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万見

- PDB-8iq5: Crystal structure of trimeric K2-2 TSP -

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データを開く

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基本情報

登録情報

データベース: PDB / ID: 8iq5

タイトル

Crystal structure of trimeric K2-2 TSP

要素

K2-2 TSP

キーワード

HYDROLASE / bacteriophage / tailspike protein / Klebsiella pneumoniae K2

生物種

Klebsiella phage VLC6 (ファージ)

手法

X線回折 /

シンクロトロン /

分子置換 / 解像度: 1.38 Å

データ登録者

Ye, T.J. / Huang, K.F. / Ko, T.P.

資金援助

台湾, 1件

引用

ジャーナル: Mbio / 年: 2024
タイトル: Klebsiella pneumoniae K2 capsular polysaccharide degradation by a bacteriophage depolymerase does not require trimer formation.
著者: Ye, T.J. / Fung, K.M. / Lee, I.M. / Ko, T.P. / Lin, C.Y. / Wong, C.L. / Tu, I.F. / Huang, T.Y. / Yang, F.L. / Chang, Y.P. / Wang, J.T. / Lin, T.L. / Huang, K.F. / Wu, S.H.

履歴

登録	2023年3月15日	登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.0	2024年2月21日	Provider: repository / タイプ: Initial release
改定 1.1	2024年3月27日	Group: Database references / カテゴリ: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
改定 1.2	2024年4月3日	Group: Database references / カテゴリ: citation / citation_author Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name

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構造の表示

構造ビューア	分子: MolmilJmol/JSmol

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ダウンロードとリンク

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ダウンロード

PDBx/mmCIF形式	8iq5.cif.gz	1.6 MB	表示	PDBx/mmCIF形式
PDB形式	pdb8iq5.ent.gz	1.1 MB	表示	PDB形式
PDBx/mmJSON形式	8iq5.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

文書・要旨	8iq5_validation.pdf.gz	9 MB	表示	wwPDB検証レポート
文書・詳細版	8iq5_full_validation.pdf.gz	9 MB	表示
XML形式データ	8iq5_validation.xml.gz	168.9 KB	表示
CIF形式データ	8iq5_validation.cif.gz	266.3 KB	表示
アーカイブディレクトリ	https://data.pdbj.org/pub/pdb/validation_reports/iq/8iq5 ftp://data.pdbj.org/pub/pdb/validation_reports/iq/8iq5	HTTPS FTP

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関連構造データ

関連構造データ	8iq9C 8iqeSC S: 精密化の開始モデル C: 同じ文献を引用 (文献)

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リンク

PDBのページ	PDBj / wwPDB / NCBI

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集合体

登録構造単位

A: K2-2 TSP

B: K2-2 TSP

C: K2-2 TSP

D: K2-2 TSP

E: K2-2 TSP

F: K2-2 TSP

ヘテロ分子

392 kDa, 6 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)

A: K2-2 TSP

B: K2-2 TSP

C: K2-2 TSP

ヘテロ分子

登録者が定義した集合体
根拠: gel filtration
196 kDa, 3 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)

D: K2-2 TSP

E: K2-2 TSP

F: K2-2 TSP

ヘテロ分子

登録者が定義した集合体
196 kDa, 3 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)	102.815, 82.838, 196.140
Angle α, β, γ (deg.)	90.000, 98.371, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

非結晶学的対称性 (NCS)

NCSドメイン:

ID	Ens-ID	詳細
d_1	ens_1	(chain "A" and (resid 15 through 21 or resid 23...
d_2	ens_1	(chain "B" and (resid 15 through 21 or resid 23...
d_3	ens_1	(chain "C" and (resid 15 through 21 or resid 23...
d_4	ens_1	(chain "D" and (resid 15 through 21 or resid 23...
d_5	ens_1	(chain "E" and (resid 15 through 21 or resid 23...
d_6	ens_1	(chain "F" and (resid 15 through 21 or resid 23...

NCSドメイン領域:

