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- PDB-5oe3: Crystal structure of the N-terminal domain of PqsA in complex wit... -

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基本情報

登録情報
データベース: PDB / ID: 5oe3
タイトルCrystal structure of the N-terminal domain of PqsA in complex with anthraniloyl-AMP (crystal form 1)
要素Anthranilate--CoA ligase
キーワードLIGASE / PQS / PqsA / Anthranilate / Anthraniloyl-AMP / Anthraniloyl-CoA / Pseudomonas Quinolone Signal / Pseudomonas aeruginosa / Quorum Sensing / Aryl-CoA ligase / ANL superfamily
機能・相同性
機能・相同性情報


anthranilate-CoA ligase / anthranilate-CoA ligase activity / acid-thiol ligase activity / secondary metabolite biosynthetic process / ATP binding
類似検索 - 分子機能
ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily
類似検索 - ドメイン・相同性
Chem-3UK / ACETATE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Anthranilate--CoA ligase
類似検索 - 構成要素
生物種Pseudomonas aeruginosa PAO1 (緑膿菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.43 Å
データ登録者Witzgall, F. / Ewert, W. / Blankenfeldt, W.
引用ジャーナル: Chembiochem / 年: 2017
タイトル: Structures of the N-Terminal Domain of PqsA in Complex with Anthraniloyl- and 6-Fluoroanthraniloyl-AMP: Substrate Activation in Pseudomonas Quinolone Signal (PQS) Biosynthesis.
著者: Witzgall, F. / Ewert, W. / Blankenfeldt, W.
履歴
登録2017年7月7日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02017年9月6日Provider: repository / タイプ: Initial release
改定 1.12017年10月25日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
改定 1.22024年5月8日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: Anthranilate--CoA ligase
B: Anthranilate--CoA ligase
C: Anthranilate--CoA ligase
D: Anthranilate--CoA ligase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)181,35531
ポリマ－177,5814
非ポリマー3,77427
水43,2362400
1
A: Anthranilate--CoA ligase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,4289
ポリマ－44,3951
非ポリマー1,0338
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Anthranilate--CoA ligase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,1697
ポリマ－44,3951
非ポリマー7746
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: Anthranilate--CoA ligase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,3927
ポリマ－44,3951
非ポリマー9976
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: Anthranilate--CoA ligase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,3668
ポリマ－44,3951
非ポリマー9717
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)71.533, 84.448, 139.011
Angle α, β, γ (deg.)90.000, 92.600, 90.000
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 2 through 12 or resid 14...
21(chain B and (resid 2 through 12 or resid 14...
31(chain C and (resid 2 through 12 or resid 14...
41(chain D and (resid 2 through 12 or resid 14...

