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- PDB-7fea: PY14 in complex with Col-D -

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基本情報

登録情報
データベース: PDB / ID: 7fea
タイトルPY14 in complex with Col-D
要素Acetyl-CoA C-acyltransferase
キーワードTRANSFERASE / Acetyl-CoA acetyltransferase
機能・相同性
機能・相同性情報


acyltransferase activity, transferring groups other than amino-acyl groups
類似検索 - 分子機能
Thiolase, active site / Thiolases active site. / Thiolase, conserved site / Thiolases signature 2. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase-like
類似検索 - ドメイン・相同性
Chem-3KI / Acetyl-CoA C-acyltransferase
類似検索 - 構成要素
生物種Massilia sp. YMA4 (バクテリア)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.4 Å
データ登録者Lin, C.C. / Ko, T.P. / Huang, K.F. / Yang, Y.L.
資金援助 台湾, 1件
組織認可番号国
Academia Sinica (Taiwan)MOST 104-2320-B-001-019-MY2 台湾
引用ジャーナル: Commun Biol / 年: 2022
タイトル: Integrated omics approach to unveil antifungal bacterial polyynes as acetyl-CoA acetyltransferase inhibitors.
著者: Lin, C.C. / Hoo, S.Y. / Ma, L.T. / Lin, C. / Huang, K.F. / Ho, Y.N. / Sun, C.H. / Lee, H.J. / Chen, P.Y. / Shu, L.J. / Wang, B.W. / Hsu, W.C. / Ko, T.P. / Yang, Y.L.
履歴
登録2021年7月19日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02022年7月27日Provider: repository / タイプ: Initial release
改定 1.12022年10月19日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22023年11月29日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

ダウンロードとリンク

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集合体

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


分子量 (理論値)分子数
合計 (水以外)171,5358
ポリマ－170,4294
非ポリマー1,1054
水30,1031671
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • 根拠: gel filtration
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area14900 Å2
ΔGint-78 kcal/mol
Surface area50430 Å2
手法PISA
単位格子
Length a, b, c (Å)66.943, 77.741, 98.117
Angle α, β, γ (deg.)70.758, 81.781, 64.995
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
41

