PDB-8xu4: The Crystal Structure of MAPK2 from Biortus.

IDまたはキーワード:

登録情報

データベース: PDB / ID: 8xu4

タイトル

The Crystal Structure of MAPK2 from Biortus.

要素

MAP kinase-activated protein kinase 2

キーワード

TRANSFERASE / Kinase / Serine/threonine-protein kinase / DNA damage / ATP-binding

機能・相同性

機能・相同性情報

calcium-dependent protein serine/threonine kinase activity / macropinocytosis / CREB phosphorylation / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / leukotriene metabolic process / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Synthesis of Leukotrienes (LT) and Eoxins (EX) / regulation of tumor necrosis factor production / regulation of tumor necrosis factor-mediated signaling pathway / calcium/calmodulin-dependent protein kinase activity ...calcium-dependent protein serine/threonine kinase activity / macropinocytosis / CREB phosphorylation / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / leukotriene metabolic process / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Synthesis of Leukotrienes (LT) and Eoxins (EX) / regulation of tumor necrosis factor production / regulation of tumor necrosis factor-mediated signaling pathway / calcium/calmodulin-dependent protein kinase activity / regulation of interleukin-6 production / mitogen-activated protein kinase binding / positive regulation of macrophage cytokine production / 3'-UTR-mediated mRNA stabilization / toll-like receptor signaling pathway / p38MAPK cascade / inner ear development / cellular response to vascular endothelial growth factor stimulus / Regulation of HSF1-mediated heat shock response / vascular endothelial growth factor receptor signaling pathway / regulation of cellular response to heat / p38MAPK events / regulation of mRNA stability / response to cytokine / activated TAK1 mediates p38 MAPK activation / Regulation of TNFR1 signaling / VEGFA-VEGFR2 Pathway / positive regulation of tumor necrosis factor production / MAPK cascade / peptidyl-serine phosphorylation / Oxidative Stress Induced Senescence / response to lipopolysaccharide / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / calmodulin binding / intracellular signal transduction / ciliary basal body / protein phosphorylation / inflammatory response / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / DNA damage response / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
類似検索 - 分子機能

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: 3.4 Å

データ登録者

Wang, F. / Cheng, W. / Yuan, Z. / Qi, J. / Shen, Z.

資金援助

1件

引用

ジャーナル: To Be Published
タイトル: The Crystal Structure of MAPK2 from Biortus.
著者: Wang, F. / Cheng, W. / Yuan, Z. / Qi, J. / Shen, Z.

履歴

登録	2024年1月12日	登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.0	2024年1月24日	Provider: repository / タイプ: Initial release

構造ビューア	分子: MolmilJmol/JSmol

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ダウンロード

PDBx/mmCIF形式	8xu4.cif.gz	699.7 KB	表示	PDBx/mmCIF形式
PDB形式	pdb8xu4.ent.gz	559.6 KB	表示	PDB形式
PDBx/mmJSON形式	8xu4.json.gz		ツリー表示	PDBx/mmJSON形式
その他	その他のダウンロード

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検証レポート

アーカイブディレクトリ	https://data.pdbj.org/pub/pdb/validation_reports/xu/8xu4 ftp://data.pdbj.org/pub/pdb/validation_reports/xu/8xu4	HTTPS FTP

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関連構造データ

類似構造データ	類似検索 - 機能・相同性F&H 検索類似検索 - 機能F&H 検索類似検索 - 相同性F&H 検索

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リンク

PDBのページ	PDBj / wwPDB / NCBI
「今月の分子」の関連する項目	#86 - 2007年2月エキソソーム (Exosomes) 類似性 (2) #148 - 2012年4月 Rasタンパク質 (Ras Protein) 類似性 (1) #254 - 2021年2月セルロース合成酵素 (Cellulose Synthase) 類似性 (1) #60 - 2004年12月ユビキチン (Ubiquitin) 類似性 (2) #205 - 2017年1月核膜孔複合体 (Nuclear Pore Complex) 類似性 (1) #213 - 2017年9月サーチュイン (Sirtuins) 類似性 (1) #195 - 2016年3月 RAFタンパク質キナーゼ (RAF Protein Kinases) 類似性 (1) #43 - 2003年7月 Srcチロシンキナーゼ (Src Tyrosine Kinase) 類似性 (1) #234 - 2019年6月 MDM2とがん (MDM2 and Cancer) 類似性 (1) #56 - 2004年8月カスパーゼ (Caspases) 類似性 (1)

PDBのページ

PDBj /

wwPDB /

NCBI

「今月の分子」の関連する項目

#86 - 2007年2月
エキソソーム (Exosomes)
類似性 (2)
#148 - 2012年4月
Rasタンパク質 (Ras Protein)
類似性 (1)
#254 - 2021年2月
セルロース合成酵素 (Cellulose Synthase)
類似性 (1)
#60 - 2004年12月
ユビキチン (Ubiquitin)
類似性 (2)
#205 - 2017年1月
核膜孔複合体 (Nuclear Pore Complex)
類似性 (1)
#213 - 2017年9月
サーチュイン (Sirtuins)
類似性 (1)
#195 - 2016年3月
RAFタンパク質キナーゼ (RAF Protein Kinases)
類似性 (1)
#43 - 2003年7月
Srcチロシンキナーゼ (Src Tyrosine Kinase)
類似性 (1)
#234 - 2019年6月
MDM2とがん (MDM2 and Cancer)
類似性 (1)
#56 - 2004年8月
カスパーゼ (Caspases)
類似性 (1)