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERPHEPHE(chain A and (resid 2 through 12 or resid 14...AA2 - 122 - 12
12LEULEUPROPRO(chain A and (resid 2 through 12 or resid 14...AA14 - 1814 - 18
13THRTHRALAALA(chain A and (resid 2 through 12 or resid 14...AA20 - 2120 - 21
14TYRTYRLEULEU(chain A and (resid 2 through 12 or resid 14...AA23 - 3323 - 33
15CYSCYSCYSCYS(chain A and (resid 2 through 12 or resid 14...AA3535
16THRTHRTHRTHR(chain A and (resid 2 through 12 or resid 14...AA3737
17ILEILELEULEU(chain A and (resid 2 through 12 or resid 14...AA39 - 4039 - 40
18GLNGLNLEULEU(chain A and (resid 2 through 12 or resid 14...AA42 - 6042 - 60
19ASPASPPROPRO(chain A and (resid 2 through 12 or resid 14...AA62 - 6462 - 64
110ALAALAPROPRO(chain A and (resid 2 through 12 or resid 14...AA67 - 8567 - 85
111SERSERSERSER(chain A and (resid 2 through 12 or resid 14...AA8787
112GLUGLUALAALA(chain A and (resid 2 through 12 or resid 14...AA89 - 9189 - 91
113ALAALACYSCYS(chain A and (resid 2 through 12 or resid 14...AA93 - 9993 - 99
114ALAALALEULEU(chain A and (resid 2 through 12 or resid 14...AA101 - 103101 - 103
115VALVALARGARG(chain A and (resid 2 through 12 or resid 14...AA105 - 106105 - 106
116ALAALAPROPRO(chain A and (resid 2 through 12 or resid 14...AA108 - 116108 - 116
117ALAALAPHEPHE(chain A and (resid 2 through 12 or resid 14...AA118 - 134118 - 134
118LEULEUALAALA(chain A and (resid 2 through 12 or resid 14...AA136 - 143136 - 143
119LEULEUHISHIS(chain A and (resid 2 through 12 or resid 14...AA145 - 151145 - 151
120GLNGLNGLNGLN(chain A and (resid 2 through 12 or resid 14...AA153153
121PROPROALAALA(chain A and (resid 2 through 12 or resid 14...AA155 - 158155 - 158
122PHEPHETYRTYR(chain A and (resid 2 through 12 or resid 14...AA160 - 163160 - 163
123THRTHRTHRTHR(chain A and (resid 2 through 12 or resid 14...AA164164
124SERSERASPASP(chain A and (resid 2 through 12 or resid 14...AA2 - 3992 - 399
125SERSERASPASP(chain A and (resid 2 through 12 or resid 14...AA2 - 3992 - 399
126SERSERASPASP(chain A and (resid 2 through 12 or resid 14...AA2 - 3992 - 399
127SERSERASPASP(chain A and (resid 2 through 12 or resid 14...AA2 - 3992 - 399
21SERSERPHEPHE(chain B and (resid 2 through 12 or resid 14...BB2 - 122 - 12
22LEULEUPROPRO(chain B and (resid 2 through 12 or resid 14...BB14 - 1814 - 18
23THRTHRALAALA(chain B and (resid 2 through 12 or resid 14...BB20 - 2120 - 21
24TYRTYRLEULEU(chain B and (resid 2 through 12 or resid 14...BB23 - 3323 - 33
25CYSCYSCYSCYS(chain B and (resid 2 through 12 or resid 14...BB3535
26THRTHRTHRTHR(chain B and (resid 2 through 12 or resid 14...BB3737
27ILEILELEULEU(chain B and (resid 2 through 12 or resid 14...BB39 - 4039 - 40
28GLNGLNLEULEU(chain B and (resid 2 through 12 or resid 14...BB42 - 6042 - 60
29ASPASPPROPRO(chain B and (resid 2 through 12 or resid 14...BB62 - 6462 - 64
210ALAALAPROPRO(chain B and (resid 2 through 12 or resid 14...BB67 - 8567 - 85
211SERSERSERSER(chain B and (resid 2 through 12 or resid 14...BB8787
212GLUGLUALAALA(chain B and (resid 2 through 12 or resid 14...BB89 - 9189 - 91
213ALAALACYSCYS(chain B and (resid 2 through 12 or resid 14...BB93 - 9993 - 99
214ALAALALEULEU(chain B and (resid 2 through 12 or resid 14...BB101 - 103101 - 103
215VALVALARGARG(chain B and (resid 2 through 12 or resid 14...BB105 - 106105 - 106
216ALAALAPROPRO(chain B and (resid 2 through 12 or resid 14...BB108 - 116108 - 116
