124	0.193	4775	0.195	4899	0.962	0.981	100	0.181
3.238-3.433	0.197	109	0.187	4561	0.187	4670	0.978	0.983	100	0.178
3.433-3.669	0.203	99	0.189	4238	0.19	4337	0.975	0.984	100	0.182
3.669-3.961	0.201	101	0.172	3995	0.172	4096	0.982	0.987	100	0.167
3.961-4.336	0.219	54	0.154	3701	0.155	3755	0.979	0.987	100	0.154
4.336-4.842	0.178	63	0.128	3346	0.129	3409	0.983	0.991	100	0.133
4.842-5.581	0.179	53	0.152	2967	0.152	3020	0.986	0.989	100	0.157
5.581-6.811	0.215	48	0.179	2520	0.18	2568	0.976	0.985	100	0.185
6.811-9.531	0.197	42	0.172	1992	0.173	2034	0.982	0.987	100	0.188
9.531-46.592	0.255	21	0.219	1163	0.219	1184	0.956	0.973	100	0.264

精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°2)	L12 (°2)	L13 (°2)	L22 (°2)	L23 (°2)	L33 (°2)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å2)	T12 (Å2)	T13 (Å2)	T22 (Å2)	T23 (Å2)	T33 (Å2)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.3784	0.2112	-0.3537	0.8251	-0.1797	1.968	-0.0239	-0.1333	0.0149	0.097	0.0108	0.0739	-0.2704	-0.3213	0.0131	0.0731	0.0245	-0.0201	0.152	0.0254	0.0336	-34.0546	-19.9811	-37.6931
2	1.3395	0.4186	0.0762	1.3814	-0.3604	2.0776	-0.0415	0.0477	0.0349	-0.1039	0.0156	0.1424	-0.0868	-0.2369	0.0259	0.0856	0.0031	-0.063	0.071	0.0055	0.0509	-32.2681	-18.6701	-70.9677
3	1.8966	0.293	-0.3523	1.2828	0.0853	2.885	0.0948	-0.1525	0.2642	-0.019	-0.058	0.0218	-0.8359	0.1571	-0.0368	0.4071	-0.0951	-0.0535	0.04	0.0017	0.0625	-15.364	3.2537	-52.6413
4	1.8091	0.1788	0.7134	0.8781	0.0441	2.1207	0.0484	-0.149	-0.1877	0.0207	-0.0297	-0.0247	0.1566	0.1221	-0.0187	0.0583	-0.0316	-0.0535	0.1296	0.0795	0.083	-12.9832	-32.2257	-35.4461
5	1.3185	0.0462	0.0841	1.9307	0.1794	2.3453	0.0557	0.0016	-0.217	-0.172	-0.0516	-0.0634	0.2928	0.2012	-0.004	0.0895	0.0262	-0.034	0.0297	0.0116	0.071	-15.0434	-35.9156	-68.6619
6	1.536	0.0516	0.1891	1.5472	0.183	2.9232	-0.0014	0.021	0.0568	-0.0596	0.1163	-0.4298	-0.4346	0.6673	-0.1149	0.1167	-0.1863	-0.0136	0.3208	0.0117	0.1609	3.6358	-11.4943	-56.0303
7	1.7148	-0.1309	0.684	0.6414	0.2782	2.135	0.0983	0.068	-0.1983	-0.0834	-0.0074	0.0019	0.1846	-0.1471	-0.0909	0.0492	-0.0113	-0.0284	0.0711	-0.0143	0.0465	23.0576	-31.5484	-21.827
8	1.6396	-0.1182	-0.0169	1.4972	-0.2548	1.3292	0.0024	-0.1983	0.1213	0.036	0.0787	0.2744	-0.1713	-0.4039	-0.0811	0.0491	0.1223	-0.0054	0.3574	-0.0068	0.1051	3.914	-11.048	-3.7184
9	2.1916	-0.0128	0.254	1.7254	-0.058	1.3966	0.0626	-0.3646	-0.3807	0.2258	0.0711	0.0547	0.1464	-0.4088	-0.1337	0.0597	-0.0559	-0.0265	0.2654	0.1276	0.093	20.0764	-35.9406	11.134
10	1.9424	-0.4376	-0.0571	1.2465	-0.2091	1.6539	0.0295	0.1144	0.1206	0.0093	-0.0432	-0.1664	-0.1667	0.252	0.0137	0.0317	-0.0238	-0.0193	0.0844	-0.0042	0.0558	43.7988	-19.6621	-16.2168
11	2.1172	-0.2473	0.1821	1.5274	0.1253	2.2842	-0.0473	-0.1306	0.5544	0.0811	0.0005	-0.053	-0.5525	-0.2134	0.0468	0.223	0.0859	-0.0485	0.0598	-0.0688	0.1809	23.5211	3.5131	-3.4744
12	1.1298	-0.1301	0.5916	1.468	0.2627	1.7562	-0.0801	-0.2224	0.0028	0.2193	0.0812	-0.1449	-0.0776	-0.1973	-0.001	0.0898	0.049	-0.06	0.1473	-0.0221	0.0433	36.8242	-19.4051	16.6616

精密化 TLSグループ

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	19 - 201
2	X-RAY DIFFRACTION	1		B	19 - 201
3	X-RAY DIFFRACTION	1		C	19 - 201
4	X-RAY DIFFRACTION	1		D	19 - 201
5	X-RAY DIFFRACTION	1		E	19 - 201
6	X-RAY DIFFRACTION	1		F	19 - 201