登録構造単位

A: MAP kinase-activated protein kinase 2

B: MAP kinase-activated protein kinase 2

C: MAP kinase-activated protein kinase 2

D: MAP kinase-activated protein kinase 2

E: MAP kinase-activated protein kinase 2

F: MAP kinase-activated protein kinase 2

G: MAP kinase-activated protein kinase 2

H: MAP kinase-activated protein kinase 2

I: MAP kinase-activated protein kinase 2

J: MAP kinase-activated protein kinase 2

K: MAP kinase-activated protein kinase 2

L: MAP kinase-activated protein kinase 2

ヘテロ分子

441 kDa, 12 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

1

A: MAP kinase-activated protein kinase 2

登録者が定義した集合体
根拠: gel filtration
36.7 kDa, 1 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

2

B: MAP kinase-activated protein kinase 2

ヘテロ分子

登録者が定義した集合体
36.8 kDa, 1 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

3

C: MAP kinase-activated protein kinase 2

ヘテロ分子

登録者が定義した集合体
36.8 kDa, 1 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

4

D: MAP kinase-activated protein kinase 2

登録者が定義した集合体
36.7 kDa, 1 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

5

E: MAP kinase-activated protein kinase 2

登録者が定義した集合体
36.7 kDa, 1 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

6

F: MAP kinase-activated protein kinase 2

登録者が定義した集合体
36.7 kDa, 1 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

7

G: MAP kinase-activated protein kinase 2

登録者が定義した集合体
36.7 kDa, 1 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

8

H: MAP kinase-activated protein kinase 2

ヘテロ分子

登録者が定義した集合体
36.8 kDa, 1 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

9

I: MAP kinase-activated protein kinase 2

登録者が定義した集合体
36.7 kDa, 1 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

10

J: MAP kinase-activated protein kinase 2

登録者が定義した集合体
36.7 kDa, 1 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

11

K: MAP kinase-activated protein kinase 2

登録者が定義した集合体
36.7 kDa, 1 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

12

L: MAP kinase-activated protein kinase 2

登録者が定義した集合体
36.7 kDa, 1 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

単位格子

Length a, b, c (Å)	139.812, 179.015, 212.397
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

非結晶学的対称性 (NCS)