Ens-ID: ens_1

Dom-ID	Component-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
d_1	1	GLU	GLU	SER	SER	A	A	15 - 21	46 - 52
d_1	2	ALA	ALA	ALA	ALA	A	A	23	54
d_1	3	LEU	LEU	LEU	LEU	A	A	25	56
d_1	4	ALA	ALA	SER	SER	A	A	27 - 31	58 - 62
d_1	5	ASP	ASP	GLY	GLY	A	A	33 - 34	64 - 65
d_1	6	LEU	LEU	LEU	LEU	A	A	36	67
d_1	7	LEU	LEU	VAL	VAL	A	A	39 - 55	70 - 86
d_1	8	SER	SER	ARG	ARG	A	A	59 - 76	90 - 107
d_1	9	LEU	LEU	VAL	VAL	A	A	78 - 80	109 - 111
d_1	10	PRO	PRO	ALA	ALA	A	A	84 - 87	115 - 118
d_1	11	MET	MET	ALA	ALA	A	A	89 - 123	120 - 154
d_1	12	TYR	TYR	PHE	PHE	A	A	125 - 127	156 - 158
d_1	13	GLY	GLY	ILE	ILE	A	A	129 - 133	160 - 164
d_1	14	VAL	VAL	SER	SER	A	A	135 - 138	166 - 169
d_1	15	ALA	ALA	ILE	ILE	A	A	140 - 142	171 - 173
d_1	16	GLY	GLY	TYR	TYR	A	A	144 - 145	175 - 176
d_1	17	GLY	GLY	VAL	VAL	A	A	147 - 149	178 - 180
d_1	18	ILE	ILE	GLY	GLY	A	A	151 - 158	182 - 189
d_1	19	VAL	VAL	TYR	TYR	A	A	161 - 168	192 - 199
d_1	20	TYR	TYR	LEU	LEU	A	A	170 - 183	201 - 214
d_1	21	GLY	GLY	ALA	ALA	A	A	185 - 191	216 - 222
d_1	22	THR	THR	THR	THR	A	A	193	224
d_1	23	GLY	GLY	GLY	GLY	A	A	195 - 202	226 - 233
d_1	24	THR	THR	VAL	VAL	A	A	205 - 206	236 - 237
d_1	25	LYS	LYS	ARG	ARG	A	A	210 - 231	241 - 262
d_1	26	GLY	GLY	TYR	TYR	A	A	233 - 242	264 - 273
d_1	27	VAL	VAL	LEU	LEU	A	A	244 - 262	275 - 293
d_1	28	SER	SER	LEU	LEU	A	A	265 - 269	296 - 300
d_1	29	PHE	PHE	CYS	CYS	A	A	271 - 317	302 - 348
d_1	30	GLY	GLY	SER	SER	A	A	319 - 367	350 - 398
d_1	31	ASP	ASP	GLU	GLU	A	A	369 - 388	400 - 419
d_1	32	GLU	GLU	ASP	ASP	A	A	390 - 444	421 - 475
d_1	33	GLY	GLY	THR	THR	A	A	446 - 449	477 - 480
d_1	34	SER	SER	VAL	VAL	A	A	451 - 453	482 - 484
d_1	35	TYR	TYR	MET	MET	A	A	455 - 468	486 - 499
d_1	36	VAL	VAL	VAL	VAL	A	A	470 - 473	501 - 504
d_1	37	VAL	VAL	GLN	GLN	A	A	475 - 481	506 - 512
d_1	38	GLN	GLN	ALA	ALA	A	A	483 - 484	514 - 515
d_1	39	THR	THR	GLY	GLY	A	A	486 - 489	517 - 520
d_1	40	PHE	PHE	SER	SER	A	A	491 - 494	522 - 525
d_1	41	MET	MET	MET	MET	A	A	496	527
d_1	42	ASN	ASN	GLY	GLY	A	A	498 - 507	529 - 538
d_1	43	VAL	VAL	VAL	VAL	A	A	509	540
d_1	44	GLY	GLY	PHE	PHE	A	A	512 - 513	543 - 544
d_1	45	ASP	ASP	LEU	LEU	A	A	515 - 521	546 - 552
d_1	46	VAL	VAL	VAL	VAL	A	A	525	556
d_1	47	ALA	ALA	ASN	ASN	A	A	527 - 528	558 - 559
d_1	48	GLY	GLY	THR	THR	A	A	530 - 532	561 - 563
d_1	49	GLY	GLY	ASN	ASN	A	A	534 - 541	565 - 572
d_1	50	LEU	LEU	PRO	PRO	A	A	543 - 548	574 - 579
d_1	51	GLY	GLY	ILE	ILE	A	A	550 - 558	581 - 589
d_1	52	THR	THR	LYS	LYS	A	A	560 - 577	591 - 608
d_1	53	GOL	GOL	GOL	GOL	A	H	601
d_2	1	GLU	GLU	SER	SER	B	B	15 - 21	46 - 52
d_2	2	ALA	ALA	ALA	ALA	B	B	23	54
d_2	3	LEU	LEU	LEU	LEU	B	B	25	56
d_2	4	ALA	ALA	SER	SER	B	B	27 - 31	58 - 62
d_2	5	ASP	ASP	GLY	GLY	B	B	33 - 34	64 - 65
d_2	6	LEU	LEU	LEU	LEU	B	B	36	67
d_2	7	LEU	LEU	VAL	VAL	B	B	39 - 55	70 - 86
d_2	8	SER	SER	ARG	ARG	B	B	59 - 76	90 - 107
d_2	9	LEU	LEU	VAL	VAL	B	B	78 - 80	109 - 111
d_2	10	PRO	PRO	ALA	ALA	B	B	84 - 87	115 - 118
d_2	11	MET	MET	ALA	ALA	B	B	89 - 123	120 - 154
d_2	12	TYR	TYR	PHE	PHE	B	B	125 - 127	156 - 158
d_2	13	GLY	GLY	ILE	ILE	B	B	129 - 133	160 - 164
d_2	14	VAL	VAL	SER	SER	B	B	135 - 138	166 - 169
d_2	15	ALA	ALA	ILE	ILE	B	B	140 - 142	171 - 173
d_2	16	GLY	GLY	TYR	TYR	B	B	144 - 145	175 - 176
d_2	17	GLY	GLY	VAL	VAL	B	B	147 - 149	178 - 180
d_2	18	ILE	ILE	GLY	GLY	B	B	151 - 158	182 - 189
d_2	19	VAL	VAL	TYR	TYR	B	B	161 - 168	192 - 199
d_2	20	TYR	TYR	LEU	LEU	B	B	170 - 183	201 - 214
d_2	21	GLY	GLY	ALA	ALA	B	B	185 - 191	216 - 222
d_2	22	THR	THR	THR	THR	B	B	193	224
d_2	23	GLY	GLY	GLY	GLY	B	B	195 - 202	226 - 233
d_2	24	THR	THR	VAL	VAL	B	B	205 - 206	236 - 237
d_2	25	LYS	LYS	ARG	ARG	B	B	210 - 231	241 - 262
d_2	26	GLY	GLY	TYR	TYR	B	B	233 - 242	264 - 273
d_2	27	VAL	VAL	LEU	LEU	B	B	244 - 262	275 - 293
d_2	28	SER	SER	LEU	LEU	B	B	265 - 269	296 - 300
d_2	29	PHE	PHE	CYS	CYS	B	B	271 - 317	302 - 348
d_2	30	GLY	GLY	SER	SER	B	B	319 - 367	350 - 398
d_2	31	ASP	ASP	GLU	GLU	B	B	369 - 388	400 - 419
d_2	32	GLU	GLU	ASP	ASP	B	B	390 - 444	421 - 475
d_2	33	GLY	GLY	THR	THR	B	B	446 - 449	477 - 480
d_2	34	SER	SER	VAL	VAL	B	B	451 - 453	482 - 484
d_2	35	TYR	TYR	MET	MET	B	B	455 - 468	486 - 499
d_2	36	VAL	VAL	VAL	VAL	B	B	470 - 473	501 - 504
d_2	37	VAL	VAL	GLN	GLN	B	B	475 - 481	506 - 512
d_2	38	GLN	GLN	ALA	ALA	B	B	483 - 484	514 - 515
d_2	39	THR	THR	GLY	GLY	B	B	486 - 489	517 - 520
d_2	40	PHE	PHE	SER	SER	B	B	491 - 494	522 - 525
d_2	41	MET	MET	MET	MET	B	B	496	527
d_2	42	ASN	ASN	GLY	GLY	B	B	498 - 507	529 - 538
d_2	43	VAL	VAL	VAL	VAL	B	B	509	540
d_2	44	GLY	GLY	PHE	PHE	B	B	512 - 513	543 - 544
d_2	45	ASP	ASP	LEU	LEU	B	B	515 - 521	546 - 552
d_2	46	VAL	VAL	VAL	VAL	B	B	525	556
d_2	47	ALA	ALA	ASN	ASN	B	B	527 - 528	558 - 559
d_2	48	GLY	GLY	THR	THR	B	B	530 - 532	561 - 563
d_2	49	GLY	GLY	ASN	ASN	B	B	534 - 541	565 - 572
d_2	50	LEU	LEU	PRO	PRO	B	B	543 - 548	574 - 579
d_2	51	GLY	GLY	ILE	ILE	B	B	550 - 558	581 - 589