217ALAALAPHEPHE(chain B and (resid 2 through 12 or resid 14...BB118 - 134118 - 134
218LEULEUALAALA(chain B and (resid 2 through 12 or resid 14...BB136 - 143136 - 143
219LEULEUHISHIS(chain B and (resid 2 through 12 or resid 14...BB145 - 151145 - 151
220GLNGLNGLNGLN(chain B and (resid 2 through 12 or resid 14...BB153153
221PROPROALAALA(chain B and (resid 2 through 12 or resid 14...BB155 - 158155 - 158
222PHEPHETHRTHR(chain B and (resid 2 through 12 or resid 14...BB160 - 164160 - 164
223VALVALSERSER(chain B and (resid 2 through 12 or resid 14...BB174 - 177174 - 177
224ARGARGCYSCYS(chain B and (resid 2 through 12 or resid 14...BB179 - 185179 - 185
225ALAALALEULEU(chain B and (resid 2 through 12 or resid 14...BB187 - 192187 - 192
226ALAALAASPASP(chain B and (resid 2 through 12 or resid 14...BB194 - 199194 - 199
227LEULEULYSLYS(chain B and (resid 2 through 12 or resid 14...BB201 - 206201 - 206
228PHEPHEPHEPHE(chain B and (resid 2 through 12 or resid 14...BB208208
229GLYGLYASNASN(chain B and (resid 2 through 12 or resid 14...BB210 - 215210 - 215
230LEULEUALAALA(chain B and (resid 2 through 12 or resid 14...BB217 - 225217 - 225
231ALAALAASPASP(chain B and (resid 2 through 12 or resid 14...BB227 - 230227 - 230
232THRTHRTHRTHR(chain B and (resid 2 through 12 or resid 14...BB232232
233PROPROGLUGLU(chain B and (resid 2 through 12 or resid 14...BB234 - 237234 - 237
234VALVALPHEPHE(chain B and (resid 2 through 12 or resid 14...BB239 - 246239 - 246
235PROPROPROPRO(chain B and (resid 2 through 12 or resid 14...BB248248
236VALVALARGARG(chain B and (resid 2 through 12 or resid 14...BB250 - 262250 - 262
237GLNGLNALAALA(chain B and (resid 2 through 12 or resid 14...BB264 - 265264 - 265
238GLUGLULEULEU(chain B and (resid 2 through 12 or resid 14...BB267 - 269267 - 269
239SERSERILEILE(chain B and (resid 2 through 12 or resid 14...BB271 - 297271 - 297
240ASPASPHISHIS(chain B and (resid 2 through 12 or resid 14...BB299 - 308299 - 308
241PHEPHEPHEPHE(chain B and (resid 2 through 12 or resid 14...BB310310
242ALAALAASNASN(chain B and (resid 2 through 12 or resid 14...BB312 - 313312 - 313
243PROPROCYSCYS(chain B and (resid 2 through 12 or resid 14...BB315 - 332315 - 332
244LEULEUARGARG(chain B and (resid 2 through 12 or resid 14...BB334 - 347334 - 347
245GLYGLYVALVAL(chain B and (resid 2 through 12 or resid 14...BB349 - 353349 - 353
246GLYGLYSERSER(chain B and (resid 2 through 12 or resid 14...BB355 - 359355 - 359
247GLYGLYASPASP(chain B and (resid 2 through 12 or resid 14...BB361 - 387361 - 387
248SERSERTYRTYR(chain B and (resid 2 through 12 or resid 14...BB389 - 392389 - 392
249HISHISASPASP(chain B and (resid 2 through 12 or resid 14...BB394 - 399394 - 399
31SERSERPHEPHE(chain C and (resid 2 through 12 or resid 14...CC2 - 122 - 12
32LEULEUPROPRO(chain C and (resid 2 through 12 or resid 14...CC14 - 1814 - 18
33THRTHRALAALA(chain C and (resid 2 through 12 or resid 14...CC20 - 2120 - 21
34TYRTYRLEULEU(chain C and (resid 2 through 12 or resid 14...CC23 - 3323 - 33
35CYSCYSCYSCYS(chain C and (resid 2 through 12 or resid 14...CC3535
36THRTHRTHRTHR(chain C and (resid 2 through 12 or resid 14...CC3737
37ILEILELEULEU(chain C and (resid 2 through 12 or resid 14...CC39 - 4039 - 40
38GLNGLNLEULEU(chain C and (resid 2 through 12 or resid 14...CC42 - 6042 - 60
39ASPASPPROPRO(chain C and (resid 2 through 12 or resid 14...CC62 - 6462 - 64
310ALAALAPROPRO(chain C and (resid 2 through 12 or resid 14...CC67 - 8567 - 85