NCSドメイン:
NCSドメイン領域:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	HIS	HIS	ASP	ASP	A	A	47 - 351	1 - 305
2	2	1	HIS	HIS	ASP	ASP	B	B	47 - 351	1 - 305
3	3	2	VAL	VAL	ASP	ASP	A	A	48 - 351	2 - 305
4	4	2	VAL	VAL	ASP	ASP	C	C	48 - 351	2 - 305
5	5	3	HIS	HIS	TRP	TRP	A	A	47 - 349	1 - 303
6	6	3	HIS	HIS	TRP	TRP	D	D	47 - 349	1 - 303
7	7	4	HIS	HIS	ASP	ASP	A	A	47 - 351	1 - 305
8	8	4	HIS	HIS	ASP	ASP	E	E	47 - 351	1 - 305
9	9	5	HIS	HIS	ASP	ASP	A	A	47 - 351	1 - 305
10	10	5	HIS	HIS	ASP	ASP	F	F	47 - 351	1 - 305
11	11	6	HIS	HIS	ARG	ARG	A	A	47 - 348	1 - 302
12	12	6	HIS	HIS	ARG	ARG	G	G	47 - 348	1 - 302
13	13	7	HIS	HIS	ASP	ASP	A	A	47 - 351	1 - 305
14	14	7	HIS	HIS	ASP	ASP	H	H	47 - 351	1 - 305
15	15	8	HIS	HIS	LYS	LYS	A	A	47 - 346	1 - 300
16	16	8	HIS	HIS	LYS	LYS	I	I	47 - 346	1 - 300
17	17	9	HIS	HIS	GLU	GLU	A	A	47 - 350	1 - 304
18	18	9	HIS	HIS	GLU	GLU	J	J	47 - 350	1 - 304
19	19	10	HIS	HIS	ARG	ARG	A	A	47 - 348	1 - 302
20	20	10	HIS	HIS	ARG	ARG	K	K	47 - 348	1 - 302
21	21	11	HIS	HIS	ASP	ASP	A	A	47 - 351	1 - 305
22	22	11	HIS	HIS	ASP	ASP	L	L	47 - 351	1 - 305
23	23	12	VAL	VAL	ASP	ASP	B	B	48 - 351	2 - 305
24	24	12	VAL	VAL	ASP	ASP	C	C	48 - 351	2 - 305
25	25	13	HIS	HIS	TRP	TRP	B	B	47 - 349	1 - 303
26	26	13	HIS	HIS	TRP	TRP	D	D	47 - 349	1 - 303
27	27	14	HIS	HIS	ASP	ASP	B	B	47 - 351	1 - 305
28	28	14	HIS	HIS	ASP	ASP	E	E	47 - 351	1 - 305
29	29	15	HIS	HIS	ASP	ASP	B	B	47 - 351	1 - 305
30	30	15	HIS	HIS	ASP	ASP	F	F	47 - 351	1 - 305
31	31	16	HIS	HIS	ARG	ARG	B	B	47 - 348	1 - 302
32	32	16	HIS	HIS	ARG	ARG	G	G	47 - 348	1 - 302
33	33	17	HIS	HIS	ASP	ASP	B	B	47 - 351	1 - 305
34	34	17	HIS	HIS	ASP	ASP	H	H	47 - 351	1 - 305
35	35	18	HIS	HIS	GLU	GLU	B	B	47 - 347	1 - 301
36	36	18	HIS	HIS	GLU	GLU	I	I	47 - 347	1 - 301
37	37	19	HIS	HIS	GLU	GLU	B	B	47 - 350	1 - 304
38	38	19	HIS	HIS	GLU	GLU	J	J	47 - 350	1 - 304
39	39	20	HIS	HIS	ARG	ARG	B	B	47 - 348	1 - 302
40	40	20	HIS	HIS	ARG	ARG	K	K	47 - 348	1 - 302
41	41	21	HIS	HIS	ASP	ASP	B	B	47 - 351	1 - 305
42	42	21	HIS	HIS	ASP	ASP	L	L	47 - 351	1 - 305
43	43	22	VAL	VAL	TRP	TRP	C	C	48 - 349	2 - 303
44	44	22	VAL	VAL	TRP	TRP	D	D	48 - 349	2 - 303
45	45	23	VAL	VAL	ASP	ASP	C	C	48 - 351	2 - 305
46	46	23	VAL	VAL	ASP	ASP	E	E	48 - 351	2 - 305
47	47	24	VAL	VAL	ASP	ASP	C	C	48 - 351	2 - 305
48	48	24	VAL	VAL	ASP	ASP	F	F	48 - 351	2 - 305
49	49	25	VAL	VAL	ARG	ARG	C	C	48 - 348	2 - 302
50	50	25	VAL	VAL	ARG	ARG	G	G	48 - 348	2 - 302
51	51	26	VAL	VAL	ASP	ASP	C	C	48 - 351	2 - 305
52	52	26	VAL	VAL	ASP	ASP	H	H	48 - 351	2 - 305
53	53	27	VAL	VAL	GLU	GLU	C	C	48 - 347	2 - 301
54	54	27	VAL	VAL	GLU	GLU	I	I	48 - 347	2 - 301
55	55	28	VAL	VAL	GLU	GLU	C	C	48 - 350	2 - 304
56	56	28	VAL	VAL	GLU	GLU	J	J	48 - 350	2 - 304
57	57	29	VAL	VAL	ARG	ARG	C	C	48 - 348	2 - 302
58	58	29	VAL	VAL	ARG	ARG	K	K	48 - 348	2 - 302
59	59	30	VAL	VAL	ASP	ASP	C	C	48 - 351	2 - 305
60	60	30	VAL	VAL	ASP	ASP	L	L	48 - 351	2 - 305
61	61	31	HIS	HIS	TRP	TRP	D	D	47 - 349	1 - 303
62	62	31	HIS	HIS	TRP	TRP	E	E	47 - 349	1 - 303
63	63	32	HIS	HIS	TRP	TRP	D	D	47 - 349	1 - 303
64	64	32	HIS	HIS	TRP	TRP	F	F	47 - 349	1 - 303
65	65	33	HIS	HIS	ARG	ARG	D	D	47 - 348	1 - 302
66	66	33	HIS	HIS	ARG	ARG	G	G	47 - 348	1 - 302