d_2	52	THR	THR	LYS	LYS	B	B	560 - 577	591 - 608
d_2	53	GOL	GOL	GOL	GOL	B	L	602
d_3	1	GLU	GLU	SER	SER	C	C	15 - 21	46 - 52
d_3	2	ALA	ALA	ALA	ALA	C	C	23	54
d_3	3	LEU	LEU	LEU	LEU	C	C	25	56
d_3	4	ALA	ALA	SER	SER	C	C	27 - 31	58 - 62
d_3	5	ASP	ASP	GLY	GLY	C	C	33 - 34	64 - 65
d_3	6	LEU	LEU	LEU	LEU	C	C	36	67
d_3	7	LEU	LEU	VAL	VAL	C	C	39 - 55	70 - 86
d_3	8	SER	SER	ARG	ARG	C	C	59 - 76	90 - 107
d_3	9	LEU	LEU	VAL	VAL	C	C	78 - 80	109 - 111
d_3	10	PRO	PRO	ALA	ALA	C	C	84 - 87	115 - 118
d_3	11	MET	MET	ALA	ALA	C	C	89 - 123	120 - 154
d_3	12	TYR	TYR	PHE	PHE	C	C	125 - 127	156 - 158
d_3	13	GLY	GLY	ILE	ILE	C	C	129 - 133	160 - 164
d_3	14	VAL	VAL	SER	SER	C	C	135 - 138	166 - 169
d_3	15	ALA	ALA	ILE	ILE	C	C	140 - 142	171 - 173
d_3	16	GLY	GLY	TYR	TYR	C	C	144 - 145	175 - 176
d_3	17	GLY	GLY	VAL	VAL	C	C	147 - 149	178 - 180
d_3	18	ILE	ILE	GLY	GLY	C	C	151 - 158	182 - 189
d_3	19	VAL	VAL	TYR	TYR	C	C	161 - 168	192 - 199
d_3	20	TYR	TYR	LEU	LEU	C	C	170 - 183	201 - 214
d_3	21	GLY	GLY	ALA	ALA	C	C	185 - 191	216 - 222
d_3	22	THR	THR	THR	THR	C	C	193	224
d_3	23	GLY	GLY	GLY	GLY	C	C	195 - 202	226 - 233
d_3	24	THR	THR	VAL	VAL	C	C	205 - 206	236 - 237
d_3	25	LYS	LYS	ARG	ARG	C	C	210 - 231	241 - 262
d_3	26	GLY	GLY	TYR	TYR	C	C	233 - 242	264 - 273
d_3	27	VAL	VAL	LEU	LEU	C	C	244 - 262	275 - 293
d_3	28	SER	SER	LEU	LEU	C	C	265 - 269	296 - 300
d_3	29	PHE	PHE	CYS	CYS	C	C	271 - 317	302 - 348
d_3	30	GLY	GLY	SER	SER	C	C	319 - 367	350 - 398
d_3	31	ASP	ASP	GLU	GLU	C	C	369 - 388	400 - 419
d_3	32	GLU	GLU	ASP	ASP	C	C	390 - 444	421 - 475
d_3	33	GLY	GLY	THR	THR	C	C	446 - 449	477 - 480
d_3	34	SER	SER	VAL	VAL	C	C	451 - 453	482 - 484
d_3	35	TYR	TYR	MET	MET	C	C	455 - 468	486 - 499
d_3	36	VAL	VAL	VAL	VAL	C	C	470 - 473	501 - 504
d_3	37	VAL	VAL	GLN	GLN	C	C	475 - 481	506 - 512
d_3	38	GLN	GLN	ALA	ALA	C	C	483 - 484	514 - 515
d_3	39	THR	THR	GLY	GLY	C	C	486 - 489	517 - 520
d_3	40	PHE	PHE	SER	SER	C	C	491 - 494	522 - 525
d_3	41	MET	MET	MET	MET	C	C	496	527
d_3	42	ASN	ASN	GLY	GLY	C	C	498 - 507	529 - 538
d_3	43	VAL	VAL	VAL	VAL	C	C	509	540
d_3	44	GLY	GLY	PHE	PHE	C	C	512 - 513	543 - 544
d_3	45	ASP	ASP	LEU	LEU	C	C	515 - 521	546 - 552
d_3	46	VAL	VAL	VAL	VAL	C	C	525	556
d_3	47	ALA	ALA	ASN	ASN	C	C	527 - 528	558 - 559
d_3	48	GLY	GLY	THR	THR	C	C	530 - 532	561 - 563
d_3	49	GLY	GLY	ASN	ASN	C	C	534 - 541	565 - 572
d_3	50	LEU	LEU	PRO	PRO	C	C	543 - 548	574 - 579
d_3	51	GLY	GLY	ILE	ILE	C	C	550 - 558	581 - 589
d_3	52	THR	THR	LYS	LYS	C	C	560 - 577	591 - 608
d_3	53	GOL	GOL	GOL	GOL	C	Q	602
d_4	1	GLU	GLU	SER	SER	D	D	15 - 21	46 - 52
d_4	2	ALA	ALA	ALA	ALA	D	D	23	54
d_4	3	LEU	LEU	LEU	LEU	D	D	25	56
d_4	4	ALA	ALA	SER	SER	D	D	27 - 31	58 - 62
d_4	5	ASP	ASP	GLY	GLY	D	D	33 - 34	64 - 65
d_4	6	LEU	LEU	LEU	LEU	D	D	36	67
d_4	7	LEU	LEU	VAL	VAL	D	D	39 - 55	70 - 86
d_4	8	SER	SER	ARG	ARG	D	D	59 - 76	90 - 107
d_4	9	LEU	LEU	VAL	VAL	D	D	78 - 80	109 - 111
d_4	10	PRO	PRO	ALA	ALA	D	D	84 - 87	115 - 118
d_4	11	MET	MET	ALA	ALA	D	D	89 - 123	120 - 154
d_4	12	TYR	TYR	PHE	PHE	D	D	125 - 127	156 - 158
d_4	13	GLY	GLY	ILE	ILE	D	D	129 - 133	160 - 164
d_4	14	VAL	VAL	SER	SER	D	D	135 - 138	166 - 169
d_4	15	ALA	ALA	ILE	ILE	D	D	140 - 142	171 - 173
d_4	16	GLY	GLY	TYR	TYR	D	D	144 - 145	175 - 176
d_4	17	GLY	GLY	VAL	VAL	D	D	147 - 149	178 - 180
d_4	18	ILE	ILE	GLY	GLY	D	D	151 - 158	182 - 189
d_4	19	VAL	VAL	TYR	TYR	D	D	161 - 168	192 - 199
d_4	20	TYR	TYR	LEU	LEU	D	D	170 - 183	201 - 214
d_4	21	GLY	GLY	ALA	ALA	D	D	185 - 191	216 - 222
d_4	22	THR	THR	THR	THR	D	D	193	224
d_4	23	GLY	GLY	GLY	GLY	D	D	195 - 202	226 - 233
d_4	24	THR	THR	VAL	VAL	D	D	205 - 206	236 - 237
d_4	25	LYS	LYS	ARG	ARG	D	D	210 - 231	241 - 262
d_4	26	GLY	GLY	TYR	TYR	D	D	233 - 242	264 - 273
d_4	27	VAL	VAL	LEU	LEU	D	D	244 - 262	275 - 293
d_4	28	SER	SER	LEU	LEU	D	D	265 - 269	296 - 300
d_4	29	PHE	PHE	CYS	CYS	D	D	271 - 317	302 - 348
d_4	30	GLY	GLY	SER	SER	D	D	319 - 367	350 - 398
d_4	31	ASP	ASP	GLU	GLU	D	D	369 - 388	400 - 419
d_4	32	GLU	GLU	ASP	ASP	D	D	390 - 444	421 - 475
d_4	33	GLY	GLY	THR	THR	D	D	446 - 449	477 - 480
d_4	34	SER	SER	VAL	VAL	D	D	451 - 453	482 - 484
d_4	35	TYR	TYR	MET	MET	D	D	455 - 468	486 - 499
d_4	36	VAL	VAL	VAL	VAL	D	D	470 - 473	501 - 504
d_4	37	VAL	VAL	GLN	GLN	D	D	475 - 481	506 - 512
d_4	38	GLN	GLN	ALA	ALA	D	D	483 - 484	514 - 515
d_4	39	THR	THR	GLY	GLY	D	D	486 - 489	517 - 520
d_4	40	PHE	PHE	SER	SER	D	D	491 - 494	522 - 525
d_4	41	MET	MET	MET	MET	D	D	496	527
d_4	42	ASN	ASN	GLY	GLY	D	D	498 - 507	529 - 538
d_4	43	VAL	VAL	VAL	VAL	D	D	509	540
d_4	44	GLY	GLY	PHE	PHE	D	D	512 - 513	543 - 544
d_4	45	ASP	ASP	LEU	LEU	D	D	515 - 521	546 - 552
d_4	46	VAL	VAL	VAL	VAL	D	D	525	556
d_4	47	ALA	ALA	ASN	ASN	D	D	527 - 528	558 - 559
d_4	48	GLY	GLY	THR	THR	D	D	530 - 532	561 - 563
d_4	49	GLY	GLY	ASN	ASN	D	D	534 - 541	565 - 572
d_4	50	LEU	LEU	PRO	PRO	D	D	543 - 548	574 - 579
d_4	51	GLY	GLY	ILE	ILE	D	D	550 - 558	581 - 589
d_4	52	THR	THR	LYS	LYS	D	D	560 - 577	591 - 608