311SERSERSERSER(chain C and (resid 2 through 12 or resid 14...CC8787
312GLUGLUALAALA(chain C and (resid 2 through 12 or resid 14...CC89 - 9189 - 91
313ALAALACYSCYS(chain C and (resid 2 through 12 or resid 14...CC93 - 9993 - 99
314ALAALALEULEU(chain C and (resid 2 through 12 or resid 14...CC101 - 103101 - 103
315VALVALARGARG(chain C and (resid 2 through 12 or resid 14...CC105 - 106105 - 106
316ALAALAPROPRO(chain C and (resid 2 through 12 or resid 14...CC108 - 116108 - 116
317ALAALAPHEPHE(chain C and (resid 2 through 12 or resid 14...CC118 - 134118 - 134
318LEULEUALAALA(chain C and (resid 2 through 12 or resid 14...CC136 - 143136 - 143
319LEULEUHISHIS(chain C and (resid 2 through 12 or resid 14...CC145 - 151145 - 151
320GLNGLNGLNGLN(chain C and (resid 2 through 12 or resid 14...CC153153
321PROPROALAALA(chain C and (resid 2 through 12 or resid 14...CC155 - 158155 - 158
322PHEPHETYRTYR(chain C and (resid 2 through 12 or resid 14...CC160 - 163160 - 163
323THRTHRTHRTHR(chain C and (resid 2 through 12 or resid 14...CC164164
324SERSERASPASP(chain C and (resid 2 through 12 or resid 14...CC2 - 3992 - 399
325SERSERASPASP(chain C and (resid 2 through 12 or resid 14...CC2 - 3992 - 399
326SERSERASPASP(chain C and (resid 2 through 12 or resid 14...CC2 - 3992 - 399
327SERSERASPASP(chain C and (resid 2 through 12 or resid 14...CC2 - 3992 - 399
41SERSERPHEPHE(chain D and (resid 2 through 12 or resid 14...DD2 - 122 - 12
42LEULEUPROPRO(chain D and (resid 2 through 12 or resid 14...DD14 - 1814 - 18
43THRTHRALAALA(chain D and (resid 2 through 12 or resid 14...DD20 - 2120 - 21
44TYRTYRLEULEU(chain D and (resid 2 through 12 or resid 14...DD23 - 3323 - 33
45CYSCYSCYSCYS(chain D and (resid 2 through 12 or resid 14...DD3535
46THRTHRTHRTHR(chain D and (resid 2 through 12 or resid 14...DD3737
47ILEILELEULEU(chain D and (resid 2 through 12 or resid 14...DD39 - 4039 - 40
48GLNGLNLEULEU(chain D and (resid 2 through 12 or resid 14...DD42 - 6042 - 60
49ASPASPPROPRO(chain D and (resid 2 through 12 or resid 14...DD62 - 6462 - 64
410ALAALAPROPRO(chain D and (resid 2 through 12 or resid 14...DD67 - 8567 - 85
411SERSERSERSER(chain D and (resid 2 through 12 or resid 14...DD8787
412GLUGLUALAALA(chain D and (resid 2 through 12 or resid 14...DD89 - 9189 - 91
413ALAALACYSCYS(chain D and (resid 2 through 12 or resid 14...DD93 - 9993 - 99
414ALAALALEULEU(chain D and (resid 2 through 12 or resid 14...DD101 - 103101 - 103
415VALVALARGARG(chain D and (resid 2 through 12 or resid 14...DD105 - 106105 - 106
416ALAALAPROPRO(chain D and (resid 2 through 12 or resid 14...DD108 - 116108 - 116
417ALAALAPHEPHE(chain D and (resid 2 through 12 or resid 14...DD118 - 134118 - 134
418LEULEUALAALA(chain D and (resid 2 through 12 or resid 14...DD136 - 143136 - 143
419LEULEUHISHIS(chain D and (resid 2 through 12 or resid 14...DD145 - 151145 - 151
420GLNGLNGLNGLN(chain D and (resid 2 through 12 or resid 14...DD153153
421PROPROALAALA(chain D and (resid 2 through 12 or resid 14...DD155 - 158155 - 158
422PHEPHETYRTYR(chain D and (resid 2 through 12 or resid 14...DD160 - 163160 - 163
423THRTHRTHRTHR(chain D and (resid 2 through 12 or resid 14...DD164164
424SERSERASPASP(chain D and (resid 2 through 12 or resid 14...DD2 - 3992 - 399
425SERSERASPASP(chain D and (resid 2 through 12 or resid 14...DD2 - 3992 - 399
426SERSERASPASP(chain D and (resid 2 through 12 or resid 14...DD2 - 3992 - 399
427SERSERASPASP(chain D and (resid 2 through 12 or resid 14...DD2 - 3992 - 399