67	67	34	HIS	HIS	TRP	TRP	D	D	47 - 349	1 - 303
68	68	34	HIS	HIS	TRP	TRP	H	H	47 - 349	1 - 303
69	69	35	HIS	HIS	GLU	GLU	D	D	47 - 347	1 - 301
70	70	35	HIS	HIS	GLU	GLU	I	I	47 - 347	1 - 301
71	71	36	HIS	HIS	TRP	TRP	D	D	47 - 349	1 - 303
72	72	36	HIS	HIS	TRP	TRP	J	J	47 - 349	1 - 303
73	73	37	HIS	HIS	ARG	ARG	D	D	47 - 348	1 - 302
74	74	37	HIS	HIS	ARG	ARG	K	K	47 - 348	1 - 302
75	75	38	HIS	HIS	TRP	TRP	D	D	47 - 349	1 - 303
76	76	38	HIS	HIS	TRP	TRP	L	L	47 - 349	1 - 303
77	77	39	HIS	HIS	LYS	LYS	E	E	47 - 353	1 - 307
78	78	39	HIS	HIS	LYS	LYS	F	F	47 - 353	1 - 307
79	79	40	HIS	HIS	ARG	ARG	E	E	47 - 348	1 - 302
80	80	40	HIS	HIS	ARG	ARG	G	G	47 - 348	1 - 302
81	81	41	HIS	HIS	LYS	LYS	E	E	47 - 353	1 - 307
82	82	41	HIS	HIS	LYS	LYS	H	H	47 - 353	1 - 307
83	83	42	HIS	HIS	GLU	GLU	E	E	47 - 347	1 - 301
84	84	42	HIS	HIS	GLU	GLU	I	I	47 - 347	1 - 301
85	85	43	HIS	HIS	GLU	GLU	E	E	47 - 350	1 - 304
86	86	43	HIS	HIS	GLU	GLU	J	J	47 - 350	1 - 304
87	87	44	HIS	HIS	ARG	ARG	E	E	47 - 348	1 - 302
88	88	44	HIS	HIS	ARG	ARG	K	K	47 - 348	1 - 302
89	89	45	HIS	HIS	LYS	LYS	E	E	47 - 353	1 - 307
90	90	45	HIS	HIS	LYS	LYS	L	L	47 - 353	1 - 307
91	91	46	HIS	HIS	ARG	ARG	F	F	47 - 348	1 - 302
92	92	46	HIS	HIS	ARG	ARG	G	G	47 - 348	1 - 302
93	93	47	HIS	HIS	LYS	LYS	F	F	47 - 353	1 - 307
94	94	47	HIS	HIS	LYS	LYS	H	H	47 - 353	1 - 307
95	95	48	HIS	HIS	GLU	GLU	F	F	47 - 347	1 - 301
96	96	48	HIS	HIS	GLU	GLU	I	I	47 - 347	1 - 301
97	97	49	HIS	HIS	GLU	GLU	F	F	47 - 350	1 - 304
98	98	49	HIS	HIS	GLU	GLU	J	J	47 - 350	1 - 304
99	99	50	HIS	HIS	ARG	ARG	F	F	47 - 348	1 - 302
100	100	50	HIS	HIS	ARG	ARG	K	K	47 - 348	1 - 302
101	101	51	HIS	HIS	LYS	LYS	F	F	47 - 353	1 - 307
102	102	51	HIS	HIS	LYS	LYS	L	L	47 - 353	1 - 307
103	103	52	HIS	HIS	ARG	ARG	G	G	47 - 348	1 - 302
104	104	52	HIS	HIS	ARG	ARG	H	H	47 - 348	1 - 302
105	105	53	HIS	HIS	GLU	GLU	G	G	47 - 347	1 - 301
106	106	53	HIS	HIS	GLU	GLU	I	I	47 - 347	1 - 301
107	107	54	HIS	HIS	ARG	ARG	G	G	47 - 348	1 - 302
108	108	54	HIS	HIS	ARG	ARG	J	J	47 - 348	1 - 302
109	109	55	HIS	HIS	ARG	ARG	G	G	47 - 348	1 - 302
110	110	55	HIS	HIS	ARG	ARG	K	K	47 - 348	1 - 302
111	111	56	HIS	HIS	ARG	ARG	G	G	47 - 348	1 - 302
112	112	56	HIS	HIS	ARG	ARG	L	L	47 - 348	1 - 302
113	113	57	HIS	HIS	LYS	LYS	H	H	47 - 346	1 - 300
114	114	57	HIS	HIS	LYS	LYS	I	I	47 - 346	1 - 300
115	115	58	HIS	HIS	GLU	GLU	H	H	47 - 350	1 - 304
116	116	58	HIS	HIS	GLU	GLU	J	J	47 - 350	1 - 304
117	117	59	HIS	HIS	ARG	ARG	H	H	47 - 348	1 - 302
118	118	59	HIS	HIS	ARG	ARG	K	K	47 - 348	1 - 302
119	119	60	HIS	HIS	GLU	GLU	H	H	47 - 354	1 - 308
120	120	60	HIS	HIS	GLU	GLU	L	L	47 - 354	1 - 308
121	121	61	HIS	HIS	GLU	GLU	I	I	47 - 347	1 - 301
122	122	61	HIS	HIS	GLU	GLU	J	J	47 - 347	1 - 301
123	123	62	HIS	HIS	GLU	GLU	I	I	47 - 347	1 - 301
124	124	62	HIS	HIS	GLU	GLU	K	K	47 - 347	1 - 301
125	125	63	HIS	HIS	GLU	GLU	I	I	47 - 347	1 - 301
126	126	63	HIS	HIS	GLU	GLU	L	L	47 - 347	1 - 301
127	127	64	HIS	HIS	ARG	ARG	J	J	47 - 348	1 - 302
128	128	64	HIS	HIS	ARG	ARG	K	K	47 - 348	1 - 302
129	129	65	HIS	HIS	GLU	GLU	J	J	47 - 350	1 - 304
130	130	65	HIS	HIS	GLU	GLU	L	L	47 - 350	1 - 304
131	131	66	HIS	HIS	GLU	GLU	K	K	47 - 347	1 - 301
132	132	66	HIS	HIS	GLU	GLU	L	L	47 - 347	1 - 301