d_4	53	GOL	GOL	GOL	GOL	D	U	601
d_5	1	GLU	GLU	SER	SER	E	E	15 - 21	46 - 52
d_5	2	ALA	ALA	ALA	ALA	E	E	23	54
d_5	3	LEU	LEU	LEU	LEU	E	E	25	56
d_5	4	ALA	ALA	SER	SER	E	E	27 - 31	58 - 62
d_5	5	ASP	ASP	GLY	GLY	E	E	33 - 34	64 - 65
d_5	6	LEU	LEU	LEU	LEU	E	E	36	67
d_5	7	LEU	LEU	VAL	VAL	E	E	39 - 55	70 - 86
d_5	8	SER	SER	ARG	ARG	E	E	59 - 76	90 - 107
d_5	9	LEU	LEU	VAL	VAL	E	E	78 - 80	109 - 111
d_5	10	PRO	PRO	ALA	ALA	E	E	84 - 87	115 - 118
d_5	11	MET	MET	ALA	ALA	E	E	89 - 123	120 - 154
d_5	12	TYR	TYR	PHE	PHE	E	E	125 - 127	156 - 158
d_5	13	GLY	GLY	ILE	ILE	E	E	129 - 133	160 - 164
d_5	14	VAL	VAL	SER	SER	E	E	135 - 138	166 - 169
d_5	15	ALA	ALA	ILE	ILE	E	E	140 - 142	171 - 173
d_5	16	GLY	GLY	TYR	TYR	E	E	144 - 145	175 - 176
d_5	17	GLY	GLY	VAL	VAL	E	E	147 - 149	178 - 180
d_5	18	ILE	ILE	GLY	GLY	E	E	151 - 158	182 - 189
d_5	19	VAL	VAL	TYR	TYR	E	E	161 - 168	192 - 199
d_5	20	TYR	TYR	LEU	LEU	E	E	170 - 183	201 - 214
d_5	21	GLY	GLY	ALA	ALA	E	E	185 - 191	216 - 222
d_5	22	THR	THR	THR	THR	E	E	193	224
d_5	23	GLY	GLY	GLY	GLY	E	E	195 - 202	226 - 233
d_5	24	THR	THR	VAL	VAL	E	E	205 - 206	236 - 237
d_5	25	LYS	LYS	ARG	ARG	E	E	210 - 231	241 - 262
d_5	26	GLY	GLY	TYR	TYR	E	E	233 - 242	264 - 273
d_5	27	VAL	VAL	LEU	LEU	E	E	244 - 262	275 - 293
d_5	28	SER	SER	LEU	LEU	E	E	265 - 269	296 - 300
d_5	29	PHE	PHE	CYS	CYS	E	E	271 - 317	302 - 348
d_5	30	GLY	GLY	SER	SER	E	E	319 - 367	350 - 398
d_5	31	ASP	ASP	GLU	GLU	E	E	369 - 388	400 - 419
d_5	32	GLU	GLU	ASP	ASP	E	E	390 - 444	421 - 475
d_5	33	GLY	GLY	THR	THR	E	E	446 - 449	477 - 480
d_5	34	SER	SER	VAL	VAL	E	E	451 - 453	482 - 484
d_5	35	TYR	TYR	MET	MET	E	E	455 - 468	486 - 499
d_5	36	VAL	VAL	VAL	VAL	E	E	470 - 473	501 - 504
d_5	37	VAL	VAL	GLN	GLN	E	E	475 - 481	506 - 512
d_5	38	GLN	GLN	ALA	ALA	E	E	483 - 484	514 - 515
d_5	39	THR	THR	GLY	GLY	E	E	486 - 489	517 - 520
d_5	40	PHE	PHE	SER	SER	E	E	491 - 494	522 - 525
d_5	41	MET	MET	MET	MET	E	E	496	527
d_5	42	ASN	ASN	GLY	GLY	E	E	498 - 507	529 - 538
d_5	43	VAL	VAL	VAL	VAL	E	E	509	540
d_5	44	GLY	GLY	PHE	PHE	E	E	512 - 513	543 - 544
d_5	45	ASP	ASP	LEU	LEU	E	E	515 - 521	546 - 552
d_5	46	VAL	VAL	VAL	VAL	E	E	525	556
d_5	47	ALA	ALA	ASN	ASN	E	E	527 - 528	558 - 559
d_5	48	GLY	GLY	THR	THR	E	E	530 - 532	561 - 563
d_5	49	GLY	GLY	ASN	ASN	E	E	534 - 541	565 - 572
d_5	50	LEU	LEU	PRO	PRO	E	E	543 - 548	574 - 579
d_5	51	GLY	GLY	ILE	ILE	E	E	550 - 558	581 - 589
d_5	52	THR	THR	LYS	LYS	E	E	560 - 577	591 - 608
d_5	53	GOL	GOL	GOL	GOL	E	BA	601
d_6	1	GLU	GLU	SER	SER	F	F	15 - 21	46 - 52
d_6	2	ALA	ALA	ALA	ALA	F	F	23	54
d_6	3	LEU	LEU	LEU	LEU	F	F	25	56
d_6	4	ALA	ALA	SER	SER	F	F	27 - 31	58 - 62
d_6	5	ASP	ASP	GLY	GLY	F	F	33 - 34	64 - 65
d_6	6	LEU	LEU	LEU	LEU	F	F	36	67
d_6	7	LEU	LEU	VAL	VAL	F	F	39 - 55	70 - 86
d_6	8	SER	SER	ARG	ARG	F	F	59 - 76	90 - 107
d_6	9	LEU	LEU	VAL	VAL	F	F	78 - 80	109 - 111
d_6	10	PRO	PRO	ALA	ALA	F	F	84 - 87	115 - 118
d_6	11	MET	MET	ALA	ALA	F	F	89 - 123	120 - 154
d_6	12	TYR	TYR	PHE	PHE	F	F	125 - 127	156 - 158
d_6	13	GLY	GLY	ILE	ILE	F	F	129 - 133	160 - 164
d_6	14	VAL	VAL	SER	SER	F	F	135 - 138	166 - 169
d_6	15	ALA	ALA	ILE	ILE	F	F	140 - 142	171 - 173
d_6	16	GLY	GLY	TYR	TYR	F	F	144 - 145	175 - 176
d_6	17	GLY	GLY	VAL	VAL	F	F	147 - 149	178 - 180
d_6	18	ILE	ILE	GLY	GLY	F	F	151 - 158	182 - 189
d_6	19	VAL	VAL	TYR	TYR	F	F	161 - 168	192 - 199
d_6	20	TYR	TYR	LEU	LEU	F	F	170 - 183	201 - 214
d_6	21	GLY	GLY	ALA	ALA	F	F	185 - 191	216 - 222
d_6	22	THR	THR	THR	THR	F	F	193	224
d_6	23	GLY	GLY	GLY	GLY	F	F	195 - 202	226 - 233
d_6	24	THR	THR	VAL	VAL	F	F	205 - 206	236 - 237
d_6	25	LYS	LYS	ARG	ARG	F	F	210 - 231	241 - 262
d_6	26	GLY	GLY	TYR	TYR	F	F	233 - 242	264 - 273
d_6	27	VAL	VAL	LEU	LEU	F	F	244 - 262	275 - 293
d_6	28	SER	SER	LEU	LEU	F	F	265 - 269	296 - 300
d_6	29	PHE	PHE	CYS	CYS	F	F	271 - 317	302 - 348
d_6	30	GLY	GLY	SER	SER	F	F	319 - 367	350 - 398
d_6	31	ASP	ASP	GLU	GLU	F	F	369 - 388	400 - 419
d_6	32	GLU	GLU	ASP	ASP	F	F	390 - 444	421 - 475
d_6	33	GLY	GLY	THR	THR	F	F	446 - 449	477 - 480
d_6	34	SER	SER	VAL	VAL	F	F	451 - 453	482 - 484
d_6	35	TYR	TYR	MET	MET	F	F	455 - 468	486 - 499
d_6	36	VAL	VAL	VAL	VAL	F	F	470 - 473	501 - 504
d_6	37	VAL	VAL	GLN	GLN	F	F	475 - 481	506 - 512
d_6	38	GLN	GLN	ALA	ALA	F	F	483 - 484	514 - 515
d_6	39	THR	THR	GLY	GLY	F	F	486 - 489	517 - 520
d_6	40	PHE	PHE	SER	SER	F	F	491 - 494	522 - 525
d_6	41	MET	MET	MET	MET	F	F	496	527
d_6	42	ASN	ASN	GLY	GLY	F	F	498 - 507	529 - 538
d_6	43	VAL	VAL	VAL	VAL	F	F	509	540
d_6	44	GLY	GLY	PHE	PHE	F	F	512 - 513	543 - 544
d_6	45	ASP	ASP	LEU	LEU	F	F	515 - 521	546 - 552
d_6	46	VAL	VAL	VAL	VAL	F	F	525	556
d_6	47	ALA	ALA	ASN	ASN	F	F	527 - 528	558 - 559
d_6	48	GLY	GLY	THR	THR	F	F	530 - 532	561 - 563
d_6	49	GLY	GLY	ASN	ASN	F	F	534 - 541	565 - 572
d_6	50	LEU	LEU	PRO	PRO	F	F	543 - 548	574 - 579
d_6	51	GLY	GLY	ILE	ILE	F	F	550 - 558	581 - 589
d_6	52	THR	THR	LYS	LYS	F	F	560 - 577	591 - 608
d_6	53	GOL	GOL	GOL	GOL	F	GA	602