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要素

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タンパク質 , 1種, 4分子 ABCD

#1: タンパク質
Anthranilate--CoA ligase


分子量: 44395.195 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Pseudomonas aeruginosa PAO1 (緑膿菌)
遺伝子: pqsA, PA0996 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9I4X3, anthranilate-CoA ligase

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非ポリマー , 6種, 2427分子

#2: 化合物
ChemComp-3UK / 5'-O-[(S)-[(2-aminobenzoyl)oxy](hydroxy)phosphoryl]adenosine


分子量: 466.342 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C17H19N6O8P
#3: 化合物
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


分子量: 106.120 Da / 分子数: 9 / 由来タイプ: 合成 / 式: C4H10O3
#4: 化合物
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


分子量: 62.068 Da / 分子数: 12 / 由来タイプ: 合成 / 式: C2H6O2
#5: 化合物 ChemComp-ACT / ACETATE ION


分子量: 59.044 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C2H3O2
#6: 化合物 ChemComp-PGE / TRIETHYLENE GLYCOL


分子量: 150.173 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C6H14O4
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 2400 / 由来タイプ: 天然 / 式: H2O

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.36 Å3/Da / 溶媒含有率: 47.92 %
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 / pH: 6.3
詳細: 100 mM tri-sodium citrate (pH 6.3), 200 mM ammonium acetate, 24.5% PEG3350

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: SLS / ビームライン: X06DA / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS 2M-F / 検出器: PIXEL / 日付: 2016年2月23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: 1.43→48.71 Å / Num. obs: 304224 / % possible obs: 100 % / 冗長度: 6.6 % / Biso Wilson estimate: 11.36 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.067 / Rrim(I) all: 0.173 / Net I/σ(I): 7.1
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.43-1.456.91.0080.6370.4131.092100
7.83-48.716.60.1020.9930.0420.1199.5

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解析

ソフトウェア
名称バージョン分類
Aimless0.5.23データスケーリング
PHENIX1.12rc2_2821精密化
PDB_EXTRACT3.22データ抽出
XDSデータ削減
PHASER位相決定
Coot0.8.8モデル構築
精密化構造決定の手法: 分子置換 / 解像度: 1.43→48.708 Å / SU ML: 0.16 / 交差検証法: FREE R-VALUE / σ(F): 1.99 / 位相誤差: 21.94
Rfactor反射数%反射
Rfree0.2158 14963 4.92 %
Rwork0.1896 --
obs0.1909 304155 99.98 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 101.19 Å2 / Biso mean: 17.0949 Å2 / Biso min: 3.55 Å2
精密化ステップサイクル: final / 解像度: 1.43→48.708 Å
タンパク質核酸リガンド溶媒全体
原子数12071 0 525 2402 14998
Biso mean--19.11 25.68 -
残基数----1574
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00413383
X-RAY DIFFRACTIONf_angle_d0.7418281
X-RAY DIFFRACTIONf_chiral_restr0.0691955
X-RAY DIFFRACTIONf_plane_restr0.0052511
X-RAY DIFFRACTIONf_dihedral_angle_d21.7195112
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A7379X-RAY DIFFRACTION6.947TORSIONAL
12B7379X-RAY DIFFRACTION6.947TORSIONAL
13C7379X-RAY DIFFRACTION6.947TORSIONAL
14D7379X-RAY DIFFRACTION6.947TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.43-1.44630.29995350.2746954910084
1.4463-1.46330.28625300.272956910099
1.4633-1.48110.27965140.2553959910113
1.4811-1.49990.27464850.25961210097
1.4999-1.51960.28464790.2489964310122
1.5196-1.54040.25665010.2382958510086
1.5404-1.56240.26285340.2318961410148
1.5624-1.58570.25984770.2305960210079
1.5857-1.61050.25324630.2227962810091
1.6105-1.63690.24714890.2174959910088
1.6369-1.66520.25055160.213960010116
1.6652-1.69540.24794750.2072969610171
1.6954-1.72810.23175140.2076956810082
1.7281-1.76330.22365000.2014960710107
1.7633-1.80170.22534940.1996960010094
1.8017-1.84360.22414960.1965965910155
1.8436-1.88970.21984600.1914966110121
1.8897-1.94080.21315330.1861959110124
1.9408-1.99790.22525100.1879958010090
1.9979-2.06240.20864880.1791967210160
2.0624-2.13610.20295030.1801961310116
2.1361-2.22160.19294890.1768969310182
2.2216-2.32270.19614810.1751966210143
2.3227-2.44520.20034920.169962110113
2.4452-2.59840.19434940.1741967010164
2.5984-2.7990.21045090.1803968210191
2.799-3.08060.20534810.175972710208
3.0806-3.52630.20094800.1722970910189
3.5263-4.44230.18675010.1636975010251
4.4423-48.73590.20085400.1836983110371
精密化 TLS