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

#1: タンパク質	MAP kinase-activated protein kinase 2 / MAPK-activated protein kinase 2 / MAPKAP kinase 2 / MAPKAP-K2 / MAPKAPK-2 / MK-2 / MK2 分子量: 36715.457 Da / 分子数: 12 / 変異: S216G / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: MAPKAPK2 / 発現宿主: Escherichia coli (大腸菌) 参照: UniProt: P49137, non-specific serine/threonine protein kinase
#2: 化合物	ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / マロン酸分子量: 104.061 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C₃H₄O₄ / タイプ: SUBJECT OF INVESTIGATION
#3: 水	ChemComp-HOH / water 分子量: 18.015 Da / 分子数: 81 / 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

-
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: 3.02 Å³/Da / 溶媒含有率: 59.22 %
結晶化	温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法詳細: 1.1M Sodium malonate dibasic monohydrate, 0.1M HEPES pH7, 0.5% v/v Jeffamine ED2003

-
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: CLSI / ビームライン: 08ID-1 / 波長: 0.953727 Å
検出器	タイプ: DECTRIS EIGER X 9M / 検出器: PIXEL / 日付: 2023年2月10日
放射	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: 0.953727 Å / 相対比: 1
反射	解像度: 3.4→48.953 Å / Num. obs: 73900 / % possible obs: 100 % / 冗長度: 11.4 % / R_merge(I) obs: 0.148 / Net I/σ(I): 13
反射シェル	解像度: 3.4→3.47 Å / R_merge(I) obs: 1.03 / Num. unique obs: 5174

-
解析

ソフトウェア

名称	バージョン	分類
REFMAC	5.8.0267	精密化
XDS		データ削減
Aimless		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: 3.4→48.953 Å / Cor.coef. F_o:F_c: 0.927 / Cor.coef. F_o:F_c free: 0.903 / WR_factor R_free: 0.247 / WR_factor R_work: 0.198 / SU B: 27.939 / SU ML: 0.438 / Average fsc free: 0.8985 / Average fsc work: 0.9159 / 交差検証法: FREE R-VALUE / ESU R Free: 0.57 / 詳細: Hydrogens have been added in their riding positions

	R_factor	反射数	%反射
R_free	0.2631	3807	5.152 %
R_work	0.2136	70093	-
all	0.216	-	-
obs	-	73900	99.947 %