NCS oper:

ID	Code	Matrix	ベクター
1	given	(0.304197422478, 0.582850053821, 0.753491700631), (-0.59182585905, -0.504176076659, 0.628926574637), (0.746462377296, -0.637253715945, 0.191576670805)	-104.244117433, -56.0608770555, 112.082215255
2	given	(0.304274410875, -0.5946810811, 0.744158245716), (0.584285297373, -0.500477542729, -0.638852815989), (0.752348173494, 0.629187286112, 0.195180902843)	-84.7897702263, 104.122481138, 92.0912836307
3	given	(-0.388414384001, -0.626476142234, -0.675767644618), (-0.622858987052, -0.361961754374, 0.693563530341), (-0.679103047078, 0.690298002012, -0.249615143507)	28.8885850941, -63.8334451513, -7.58769279207
4	given	(-0.252742443312, 0.519848652869, -0.816013869649), (0.544132668372, -0.621008810614, -0.564152192542), (-0.800025559941, -0.586605007864, -0.125911350522)	28.7720545116, 99.0207793159, -3.13018662129
5	given	(-0.993741307451, 0.109658963832, -0.0212867450881), (0.111145690761, 0.989700067929, -0.0902242260464), (0.0111735979189, -0.092025470342, -0.995693960772)	-65.3217379923, 13.9087140151, 98.9501106478

-
要素

#1: タンパク質	K2-2 TSP 分子量: 64872.395 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Klebsiella phage VLC6 (ファージ) / 遺伝子: VLC6_58 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
#2: 化合物	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / トリス(ヒドロキシメチル)メチルアンモニウム分子量: 122.143 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C₄H₁₂NO₃ / タイプ: SUBJECT OF INVESTIGATION / コメント: pH緩衝剤*YM
#3: 化合物	... ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル分子量: 92.094 Da / 分子数: 25 / 由来タイプ: 合成 / 式: C₃H₈O₃ / タイプ: SUBJECT OF INVESTIGATION
#4: 化合物	ChemComp-BCN / BICINE / N,N-ビス(2-ヒドロキシエチル)グリシン分子量: 163.172 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C₆H₁₃NO₄ / タイプ: SUBJECT OF INVESTIGATION / コメント: pH緩衝剤*YM
#5: 水	ChemComp-HOH / water 分子量: 18.015 Da / 分子数: 5165 / 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: 2.12 Å³/Da / 溶媒含有率: 42.06 %
結晶化	温度: 288 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 0.1 M Bicine pH 9.0, 22% PEG-6000

-
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: NSRRC / ビームライン: TPS 05A / 波長: 1 Å
検出器	タイプ: RAYONIX MX300-HS / 検出器: CCD / 日付: 2022年7月5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: 1 Å / 相対比: 1
反射	解像度: 1.38→30 Å / Num. obs: 651990 / % possible obs: 98.1 % / 冗長度: 4 % / B_iso Wilson estimate: 12.95 Å² / R_merge(I) obs: 0.078 / R_pim(I) all: 0.044 / R_rim(I) all: 0.089 / R_sym value: 0.058 / Χ²: 1.259 / Net I/σ(I): 24.1
反射シェル	解像度: 1.38→1.43 Å / R_merge(I) obs: 0.56 / Num. unique obs: 63676 / CC_1/2: 0.653 / R_pim(I) all: 0.402 / R_rim(I) all: 0.693 / R_sym value: 0.6 / Χ²: 0.556

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解析

ソフトウェア

名称	バージョン	分類
PHENIX	1.19.2_4158	精密化
HKL-2000		データスケーリング
HKL-2000		データ削減
MOLREP		位相決定

精密化

構造決定の手法:

分子置換
開始モデル: 8IQE

8iqe

解像度: 1.38→25.42 Å / SU ML: 0.105 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 14.7109
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2

	R_factor	反射数	%反射
R_free	0.1578	2000	0.31 %
R_work	0.1341	649918	-
obs	0.1341	651918	98.07 %

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 BULK SOLVENT MODEL

原子変位パラメータ

B_iso mean: 17.42 Å²

精密化ステップ

サイクル: LAST / 解像度: 1.38→25.42 Å

	タンパク質	核酸	リガンド	溶媒	全体
原子数	25074	0	177	5167	30418

拘束条件

Refine-ID	タイプ	Dev ideal	数
X-RAY DIFFRACTION	f_bond_d	0.0123	26278
X-RAY DIFFRACTION	f_angle_d	1.2436	35743
X-RAY DIFFRACTION	f_chiral_restr	0.1135	4011
X-RAY DIFFRACTION	f_plane_restr	0.0109	4649
X-RAY DIFFRACTION	f_dihedral_angle_d	12.3458	9240

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	タイプ	Rms dev position (Å)
ens_1	d_2	A	X-RAY DIFFRACTION	Torsion NCS	0.570009709563
ens_1	d_3	A	X-RAY DIFFRACTION	Torsion NCS	1.55314647223
ens_1	d_4	A	X-RAY DIFFRACTION	Torsion NCS	1.53898178637
ens_1	d_5	A	X-RAY DIFFRACTION	Torsion NCS	2.06466388732
ens_1	d_6	A	X-RAY DIFFRACTION	Torsion NCS	1.52455294079

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 (%)
1.38-1.42	0.2302	138	0.2132	44711	X-RAY DIFFRACTION	95.15
1.42-1.45	0.212	141	0.1923	45748	X-RAY DIFFRACTION	96.74
1.45-1.5	0.2032	140	0.1737	45724	X-RAY DIFFRACTION	97.02
1.5-1.55	0.2038	141	0.1565	45930	X-RAY DIFFRACTION	97.27
1.55-1.6	0.1627	142	0.1435	46021	X-RAY DIFFRACTION	97.56
1.6-1.66	0.1777	143	0.1376	46214	X-RAY DIFFRACTION	97.81
1.66-1.74	0.1641	142	0.133	46301	X-RAY DIFFRACTION	98.08
1.74-1.83	0.1537	143	0.1291	46530	X-RAY DIFFRACTION	98.34
1.83-1.95	0.1666	143	0.126	46580	X-RAY DIFFRACTION	98.61
1.95-2.1	0.1155	144	0.1208	46808	X-RAY DIFFRACTION	98.88
2.1-2.31	0.144	144	0.1235	46955	X-RAY DIFFRACTION	99.11
2.31-2.64	0.145	145	0.1323	47157	X-RAY DIFFRACTION	99.36
2.64-3.33	0.1639	146	0.1317	47360	X-RAY DIFFRACTION	99.51
3.33-25.42	0.151	148	0.1263	47879	X-RAY DIFFRACTION	99.51