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

IDL11 (°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)
10.3198-0.0140.17790.20060.12310.1670.0648-0.030.13940.037-0.04930.0827-0.0598-0.0664-0.02420.09650.01580.03110.0624-0.01370.094913.90515.074917.9034
20.19320.01380.05520.2204-0.17170.14430.02810.02750.0528-0.0272-0.00190.1244-0.0009-0.10760.05930.08050.0150.00240.05610.00680.098111.5581-0.26637.9017
30.36060.087-0.04290.6886-0.05730.56850.01030.05060.0105-0.11760.03060.0311-0.0314-0.07150.00040.1015-0.0024-0.00310.05690.00320.072416.2568-6.67753.1071
40.34910.04640.15420.1825-0.10580.28410.0939-0.0171-0.06480.0142-0.0694-0.00940.07330.06820.00510.0831-0.0013-0.00590.0697-0.00050.059725.4418-7.776417.8253
50.2250.09050.16380.05650.01040.14590.0333-0.01610.05990.04510.0282-0.01440.00550.0620.00050.0859-0.00530.0180.061-0.01130.075526.8037.041613.0449
60.44020.0392-0.29230.0649-0.12270.38630.1092-0.0590.23310.0336-0.0522-0.0045-0.17210.08170.06990.1478-0.01790.04620.0601-0.00670.101939.202514.810211.8271
70.40720.0134-0.28730.1271-0.03570.24990.0278-0.1303-0.05090.0592-0.0427-0.03310.00390.1299-0.0010.0959-0.0152-0.01020.09520.00210.050839.50080.554525.0145
80.2819-0.02610.00430.2913-0.18780.225-0.0301-0.1048-0.07780.00330.0107-0.09750.07510.12290.00110.09660.0301-0.00970.10440.00860.095740.7373-14.191924.8981
90.2017-0.18690.04770.4149-0.18260.41340.13850.0345-0.20140.0159-0.0394-0.21850.12980.17550.04970.15620.0188-0.02870.13030.01390.127742.9444-11.335322.4361
100.2416-0.03370.21570.1697-0.09390.2470.06280.0350.2109-0.0457-0.0248-0.136-0.03810.11790.01040.1137-0.03240.03650.12020.00710.158254.60358.584251.423
110.12780.0984-0.07220.67410.26660.293-0.0305-0.10110.1510.11980.0753-0.1268-0.00020.15710.06630.0406-0.02690.00450.0923-0.0250.110156.42162.872162.0403
120.4948-0.07910.19440.5276-0.03660.2683-0.0136-0.10290.020.12670.0312-0.0522-0.06980.1117-0.02660.0897-0.00040.00370.1051-0.01460.086452.2616-2.989966.3576
130.15470.0188-0.04080.058-0.07030.0910.00960.0584-0.0274-0.0208-0.06050.0126-0.03240.0623-0.00010.05790.0116-0.00280.0763-0.00050.070642.7396-4.847251.8988
140.371-0.0830.10670.12640.16090.29610.0499-0.03390.160.03070.005-0.0342-0.03620.10380.03190.0658-0.01550.01370.0683-0.00070.093241.611910.004955.6425
150.7155-0.0896-0.3610.2890.07340.46060.19270.12820.2103-0.0863-0.0521-0.0676-0.2083-0.13260.32550.10210.00520.03930.04490.01560.082529.116312.262951.926
160.23530.09320.05880.1385-0.01580.137-0.07220.1316-0.0748-0.06920.0196-0.00510.0425-0.0434-0.0670.0869-0.0304-0.01290.1035-0.00570.071828.2099-11.512745.378
170.3690.23810.02710.25030.13020.27650.0425-0.095-0.12670.0020.04420.04840.0761-0.17640.02170.0932-0.0213-0.00510.13270.01140.091425.0516-7.84547.2097