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: 110.328 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.281 Å²	-0 Å²	0 Å²
2-	-	-3.018 Å²	-0 Å²
3-	-	-	-0.263 Å²

精密化ステップ

サイクル: LAST / 解像度: 3.4→48.953 Å

	タンパク質	核酸	リガンド	溶媒	全体
原子数	27342	0	21	81	27444

拘束条件

Refine-ID	タイプ	Dev ideal	Dev ideal target	数
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	27924
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	27162
X-RAY DIFFRACTION	r_angle_refined_deg	1.348	1.651	37597
X-RAY DIFFRACTION	r_angle_other_deg	1.242	1.582	62729
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.876	5	3288
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	22.118	21.954	1484
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.434	15	5346
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.789	15	201
X-RAY DIFFRACTION	r_chiral_restr	0.063	0.2	3613
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	30466
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	6276
X-RAY DIFFRACTION	r_nbd_refined	0.195	0.2	5125
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.186	0.2	24864
X-RAY DIFFRACTION	r_nbtor_refined	0.16	0.2	13838
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.074	0.2	13864
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.115	0.2	346
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.085	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.292	0.2	127
X-RAY DIFFRACTION	r_nbd_other	0.256	0.2	510
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.19	0.2	31
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.032	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	8.469	11.262	13317
X-RAY DIFFRACTION	r_mcbond_other	8.466	11.262	13316
X-RAY DIFFRACTION	r_mcangle_it	13.044	16.887	16550
X-RAY DIFFRACTION	r_mcangle_other	13.044	16.887	16551
X-RAY DIFFRACTION	r_scbond_it	8.858	12.135	14607
X-RAY DIFFRACTION	r_scbond_other	8.858	12.135	14606
X-RAY DIFFRACTION	r_scangle_it	13.713	17.897	21047
X-RAY DIFFRACTION	r_scangle_other	13.713	17.897	21048
X-RAY DIFFRACTION	r_lrange_it	21.146	213.572	112684
X-RAY DIFFRACTION	r_lrange_other	21.147	213.58	112670
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.107	0.05	9026
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.104	0.05	8998
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.11	0.05	8776
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.116	0.05	8744
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.118	0.05	8560
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.108	0.05	8503
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.117	0.05	8489
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.105	0.05	8453
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.116	0.05	8543
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.108	0.05	8434
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.117	0.05	8345
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.101	0.05	9113
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.105	0.05	9097
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.12	0.05	8832
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.116	0.05	8712
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.114	0.05	8592
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.111	0.05	8543
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.1	0.05	8576
X-RAY DIFFRACTION	r_ncsr_local_group_19	0.12	0.05	8596
X-RAY DIFFRACTION	r_ncsr_local_group_20	0.117	0.05	8457
X-RAY DIFFRACTION	r_ncsr_local_group_21	0.121	0.05	8418
X-RAY DIFFRACTION	r_ncsr_local_group_22	0.105	0.05	8971
X-RAY DIFFRACTION	r_ncsr_local_group_23	0.117	0.05	8794
X-RAY DIFFRACTION	r_ncsr_local_group_24	0.115	0.05	8713
X-RAY DIFFRACTION	r_ncsr_local_group_25	0.113	0.05	8567
X-RAY DIFFRACTION	r_ncsr_local_group_26	0.107	0.05	8580
X-RAY DIFFRACTION	r_ncsr_local_group_27	0.1	0.05	8526
X-RAY DIFFRACTION	r_ncsr_local_group_28	0.119	0.05	8617
X-RAY DIFFRACTION	r_ncsr_local_group_29	0.112	0.05	8462
X-RAY DIFFRACTION	r_ncsr_local_group_30	0.113	0.05	8454
X-RAY DIFFRACTION	r_ncsr_local_group_31	0.117	0.05	8673
X-RAY DIFFRACTION	r_ncsr_local_group_32	0.12	0.05	8649
X-RAY DIFFRACTION	r_ncsr_local_group_33	0.113	0.05	8548
X-RAY DIFFRACTION	r_ncsr_local_group_34	0.108	0.05	8431
X-RAY DIFFRACTION	r_ncsr_local_group_35	0.1	0.05	8464
X-RAY DIFFRACTION	r_ncsr_local_group_36	0.118	0.05	8586
X-RAY DIFFRACTION	r_ncsr_local_group_37	0.11	0.05	8471
X-RAY DIFFRACTION	r_ncsr_local_group_38	0.118	0.05	8333
X-RAY DIFFRACTION	r_ncsr_local_group_39	0.119	0.05	8794
X-RAY DIFFRACTION	r_ncsr_local_group_40	0.117	0.05	8564
X-RAY DIFFRACTION	r_ncsr_local_group_41	0.113	0.05	8665
X-RAY DIFFRACTION	r_ncsr_local_group_42	0.104	0.05	8512
X-RAY DIFFRACTION	r_ncsr_local_group_43	0.116	0.05	8439
X-RAY DIFFRACTION	r_ncsr_local_group_44	0.118	0.05	8435
X-RAY DIFFRACTION	r_ncsr_local_group_45	0.119	0.05	8447
X-RAY DIFFRACTION	r_ncsr_local_group_46	0.112	0.05	8549
X-RAY DIFFRACTION	r_ncsr_local_group_47	0.112	0.05	8603
X-RAY DIFFRACTION	r_ncsr_local_group_48	0.1	0.05	8511
X-RAY DIFFRACTION	r_ncsr_local_group_49	0.108	0.05	8519
X-RAY DIFFRACTION	r_ncsr_local_group_50	0.113	0.05	8373
X-RAY DIFFRACTION	r_ncsr_local_group_51	0.118	0.05	8453
X-RAY DIFFRACTION	r_ncsr_local_group_52	0.115	0.05	8362
X-RAY DIFFRACTION	r_ncsr_local_group_53	0.106	0.05	8345
X-RAY DIFFRACTION	r_ncsr_local_group_54	0.119	0.05	8431
X-RAY DIFFRACTION	r_ncsr_local_group_55	0.111	0.05	8457
X-RAY DIFFRACTION	r_ncsr_local_group_56	0.119	0.05	8353
X-RAY DIFFRACTION	r_ncsr_local_group_57	0.107	0.05	8316
X-RAY DIFFRACTION	r_ncsr_local_group_58	0.113	0.05	8221
X-RAY DIFFRACTION	r_ncsr_local_group_59	0.124	0.05	8121
X-RAY DIFFRACTION	r_ncsr_local_group_60	0.12	0.05	8280
X-RAY DIFFRACTION	r_ncsr_local_group_61	0.103	0.05	8300
X-RAY DIFFRACTION	r_ncsr_local_group_62	0.105	0.05	8179
X-RAY DIFFRACTION	r_ncsr_local_group_63	0.109	0.05	8124
X-RAY DIFFRACTION	r_ncsr_local_group_64	0.112	0.05	8317
X-RAY DIFFRACTION	r_ncsr_local_group_65	0.115	0.05	8441
X-RAY DIFFRACTION	r_ncsr_local_group_66	0.121	0.05	8260