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	0.0575490933225	-0.0318110609769	-0.0554904688708	0.180214377001	0.0109194527155	0.250131638606	-0.00406964323185	-0.0388553028289	0.0876111556193	0.252052497877	0.0219747876493	-0.294671609064	-0.166743228238	0.361283433574	0.00999687969222	0.205630846856	-0.0150309785227	-0.0605653912631	0.223765387518	0.0217578301969	0.17510958796	-19.183773232	6.67477766448	120.054012798
2	0.353955403731	0.138235569397	0.164882497457	0.343274647038	-0.0630809169832	0.375343382168	0.0360184650799	-0.0105573334385	-0.0485393536962	0.0893508481311	-0.0232023249069	-0.0551828128539	0.0593522250307	0.0593284351401	-8.19747895295E-5	0.111009772689	0.00657807372637	-0.0208715959501	0.111691190566	0.012232222047	0.104183715671	-31.9920532393	3.11892705534	108.84167426
3	0.557033105434	-0.240773934342	-0.0674891596436	0.480904434429	0.2396035208	0.498783226455	-0.00349493361013	-0.0873447621642	-0.0955963988138	0.0905301972659	0.000129047229594	0.0314899980414	0.107971473077	-0.0114713743046	-0.0369708138062	0.0949649200606	-0.00335230567232	-0.0044625093916	0.0971536073766	0.0156663731542	0.0980128661421	-46.9366787002	0.304955126095	99.1236025307
4	0.31116954718	-9.45283617635E-5	0.205519078166	0.147683026938	-0.00382623806751	0.295514738817	0.028882409407	0.0432388258991	-0.0385300050507	-0.0419787350617	-0.00226037720112	-0.00326052805799	0.0532837622605	0.0149109523312	0.000162615462984	0.0767761415858	0.00125666274465	0.00192734152968	0.0789352734859	-0.00533396209051	0.0859370627148	-52.9746342325	-0.435132220013	74.9303935974
5	0.422180183967	0.00172210902174	-0.0441140626237	0.300165383596	-0.073066426103	0.252122543879	0.0428836904337	0.013963399334	-0.0484407188616	0.00769442396193	-0.029060501359	-0.0030174823292	0.0862921937168	-0.0343291524703	2.06420301116E-6	0.160156205312	0.00107239145661	-0.0147151083754	0.12440503575	-0.00703342046856	0.120711886983	-74.6168481742	-5.40984676019	46.2947983524
6	0.234506419825	0.0280863219699	0.00522789216165	0.0335942374506	0.0445724404725	0.113716717229	0.0356229671254	0.101277265984	0.026840596849	-0.0816917009461	-0.0432794855241	-0.100746383936	0.0147529722399	0.0141289252365	-3.77706543208E-6	0.160765162374	0.0225446480016	-0.00661538155647	0.142981026293	-0.0232508030521	0.135327869253	-63.5941706771	0.529587141991	42.6085643788
7	0.208712770741	0.0708829918306	0.00581802800379	0.105629071591	-0.084485005006	0.0974071504788	0.0352576321224	0.0719651842924	0.0299098616239	-0.010305551418	-0.0389828942726	-0.0195928688697	0.0185979143338	0.0272035606432	2.37207194327E-5	0.1404919595	0.00978806711106	-0.0095499395931	0.123536485541	-0.0130028466607	0.122131303715	-64.6505919422	0.479257955338	46.8730796769
8	0.341064526753	0.19734710237	0.137615934063	0.166924885514	0.177891592861	0.293516881669	0.0769205758796	-0.0175086133793	0.00341935575467	0.0167380616101	-0.0195935799244	-0.0596963943662	-0.0279637020368	0.132621414335	3.16701582923E-5	0.109835749709	-0.0357838559279	-0.012563921844	0.137902919357	-0.00706925421597	0.143041221866	-16.8469647398	29.907786929	112.392341339
9	0.280058003406	0.0671779353235	0.101707642714	0.242530530344	-0.0197331246129	0.139102134661	-0.0124937861227	-0.0733724108167	0.0158186518858	0.0733756396269	-0.0241756993106	-0.0316346060756	-0.0461570063605	0.0267969282889	-0.00545507050475	0.0954838031223	-0.00948301311087	-0.0182651232768	0.107226998732	-0.00689115613725	0.117686284477	-36.5169352433	28.1860310117	106.485169492
10	0.457442700815	0.17624938958	-0.361357050344	0.284988366705	-0.259358910215	0.877304408835	0.00886207565625	-0.0394102654649	0.120700617168	0.0453996269343	0.00681687979999	-0.00130538882769	-0.132404273173	0.0131814476602	0.0370342166883	0.0791071777954	-0.00135432200369	-0.0174443027914	0.0758085088133	-0.0140897074879	0.112607037136	-43.6147173885	33.9182065007	95.9416596669
11	0.353199623263	0.0504275680969	0.309562182393	0.136929317011	0.0627175850318	0.391932173212	-0.0221644557175	-0.0455588352747	0.026651560467	-0.0166222433758	-0.0043920248875	0.0171378897373	-0.0185819744337	-0.092606835323	-0.00250517218791	0.0555616961291	0.0112513277823	-0.000708647599256	0.0811019847882	-0.00661870492929	0.0814028269181	-64.1470202578	22.821699305	87.0421498092
12	0.265200581958	0.0419447391627	0.0249625568639	0.381937928575	-0.0555524411526	0.347684674764	-0.00288448326063	-0.0767716915636	0.0900350725888	-0.0142842195666	-0.00657308435152	0.0314640545255	-0.0136001994001	-0.0366831411248	2.14641830667E-5	0.095508224867	0.00827977479729	0.00182101632192	0.143022051282	-0.0164426371037	0.125840646424	-95.1757044338	19.7641013833	68.8679195313
13	0.183858905968	-0.0847649985663	0.209409885251	0.461774920194	-0.0822362067345	0.308765422344	-0.00621291121073	-0.0431513930417	-0.00239074564522	0.0120770984699	0.0212661021245	0.0160676305545	0.0935614006317	-0.0347331012782	9.93935401329E-5	0.0872232144232	-0.00224207391128	0.00187079950459	0.147295406488	0.000549054590659	0.0965399111414	-89.4584386025	9.73262182135	72.5601283766
14	0.383599267807	-0.0711350703402	0.144555497362	0.219842692849	-0.145477854396	0.125363765182	-0.0102728093291	-0.0177281281615	-0.0160899831439	0.0728581606656	-0.0116301507682	-0.10785429124	0.0419416368899	0.0332483517941	-7.70994403507E-5	0.097264846281	0.022598823888	-0.0132622738241	0.141069739298	0.00546488545414	0.159131596551	-7.67194081711	9.79591286967	102.448191869
15	0.149058887906	-0.0239855836866	0.052728073965	0.222843790326	-0.125648543204	0.326741274507	-0.00271147201785	0.0515814704344	0.0255918408719	0.0389232282324	0.00111908981983	-0.0720611314848	-0.0629089866275	0.0886073604188	-0.00137409981462	0.0770196025634	0.000612300694125	-0.00087004854728	0.147808467249	0.00552342867184	0.139366839883	-18.6147438358	18.5274970478	87.3542212385
16	0.275256655898	0.171361871948	0.120954029174	0.960035190715	0.0676375237344	0.201452578604	-0.00509417297962	0.0757608725565	-0.0104176688138	-0.0786539118882	-0.00646442819193	-0.115886729504	0.00895637011991	0.110660158742	0.000595061358183	0.0719859096416	0.012264408144	0.0107712858001	0.14346623264	0.00599858466664	0.115912649015	-25.3591472881	13.3980930347	76.2946609324
17	0.438733383175	-0.0633878128663	0.244618802415	0.0908321899008	-0.0710588849764	0.32597198095	-0.0267642277223	0.079382684844	0.0540169564511	-0.0353755376629	-0.00370500531251	-0.00339696277496	-0.0387839650904	0.0455184348064	-0.00107999485331	0.0823228986824	-0.00715030090662	0.00318008056133	0.0917338540171	0.0132480854623	0.0869290834089	-44.8374925672	25.3535468169	66.3644601821
18	0.3626754267	0.0494273872133	-0.0223871753168	0.341614332896	0.147948293291	0.271711564483	-0.00568906752005	0.100146258014	0.038070459943	-0.0454179444176	-0.0292547030211	-0.0327093630542	-0.0444703017814	0.0199021990474	-1.9073550341E-5	0.140109842185	0.00221805123789	-0.00435660515945	0.149066265727	0.0309262234541	0.121272150919	-69.9359067788	34.0256530138	41.5478688417
19	0.374694457408	0.00830125609681	0.0886913215592	0.218983241322	0.266077426371	0.375822188255	-0.0131620904005	-0.00862650825179	0.0860606360793	-0.0143364045036	-0.0384356238329	0.0255620536684	-0.0759111170189	-0.000426037204021	-1.72273346042E-5	0.114183145847	-0.00312941643818	-0.0184738400408	0.0904352340845	0.0248943868517	0.106644237493	-71.579068059	37.6868500807	53.3157758804
20	0.109843730018	-0.101867386058	0.0383012622674	0.113674448197	-0.011111515927	0.139769053466	-0.00943976396134	0.0665713724462	-0.0576990944991	0.00379765506158	0.00177366007059	0.143285096982	0.0274161330372	-0.147650827912	0.000131174569995	0.116010516537	0.0105315391906	-0.00531275473786	0.119444851929	0.00360507832258	0.123548071062	-49.2306807082	28.8029414633	-19.598965507
21	0.386136793852	0.041775776797	0.235516622887	0.216341516568	-0.0521818385013	0.207797216082	-0.0198791411061	0.0252871876272	0.028086985359	-0.0209211858661	0.00762385265308	0.0192295131965	-0.0231040207565	-0.00826492172196	4.97961716968E-5	0.116624656169	0.00957218662075	0.00013024064296	0.102830548517	0.00689844250995	0.0938071267971	-34.0251108234	30.5196082286	-11.0026237622
22	0.222882357716	0.00880749381137	0.10611967903	0.184254004855	-0.00422026328717	0.236971176965	0.00980706920446	0.0326433149459	0.0670061959695	-0.0466107396277	0.00243547449993	-0.0183057785087	-0.0994155861206	0.0212850616097	0.00251458418307	0.108188399063	0.000790013208093	0.0063156955427	0.0863095916059	0.0095503246014	0.0960131261907	-20.2520421069	33.8513541369	-0.183277101385