180.73180.21560.15230.14540.01160.38220.0604-0.1203-0.4859-0.0741-0.0036-0.2527-0.01990.24110.25050.07260.0464-0.04050.02380.06090.148923.217539.268212.6264
190.6240.1145-0.13750.2831-0.13110.3111-0.03030.085-0.0405-0.08650.0218-0.03990.09610.0548-0.00010.10890.0019-0.00550.0689-0.00470.079819.538447.26982.6041
200.55490.3195-0.0590.1983-0.00660.30740.1039-0.2105-0.13430.0571-0.0948-0.07220.0534-0.00610.00650.0812-0.0169-0.01420.07670.01990.06619.103242.642816.986
210.1262-0.1473-0.13070.19210.17350.15790.25230.1134-0.5993-0.13620.00330.0480.0856-0.00820.56410.17690.0233-0.11130.1161-0.01660.30765.712928.02435.2216
220.6925-0.050.34460.1424-0.0730.26150.2056-0.2129-0.26980.0154-0.10940.03150.2169-0.10580.19770.1402-0.0354-0.04070.08120.02350.0741-4.832533.581419.4153
230.16570.0598-0.02030.1525-0.00350.1441-0.0313-0.10940.123-0.0477-0.00940.0695-0.0061-0.1238-0.04550.07790.01430.00970.1248-0.02550.0967-4.803356.379624.3146
240.3732-0.2501-0.02830.3059-0.10060.08530.04470.02340.11340.01220.0170.0903-0.0769-0.17810.00330.1123-0.0130.01160.1126-0.01230.091-7.924352.811322.4168
250.2117-0.1477-0.05210.2501-0.04540.21730.06230.0474-0.2675-0.0827-0.00160.15060.1057-0.10820.05450.0867-0.024-0.04220.08850.00090.140846.580240.120250.8558
260.44820.04320.07360.3635-0.22510.1618-0.0336-0.0916-0.18780.05180.09210.13740.0739-0.08260.05950.0767-0.0132-0.00230.09350.02710.129944.287245.413761.3865
270.5095-0.42270.23920.3448-0.28270.3531-0.085-0.2092-0.0710.1140.1169-0.02590.0142-0.0349-0.00730.07010.0189-0.0110.0973-0.00110.065253.930752.984166.419
280.4519-0.0653-0.19390.69240.07880.2849-0.0042-0.1426-0.00790.17940.01870.06640.0969-0.0401-0.01970.1375-0.00090.00510.16820.03580.120844.575949.223167.0873
290.3371-0.24270.06220.204-0.07870.04270.0542-0.0067-0.01710.0123-0.0154-0.0220.002-0.07340.00940.0698-0.0037-0.00620.0662-0.00810.063759.563546.940152.5503
300.39190.02650.18420.2081-0.13650.18210.1446-0.035-0.2567-0.0038-0.04560.06610.08510.00470.1670.0973-0.0033-0.05520.06170.00430.123367.880332.979556.8781
310.2464-0.03890.2160.2092-0.08310.16530.06550.1079-0.0561-0.0422-0.0116-0.02660.06280.16320.01980.08190.0313-0.00320.1049-0.01970.059572.291645.29344.4133
320.23030.0758-0.05660.16590.05240.1316-0.03060.08330.0964-0.05530.0132-0.0404-0.10780.1124-0.05840.0838-0.01820.01730.1410.00780.081473.204160.639945.4634
330.24110.1867-0.00890.2149-0.08420.14620.01640.0080.09550.06930.0165-0.1431-0.09480.23750.00190.0699-0.0199-0.01020.1317-0.00010.087675.993257.050747.4635
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 27 )A2 - 27