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	0.10705	0.05009
1	2	B	X-RAY DIFFRACTION	Local ncs	0.10705	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.10385	0.05009
2	4	C	X-RAY DIFFRACTION	Local ncs	0.10385	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.11015	0.05009
3	6	D	X-RAY DIFFRACTION	Local ncs	0.11015	0.05009
4	7	A	X-RAY DIFFRACTION	Local ncs	0.11647	0.05009
4	8	E	X-RAY DIFFRACTION	Local ncs	0.11647	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.11764	0.05009
5	10	F	X-RAY DIFFRACTION	Local ncs	0.11764	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.10756	0.05009
6	12	G	X-RAY DIFFRACTION	Local ncs	0.10756	0.05009
7	13	A	X-RAY DIFFRACTION	Local ncs	0.11744	0.05009
7	14	H	X-RAY DIFFRACTION	Local ncs	0.11744	0.05009
8	15	A	X-RAY DIFFRACTION	Local ncs	0.10464	0.05009
8	16	I	X-RAY DIFFRACTION	Local ncs	0.10464	0.05009
9	17	A	X-RAY DIFFRACTION	Local ncs	0.11556	0.05009
9	18	J	X-RAY DIFFRACTION	Local ncs	0.11556	0.05009
10	19	A	X-RAY DIFFRACTION	Local ncs	0.10785	0.05009
10	20	K	X-RAY DIFFRACTION	Local ncs	0.10785	0.05009
11	21	A	X-RAY DIFFRACTION	Local ncs	0.11741	0.05009
11	22	L	X-RAY DIFFRACTION	Local ncs	0.11741	0.05009
12	23	B	X-RAY DIFFRACTION	Local ncs	0.10062	0.05009
12	24	C	X-RAY DIFFRACTION	Local ncs	0.10062	0.05009
13	25	B	X-RAY DIFFRACTION	Local ncs	0.10509	0.05009
13	26	D	X-RAY DIFFRACTION	Local ncs	0.10509	0.05009
14	27	B	X-RAY DIFFRACTION	Local ncs	0.1196	0.05009
14	28	E	X-RAY DIFFRACTION	Local ncs	0.1196	0.05009
15	29	B	X-RAY DIFFRACTION	Local ncs	0.11583	0.05009
15	30	F	X-RAY DIFFRACTION	Local ncs	0.11583	0.05009
16	31	B	X-RAY DIFFRACTION	Local ncs	0.1143	0.05009
16	32	G	X-RAY DIFFRACTION	Local ncs	0.1143	0.05009
17	33	B	X-RAY DIFFRACTION	Local ncs	0.11125	0.05009
17	34	H	X-RAY DIFFRACTION	Local ncs	0.11125	0.05009
18	35	B	X-RAY DIFFRACTION	Local ncs	0.10032	0.0501
18	36	I	X-RAY DIFFRACTION	Local ncs	0.10032	0.0501
19	37	B	X-RAY DIFFRACTION	Local ncs	0.12032	0.05009
19	38	J	X-RAY DIFFRACTION	Local ncs	0.12032	0.05009
20	39	B	X-RAY DIFFRACTION	Local ncs	0.11725	0.05009
20	40	K	X-RAY DIFFRACTION	Local ncs	0.11725	0.05009
21	41	B	X-RAY DIFFRACTION	Local ncs	0.12118	0.05009
21	42	L	X-RAY DIFFRACTION	Local ncs	0.12118	0.05009
22	43	C	X-RAY DIFFRACTION	Local ncs	0.10548	0.05009
22	44	D	X-RAY DIFFRACTION	Local ncs	0.10548	0.05009
23	45	C	X-RAY DIFFRACTION	Local ncs	0.11705	0.05009
23	46	E	X-RAY DIFFRACTION	Local ncs	0.11705	0.05009
24	47	C	X-RAY DIFFRACTION	Local ncs	0.11456	0.05009
24	48	F	X-RAY DIFFRACTION	Local ncs	0.11456	0.05009
25	49	C	X-RAY DIFFRACTION	Local ncs	0.1129	0.05009
25	50	G	X-RAY DIFFRACTION	Local ncs	0.1129	0.05009
26	51	C	X-RAY DIFFRACTION	Local ncs	0.10681	0.05009
26	52	H	X-RAY DIFFRACTION	Local ncs	0.10681	0.05009
27	53	C	X-RAY DIFFRACTION	Local ncs	0.10033	0.05009
27	54	I	X-RAY DIFFRACTION	Local ncs	0.10033	0.05009
28	55	C	X-RAY DIFFRACTION	Local ncs	0.11889	0.05009
28	56	J	X-RAY DIFFRACTION	Local ncs	0.11889	0.05009
29	57	C	X-RAY DIFFRACTION	Local ncs	0.11236	0.05009
29	58	K	X-RAY DIFFRACTION	Local ncs	0.11236	0.05009
30	59	C	X-RAY DIFFRACTION	Local ncs	0.11333	0.05009
30	60	L	X-RAY DIFFRACTION	Local ncs	0.11333	0.05009
31	61	D	X-RAY DIFFRACTION	Local ncs	0.11745	0.05009
31	62	E	X-RAY DIFFRACTION	Local ncs	0.11745	0.05009
32	63	D	X-RAY DIFFRACTION	Local ncs	0.12028	0.05009
32	64	F	X-RAY DIFFRACTION	Local ncs	0.12028	0.05009
33	65	D	X-RAY DIFFRACTION	Local ncs	0.1129	0.05009
33	66	G	X-RAY DIFFRACTION	Local ncs	0.1129	0.05009
34	67	D	X-RAY DIFFRACTION	Local ncs	0.10791	0.05009
34	68	H	X-RAY DIFFRACTION	Local ncs	0.10791	0.05009
35	69	D	X-RAY DIFFRACTION	Local ncs	0.10047	0.05009
35	70	I	X-RAY DIFFRACTION	Local ncs	0.10047	0.05009
36	71	D	X-RAY DIFFRACTION	Local ncs	0.11807	0.05009
36	72	J	X-RAY DIFFRACTION	Local ncs	0.11807	0.05009
37	73	D	X-RAY DIFFRACTION	Local ncs	0.10974	0.05009
37	74	K	X-RAY DIFFRACTION	Local ncs	0.10974	0.05009
38	75	D	X-RAY DIFFRACTION	Local ncs	0.1183	0.05009
38	76	L	X-RAY DIFFRACTION	Local ncs	0.1183	0.05009
39	77	E	X-RAY DIFFRACTION	Local ncs	0.11909	0.05009
39	78	F	X-RAY DIFFRACTION	Local ncs	0.11909	0.05009
40	79	E	X-RAY DIFFRACTION	Local ncs	0.11706	0.05009
40	80	G	X-RAY DIFFRACTION	Local ncs	0.11706	0.05009
41	81	E	X-RAY DIFFRACTION	Local ncs	0.11329	0.05009
41	82	H	X-RAY DIFFRACTION	Local ncs	0.11329	0.05009
42	83	E	X-RAY DIFFRACTION	Local ncs	0.10395	0.05009
42	84	I	X-RAY DIFFRACTION	Local ncs	0.10395	0.05009
43	85	E	X-RAY DIFFRACTION	Local ncs	0.11621	0.05009
43	86	J	X-RAY DIFFRACTION	Local ncs	0.11621	0.05009
44	87	E	X-RAY DIFFRACTION	Local ncs	0.118	0.05009
44	88	K	X-RAY DIFFRACTION	Local ncs	0.118	0.05009
45	89	E	X-RAY DIFFRACTION	Local ncs	0.11925	0.05009
45	90	L	X-RAY DIFFRACTION	Local ncs	0.11925	0.05009
46	91	F	X-RAY DIFFRACTION	Local ncs	0.11157	0.05009
46	92	G	X-RAY DIFFRACTION	Local ncs	0.11157	0.05009
47	93	F	X-RAY DIFFRACTION	Local ncs	0.11194	0.05009
47	94	H	X-RAY DIFFRACTION	Local ncs	0.11194	0.05009
48	95	F	X-RAY DIFFRACTION	Local ncs	0.09968	0.05009
48	96	I	X-RAY DIFFRACTION	Local ncs	0.09968	0.05009
49	97	F	X-RAY DIFFRACTION	Local ncs	0.10803	0.05009
49	98	J	X-RAY DIFFRACTION	Local ncs	0.10803	0.05009
50	99	F	X-RAY DIFFRACTION	Local ncs	0.11338	0.05009
50	100	K	X-RAY DIFFRACTION	Local ncs	0.11338	0.05009
51	101	F	X-RAY DIFFRACTION	Local ncs	0.11786	0.05009
51	102	L	X-RAY DIFFRACTION	Local ncs	0.11786	0.05009
52	103	G	X-RAY DIFFRACTION	Local ncs	0.11522	0.05009
52	104	H	X-RAY DIFFRACTION	Local ncs	0.11522	0.05009
53	105	G	X-RAY DIFFRACTION	Local ncs	0.1061	0.05009
53	106	I	X-RAY DIFFRACTION	Local ncs	0.1061	0.05009
54	107	G	X-RAY DIFFRACTION	Local ncs	0.11913	0.05009
54	108	J	X-RAY DIFFRACTION	Local ncs	0.11913	0.05009
55	109	G	X-RAY DIFFRACTION	Local ncs	0.11143	0.05009
55	110	K	X-RAY DIFFRACTION	Local ncs	0.11143	0.05009
56	111	G	X-RAY DIFFRACTION	Local ncs	0.11921	0.05009
56	112	L	X-RAY DIFFRACTION	Local ncs	0.11921	0.05009
57	113	H	X-RAY DIFFRACTION	Local ncs	0.107	0.05009
57	114	I	X-RAY DIFFRACTION	Local ncs	0.107	0.05009
58	115	H	X-RAY DIFFRACTION	Local ncs	0.1133	0.05009
58	116	J	X-RAY DIFFRACTION	Local ncs	0.1133	0.05009
59	117	H	X-RAY DIFFRACTION	Local ncs	0.12364	0.05009
59	118	K	X-RAY DIFFRACTION	Local ncs	0.12364	0.05009
60	119	H	X-RAY DIFFRACTION	Local ncs	0.1203	0.05009
60	120	L	X-RAY DIFFRACTION	Local ncs	0.1203	0.05009
61	121	I	X-RAY DIFFRACTION	Local ncs	0.10321	0.05009
61	122	J	X-RAY DIFFRACTION	Local ncs	0.10321	0.05009
62	123	I	X-RAY DIFFRACTION	Local ncs	0.10489	0.05009
62	124	K	X-RAY DIFFRACTION	Local ncs	0.10489	0.05009
63	125	I	X-RAY DIFFRACTION	Local ncs	0.10936	0.05009
63	126	L	X-RAY DIFFRACTION	Local ncs	0.10936	0.05009
64	127	J	X-RAY DIFFRACTION	Local ncs	0.11244	0.05009
64	128	K	X-RAY DIFFRACTION	Local ncs	0.11244	0.05009
65	129	J	X-RAY DIFFRACTION	Local ncs	0.1145	0.05009
65	130	L	X-RAY DIFFRACTION	Local ncs	0.1145	0.05009
66	131	K	X-RAY DIFFRACTION	Local ncs	0.12076	0.05009
66	132	L	X-RAY DIFFRACTION	Local ncs	0.12076	0.05009