23	0.4027592969	-0.0693742168239	0.164202818941	0.0560143789002	-0.0724632186628	0.2194488698	-0.0029447978995	0.01955721301	-0.00322466712592	-0.00281680706257	-0.00731490706849	-0.0261844449649	0.00847411683709	0.0467784574038	1.45295745432E-5	0.100076099421	0.00175440441861	0.00756683439663	0.0932320331854	0.00459466104012	0.0977467845753	-0.87983543671	21.4642294949	9.51270779661
24	0.192352818729	-0.0221602020236	0.0910153416712	0.333639303855	0.0675513301995	0.346851990622	-0.00966919495843	0.0110344862958	0.101713854605	0.00323848290359	0.00800303380754	-0.0439790309996	-0.0022622173273	0.0587268494738	-8.42330685694E-5	0.104047317894	0.00400480205409	0.00985354605913	0.140709564391	0.0149354313137	0.133946535111	30.0022612715	16.5156983003	27.7206673161
25	0.109346732637	0.0339113559249	0.0798720565794	0.243163169376	0.0890436221548	0.112009399827	-0.0112187522062	0.0367248520164	0.0235756259947	0.00141082931062	0.019426147042	0.000686232833133	0.100423637617	8.0520118599E-5	1.15058121767E-5	0.110715237729	0.0143903466977	0.0139807175614	0.157648486013	0.00101113302227	0.111007188194	24.2221813228	4.82512229098	25.6708200328
26	0.100452771399	0.0237707287951	0.0828623603149	0.155213930607	-0.0146692267382	0.139088615714	0.0143870757257	0.00181957962606	-0.000710701805246	-0.00215816048268	0.00165154306975	0.00111589699561	0.0794459805262	0.0217972574469	9.45546705109E-7	0.108331318822	0.00854538623398	0.0126465538654	0.139132125032	0.0055683997279	0.116011515418	21.7651710848	8.74018200085	25.0581711733
27	0.15577185665	0.104689263187	0.00987594588575	0.369047812448	-0.0726992573065	0.0727698382625	-0.000909732881868	0.143707509727	-0.0446154930729	-0.29626778282	0.00312752160179	0.159474849442	0.054975333793	-0.15108516024	-0.000814618904099	0.145822866763	-0.00735261001724	-0.0166370799007	0.145440598983	-0.00248166376321	0.172092295903	-60.7991960843	16.9585612894	-6.30091152947
28	0.300825149301	-0.0119246592083	0.111887276365	0.255631096291	-0.0123943503846	0.459363805051	-0.00894054182587	-0.00965044793553	-0.0189852846064	-0.00533834341736	0.0133233955227	0.0357340303651	0.00360177436829	-0.0798839342111	-6.89499178181E-6	0.0999847697814	-0.00342266496497	0.00479482991256	0.109109504093	0.00352642983772	0.106891881215	-50.3047340954	18.3271761494	7.08007196211
29	0.19690054637	-0.0722962489171	0.0914802085532	0.171665043313	-0.0391142648858	0.240049999104	-0.0176032798748	-0.0485122755507	-0.0400919976939	0.0715765672099	0.0251368216662	0.070371544736	0.00554746001541	-0.0881620531952	-0.000210209170246	0.0966561199086	0.000588089939847	0.0129161567009	0.109611346477	0.00925042414171	0.0988270219008	-40.1247595443	17.2734730605	21.4429565157
30	0.412521149312	0.044101178589	0.243520820358	0.0844172374639	0.0417731573642	0.289647453896	-0.0212435441022	-0.044933202497	0.0195546139579	0.0217117867173	0.00775112377745	-0.0176755296806	-0.0367533803416	-0.0101106436677	0.000103266215353	0.104946214304	0.00724731301973	0.0030438382525	0.0875990402923	0.00079244686407	0.0753640303787	-19.3127018941	28.0714008393	30.0312372063
31	0.341471750862	-0.0934273707496	-0.0420323548352	0.326028972333	-0.113131836968	0.311123500977	-0.00224933783419	-0.0327963127828	0.0298840335605	0.0398903150502	-0.00587343664466	-0.0155567575416	-0.013647240399	-0.0171596434938	-1.79650623469E-5	0.136769708634	0.000905857439046	-0.010804551439	0.121871435636	-0.0144456124906	0.109032332456	6.78848772438	35.8279493868	53.7454446475
32	0.114737445926	-0.0512206658218	-0.0390656445511	0.154597075254	-0.139602639827	0.20163409269	0.0251895112331	0.0599939285965	0.0514126123548	-0.0209558995155	-0.0375684359303	-0.0668569374608	-0.0591403992487	0.00297357459595	2.77866608558E-5	0.169664798289	0.0017536268693	-0.020275938694	0.112425637861	-0.00417366179925	0.130903609024	10.6579394242	39.7004767251	41.5315039904
33	0.193795348875	-0.032193810577	-0.0126437531599	0.0899292509566	-0.103111581136	0.158108019319	-0.0201535280793	0.0329377821528	0.030994582548	0.00109800250224	-0.0149920500144	-0.0425059047597	-0.0340740802663	0.0292246086699	3.11426110459E-6	0.148263266651	-8.06226744998E-5	-0.0138146850302	0.116710235787	-0.0100953228356	0.112317248316	6.88589200066	37.0800264705	42.1405231176
34	0.101063667116	0.0467468067864	-0.00308792131931	0.0715601570112	0.0193517937955	0.0983307109829	0.0111603580868	0.0789210083035	0.100980263715	-0.184208313997	0.0082546485176	0.169879024768	-0.135686468133	-0.0631094333173	0.000770178538301	0.206697817116	-0.0247209920158	-0.0204593215087	0.143244838266	-0.00685719769488	0.134703373765	-48.3173020646	7.58763423853	-21.0250833247
35	0.116879276373	-0.0514273176347	0.0560660296727	0.0736419565884	-0.0422449223555	0.0383803685696	0.00713400134477	0.14946939735	-0.0493376018011	-0.216426781448	-0.0420470592985	0.0201908486254	-0.0210484297957	0.152489071059	7.88316584673E-5	0.211320846565	0.00226159382367	-0.0122117451272	0.152804081443	-0.0221330086893	0.122410739198	-38.0408391206	7.02240779797	-21.8381583704
36	0.179409512196	-0.067179408851	0.0662546934114	0.0827310551645	-0.0252975157617	0.209795413441	-0.00935601277857	0.0426046414916	-0.0547468416351	0.0137443797077	0.0183955277728	0.046100766489	0.0780096189037	-0.0659136129646	-3.06385230112E-6	0.134031502241	-0.0102232578739	0.00016233648593	0.108199694746	-0.00787988416343	0.112883051	-34.0115016884	1.6552966676	-3.97378759805
37	0.178852571256	0.0792681702681	0.101441012732	0.251020384468	-0.0135516176925	0.222480763976	-0.0154130273116	0.0590391437233	-0.134959052091	-0.0625435402242	-0.0103214842744	-0.0620916052309	0.10330629367	0.0129989543243	-0.000306644107664	0.129563497141	0.00986888857665	0.00879622649434	0.0911024456016	-0.00821541999273	0.124589997312	-20.7464263448	0.295953397391	-0.32332719805
38	0.14033311186	0.101871889514	-0.0168186381431	0.0749993911698	0.000217207535801	0.165467301726	0.0178996372958	0.0262165613329	-0.0656505654265	-0.0210556691944	-0.00507484395182	-0.00432805258846	0.0530398112376	-0.00282476983068	8.68022041918E-6	0.107591904246	0.00917663397393	0.000344603017856	0.0770628989135	0.00213354598164	0.110626347845	-21.5532163791	-0.583455265857	9.91721023063
39	0.0848112125427	0.0035843003898	0.0857654473943	0.115005368944	-0.0140812340882	0.0932739868491	0.0241578047196	-0.00479876131124	-0.0564062736452	-0.0596342822887	-0.0109679867959	-0.0261508000503	0.0565394503184	0.045052411088	-7.640659698E-6	0.116744926093	0.00937781767834	0.00553928201198	0.0987293939549	0.0086486837899	0.115443957036	-15.4768702018	1.08556198879	15.3053431823
40	0.152208719671	0.0251719532643	0.175712192987	0.17868252971	0.0432232404303	0.202073547881	0.0331097598983	-0.0227699069333	-0.0617242820414	0.0220250931405	-0.0132727207465	-0.00657653819498	0.0472475922149	-0.0212818619139	-8.72421811968E-6	0.114174785025	0.00455995373845	0.000598531978872	0.111609106974	0.0226540313696	0.118296887881	-12.7204076999	0.543878833083	28.9416210729
41	0.141417326666	0.0336628796456	0.0660945899476	0.0259818399528	-0.0245297163205	0.119320532061	0.0141904548463	-0.027324876229	0.0167717930986	0.00209743090095	-0.00352946033737	0.0450608552891	0.00235802188508	-0.0479958031888	1.75444585417E-5	0.123429000254	0.00361410278378	-0.00177970857944	0.125136323515	0.0201747577749	0.116602839388	-7.0951523795	2.31814136004	39.6737005008
42	0.42243478644	0.0547598434219	-0.011843336028	0.307599357417	0.117269999367	0.269555808289	0.0390621959746	0.00578455697137	-0.0360056226761	0.0166943459402	-0.0101836320413	-0.0172793213434	0.0958708581905	0.0314545860269	-6.97830444036E-5	0.158812191704	0.00766484563016	-0.00941860764202	0.121993569439	0.0128283811007	0.121267048971	7.03526741742	-3.93364118187	52.4544457578
43	0.188434096694	-0.0870576824826	-0.0557987218714	0.0994243611728	0.0840460062168	0.136093421124	0.00809638065068	-0.0505844348507	0.0342043796513	0.0419648531969	-0.0151093947409	0.0851180513952	0.0262634464054	-0.00647281791981	-4.12345497151E-5	0.154269882174	-0.0104968855634	-0.00266256533333	0.135690856416	0.0282881387668	0.13614995087	-3.12711650624	4.04013848125	55.7601904006
44	0.228952249575	-0.0206967053752	0.00690882132034	0.142396236047	0.129271405835	0.132145504252	0.00769744867424	-0.0573677652565	0.050983174709	0.00375181596163	-0.0171145992619	0.0309197767482	0.0171802933556	-0.013197021142	2.82762847338E-5	0.127900964314	0.00073167066221	-0.00513637196159	0.117049992456	0.0236599410574	0.113376568399	-2.23718594135	2.96648435148	51.3601168148