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 63 )A28 - 63
3X-RAY DIFFRACTION3chain 'A' and (resid 64 through 157 )A64 - 157
4X-RAY DIFFRACTION4chain 'A' and (resid 158 through 189 )A158 - 189
5X-RAY DIFFRACTION5chain 'A' and (resid 190 through 235 )A190 - 235
6X-RAY DIFFRACTION6chain 'A' and (resid 236 through 293 )A236 - 293
7X-RAY DIFFRACTION7chain 'A' and (resid 294 through 335 )A294 - 335
8X-RAY DIFFRACTION8chain 'A' and (resid 336 through 366 )A336 - 366
9X-RAY DIFFRACTION9chain 'A' and (resid 367 through 399 )A367 - 399
10X-RAY DIFFRACTION10chain 'B' and (resid 2 through 27 )B2 - 27
11X-RAY DIFFRACTION11chain 'B' and (resid 28 through 63 )B28 - 63
12X-RAY DIFFRACTION12chain 'B' and (resid 64 through 157 )B64 - 157
13X-RAY DIFFRACTION13chain 'B' and (resid 158 through 189 )B158 - 189
14X-RAY DIFFRACTION14chain 'B' and (resid 190 through 235 )B190 - 235
15X-RAY DIFFRACTION15chain 'B' and (resid 236 through 335 )B236 - 335
16X-RAY DIFFRACTION16chain 'B' and (resid 336 through 366 )B336 - 366
17X-RAY DIFFRACTION17chain 'B' and (resid 367 through 399 )B367 - 399
18X-RAY DIFFRACTION18chain 'C' and (resid 2 through 63 )C2 - 63
19X-RAY DIFFRACTION19chain 'C' and (resid 64 through 155 )C64 - 155
20X-RAY DIFFRACTION20chain 'C' and (resid 156 through 223 )C156 - 223
21X-RAY DIFFRACTION21chain 'C' and (resid 224 through 246 )C224 - 246
22X-RAY DIFFRACTION22chain 'C' and (resid 247 through 335 )C247 - 335
23X-RAY DIFFRACTION23chain 'C' and (resid 336 through 366 )C336 - 366
24X-RAY DIFFRACTION24chain 'C' and (resid 367 through 399 )C367 - 399
25X-RAY DIFFRACTION25chain 'D' and (resid 2 through 27 )D2 - 27
26X-RAY DIFFRACTION26chain 'D' and (resid 28 through 63 )D28 - 63
27X-RAY DIFFRACTION27chain 'D' and (resid 64 through 106 )D64 - 106
28X-RAY DIFFRACTION28chain 'D' and (resid 107 through 157 )D107 - 157
29X-RAY DIFFRACTION29chain 'D' and (resid 158 through 209 )D158 - 209
30X-RAY DIFFRACTION30chain 'D' and (resid 210 through 293 )D210 - 293
31X-RAY DIFFRACTION31chain 'D' and (resid 294 through 335 )D294 - 335
32X-RAY DIFFRACTION32chain 'D' and (resid 336 through 366 )D336 - 366
33X-RAY DIFFRACTION33chain 'D' and (resid 367 through 399 )D367 - 399

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万見について

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お知らせ

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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

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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

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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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

他の情報も見る