LS精密化シェル

解像度 (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.4-3.488	0.32	259	0.282	5174	X-RAY DIFFRACTION	100
3.488-3.584	0.325	247	0.263	5007	X-RAY DIFFRACTION	100
3.584-3.688	0.302	268	0.247	4840	X-RAY DIFFRACTION	100
3.688-3.801	0.244	256	0.226	4740	X-RAY DIFFRACTION	100
3.801-3.926	0.266	261	0.209	4535	X-RAY DIFFRACTION	100
3.926-4.063	0.286	220	0.201	4456	X-RAY DIFFRACTION	100
4.063-4.217	0.234	240	0.195	4291	X-RAY DIFFRACTION	100
4.217-4.389	0.227	232	0.177	4123	X-RAY DIFFRACTION	100
4.389-4.583	0.226	233	0.182	3941	X-RAY DIFFRACTION	100
4.583-4.807	0.227	207	0.176	3814	X-RAY DIFFRACTION	99.9751
4.807-5.067	0.225	178	0.183	3630	X-RAY DIFFRACTION	100
5.067-5.373	0.292	172	0.216	3429	X-RAY DIFFRACTION	100
5.373-5.744	0.331	193	0.236	3218	X-RAY DIFFRACTION	100
5.744-6.203	0.287	161	0.232	3023	X-RAY DIFFRACTION	99.9686
6.203-6.794	0.279	143	0.207	2791	X-RAY DIFFRACTION	100
6.794-7.593	0.319	155	0.219	2534	X-RAY DIFFRACTION	100
7.593-8.764	0.25	141	0.199	2243	X-RAY DIFFRACTION	100
8.764-10.722	0.216	101	0.196	1934	X-RAY DIFFRACTION	100
10.722-15.117	0.237	95	0.214	1499	X-RAY DIFFRACTION	100
15.117-48.953	0.364	45	0.382	871	X-RAY DIFFRACTION	96.2185

-
お知らせ

-
2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

-
2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

+
2020年3月5日: 新型コロナウイルスの構造データ

+
2019年1月31日: EMDBのIDの桁数の変更

+
2017年7月12日: PDB大規模アップデート

すべてのお知らせ

-
万見 (Yorodumi)

幾万の構造データを、幾万の視点から

万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

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万見について

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お知らせ

-
2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

-
2020年8月12日: 新型コロナ情報

+
2020年3月5日: 新型コロナウイルスの構造データ

+
2019年1月31日: EMDBのIDの桁数の変更

+
2017年7月12日: PDB大規模アップデート

-
万見 (Yorodumi)

-ムービー

-構造ビューア

+ビューアのログ

-このページ

-このウェブサイト

-オプション

+データを開く

-基本情報

-構造の表示

-ダウンロードとリンク

-ダウンロード

-検証レポート

-関連構造データ

-リンク

-集合体

-要素

-実験情報

-実験

-試料調製

-データ収集

-解析

+万見について

-お知らせ

-2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

-2020年8月12日: 新型コロナ情報

+2020年3月5日: 新型コロナウイルスの構造データ

+2019年1月31日: EMDBのIDの桁数の変更

+2017年7月12日: PDB大規模アップデート

-万見 (Yorodumi)

-
ムービー

-
構造ビューア

+
ビューアのログ

-
このページ

-
このウェブサイト

-
オプション

+
データを開く

-
基本情報

-
構造の表示

-
ダウンロードとリンク

-
ダウンロード

-
検証レポート

-
関連構造データ

-
リンク

-
集合体

-
要素

-
実験情報

-
実験

-
試料調製

-
データ収集

-
解析

+
万見について

-
お知らせ

-
2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

-
2020年8月12日: 新型コロナ情報

+
2020年3月5日: 新型コロナウイルスの構造データ

+
2019年1月31日: EMDBのIDの桁数の変更

+
2017年7月12日: PDB大規模アップデート

-
万見 (Yorodumi)