精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 15 through 50 )	A	A	15 - 50	1 - 36
2	2	chain 'A' and (resid 51 through 152 )	A	A	51 - 152	37 - 138
3	3	chain 'A' and (resid 153 through 216 )	A	A	153 - 216	139 - 202
4	4	chain 'A' and (resid 217 through 430 )	A	A	217 - 430	203 - 416
5	5	chain 'A' and (resid 431 through 489 )	A	A	431 - 489	417 - 475
6	6	chain 'A' and (resid 490 through 533 )	A	A	490 - 533	476 - 519
7	7	chain 'A' and (resid 534 through 577 )	A	A	534 - 577	520 - 563
8	8	chain 'B' and (resid 15 through 86 )	B	B	15 - 86	1 - 72
9	9	chain 'B' and (resid 87 through 152 )	B	B	87 - 152	73 - 138
10	10	chain 'B' and (resid 153 through 216 )	B	B	153 - 216	139 - 202
11	11	chain 'B' and (resid 217 through 430 )	B	B	217 - 430	203 - 416
12	12	chain 'B' and (resid 431 through 489 )	B	B	431 - 489	417 - 475
13	13	chain 'B' and (resid 490 through 577 )	B	B	490 - 577	476 - 563
14	14	chain 'C' and (resid 15 through 86 )	C	C	15 - 86	1 - 72
15	15	chain 'C' and (resid 87 through 152 )	C	C	87 - 152	73 - 138
16	16	chain 'C' and (resid 153 through 216 )	C	C	153 - 216	139 - 202
17	17	chain 'C' and (resid 217 through 430 )	C	C	217 - 430	203 - 416
18	18	chain 'C' and (resid 431 through 489 )	C	C	431 - 489	417 - 475
19	19	chain 'C' and (resid 490 through 577 )	C	C	490 - 577	476 - 563
20	20	chain 'D' and (resid 14 through 50 )	D	D	14 - 50	1 - 37
21	21	chain 'D' and (resid 51 through 152 )	D	D	51 - 152	38 - 139
22	22	chain 'D' and (resid 153 through 216 )	D	D	153 - 216	140 - 203
23	23	chain 'D' and (resid 217 through 430 )	D	D	217 - 430	204 - 417
24	24	chain 'D' and (resid 431 through 489 )	D	D	431 - 489	418 - 476
25	25	chain 'D' and (resid 490 through 534 )	D	D	490 - 534	477 - 521
26	26	chain 'D' and (resid 535 through 577 )	D	D	535 - 577	522 - 564
27	27	chain 'E' and (resid 15 through 50 )	E	E	15 - 50	1 - 36
28	28	chain 'E' and (resid 51 through 152 )	E	E	51 - 152	37 - 138
29	29	chain 'E' and (resid 153 through 216 )	E	E	153 - 216	139 - 202
30	30	chain 'E' and (resid 217 through 430 )	E	E	217 - 430	203 - 416
31	31	chain 'E' and (resid 431 through 489 )	E	E	431 - 489	417 - 475
32	32	chain 'E' and (resid 490 through 533 )	E	E	490 - 533	476 - 519
33	33	chain 'E' and (resid 534 through 577 )	E	E	534 - 577	520 - 563
34	34	chain 'F' and (resid 15 through 50 )	F	F	15 - 50	1 - 36
35	35	chain 'F' and (resid 51 through 86 )	F	F	51 - 86	37 - 72
36	36	chain 'F' and (resid 87 through 152 )	F	F	87 - 152	73 - 138
37	37	chain 'F' and (resid 153 through 216 )	F	F	153 - 216	139 - 202
38	38	chain 'F' and (resid 217 through 258 )	F	F	217 - 258	203 - 244
39	39	chain 'F' and (resid 259 through 307 )	F	F	259 - 307	245 - 293
40	40	chain 'F' and (resid 308 through 386 )	F	F	308 - 386	294 - 372
41	41	chain 'F' and (resid 387 through 430 )	F	F	387 - 430	373 - 416
42	42	chain 'F' and (resid 431 through 489 )	F	F	431 - 489	417 - 475
43	43	chain 'F' and (resid 490 through 533 )	F	F	490 - 533	476 - 519
44	44	chain 'F' and (resid 534 through 577 )	F	F	534 - 577	520 - 563

+
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

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://pdbjlvh1.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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このページ

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データを開く

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基本情報

-
構造の表示

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ダウンロードとリンク

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ダウンロード

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検証レポート

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関連構造データ

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リンク

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集合体

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要素

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実験情報

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実験

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試料調製

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データ収集

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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)

-
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)