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
11VALVALPHEPHE(chain 'A' and (resid 2 through 19 or resid 21...AA2 - 192 - 19
12GLYGLYLEULEU(chain 'A' and (resid 2 through 19 or resid 21...AA21 - 4021 - 40
13ARGARGILEILE(chain 'A' and (resid 2 through 19 or resid 21...AA42 - 10442 - 104
14SERSERASNASN(chain 'A' and (resid 2 through 19 or resid 21...AA106 - 119106 - 119
15ASPASPLEULEU(chain 'A' and (resid 2 through 19 or resid 21...AA121 - 126121 - 126
16PROPROPROPRO(chain 'A' and (resid 2 through 19 or resid 21...AA128128
17LEULEUARGARG(chain 'A' and (resid 2 through 19 or resid 21...AA130 - 135130 - 135
18GLYGLYSERSER(chain 'A' and (resid 2 through 19 or resid 21...AA137 - 155137 - 155
19GLNGLNARGARG(chain 'A' and (resid 2 through 19 or resid 21...AA157 - 174157 - 174
110ALAALAASPASP(chain 'A' and (resid 2 through 19 or resid 21...AA176 - 178176 - 178
111PHEPHETHRTHR(chain 'A' and (resid 2 through 19 or resid 21...AA180 - 183180 - 183
112GLNGLNGLNGLN(chain 'A' and (resid 2 through 19 or resid 21...AA185185
113ARGARGPROPRO(chain 'A' and (resid 2 through 19 or resid 21...AA187 - 203187 - 203
114THRTHRPROPRO(chain 'A' and (resid 2 through 19 or resid 21...AA205 - 223205 - 223
115THRTHRARGARG(chain 'A' and (resid 2 through 19 or resid 21...AA225 - 238225 - 238
116GLYGLYLEULEU(chain 'A' and (resid 2 through 19 or resid 21...AA241 - 271241 - 271
117PROPROLEULEU(chain 'A' and (resid 2 through 19 or resid 21...AA273 - 275273 - 275
118ILEILELEULEU(chain 'A' and (resid 2 through 19 or resid 21...AA277 - 302277 - 302
119ALAALATRPTRP(chain 'A' and (resid 2 through 19 or resid 21...AA305 - 307305 - 307
120VALVALASPASP(chain 'A' and (resid 2 through 19 or resid 21...AA309 - 330309 - 330
121LEULEUPROPRO(chain 'A' and (resid 2 through 19 or resid 21...AA332 - 336332 - 336
122ARGARGGLYGLY(chain 'A' and (resid 2 through 19 or resid 21...AA338 - 353338 - 353
123GLYGLYTHRTHR(chain 'A' and (resid 2 through 19 or resid 21...AA356 - 361356 - 361
124VALVALGLUGLU(chain 'A' and (resid 2 through 19 or resid 21...AA363 - 372363 - 372
125ARGARGLEULEU(chain 'A' and (resid 2 through 19 or resid 21...AA374 - 379374 - 379
126GLYGLYLEULEU(chain 'A' and (resid 2 through 19 or resid 21...AA383 - 396383 - 396
1273KI3KI3KI3KI(chain 'A' and (resid 2 through 19 or resid 21...AE501
21VALVALPHEPHE(chain 'B' and (resid 2 through 19 or resid 21...BB2 - 192 - 19
22GLYGLYLEULEU(chain 'B' and (resid 2 through 19 or resid 21...BB21 - 4021 - 40
23ARGARGILEILE(chain 'B' and (resid 2 through 19 or resid 21...BB42 - 10442 - 104
24SERSERASNASN(chain 'B' and (resid 2 through 19 or resid 21...BB106 - 119106 - 119
25ASPASPLEULEU(chain 'B' and (resid 2 through 19 or resid 21...BB121 - 126121 - 126
26PROPROPROPRO(chain 'B' and (resid 2 through 19 or resid 21...BB128128
27LEULEUARGARG(chain 'B' and (resid 2 through 19 or resid 21...BB130 - 135130 - 135
28GLYGLYSERSER(chain 'B' and (resid 2 through 19 or resid 21...BB137 - 155137 - 155
29GLNGLNARGARG(chain 'B' and (resid 2 through 19 or resid 21...BB157 - 174157 - 174
210ALAALAASPASP(chain 'B' and (resid 2 through 19 or resid 21...BB176 - 178176 - 178
211PHEPHETHRTHR(chain 'B' and (resid 2 through 19 or resid 21...BB180 - 183180 - 183
212GLNGLNGLNGLN(chain 'B' and (resid 2 through 19 or resid 21...BB185185
213ARGARGPROPRO(chain 'B' and (resid 2 through 19 or resid 21...BB187 - 203187 - 203
214THRTHRPROPRO(chain 'B' and (resid 2 through 19 or resid 21...BB205 - 223205 - 223
215THRTHRARGARG(chain 'B' and (resid 2 through 19 or resid 21...BB225 - 238225 - 238
216GLYGLYLEULEU(chain 'B' and (resid 2 through 19 or resid 21...BB241 - 271241 - 271
217PROPROLEULEU(chain 'B' and (resid 2 through 19 or resid 21...BB273 - 275273 - 275
218ILEILELEULEU(chain 'B' and (resid 2 through 19 or resid 21...BB277 - 302277 - 302
219ALAALATRPTRP(chain 'B' and (resid 2 through 19 or resid 21...BB305 - 307305 - 307
220VALVALASPASP(chain 'B' and (resid 2 through 19 or resid 21...BB309 - 330309 - 330
221LEULEUPROPRO(chain 'B' and (resid 2 through 19 or resid 21...BB332 - 336332 - 336
222ARGARGGLYGLY(chain 'B' and (resid 2 through 19 or resid 21...BB338 - 353338 - 353
223GLYGLYTHRTHR(chain 'B' and (resid 2 through 19 or resid 21...BB356 - 361356 - 361
224VALVALGLUGLU(chain 'B' and (resid 2 through 19 or resid 21...BB363 - 372363 - 372
225ARGARGLEULEU(chain 'B' and (resid 2 through 19 or resid 21...BB374 - 379374 - 379
226GLYGLYLEULEU(chain 'B' and (resid 2 through 19 or resid 21...BB383 - 396383 - 396
2273KI3KI3KI3KI(chain 'B' and (resid 2 through 19 or resid 21...BF501
31VALVALPHEPHE(chain 'C' and (resid 2 through 19 or resid 21...CC2 - 192 - 19
32GLYGLYLEULEU(chain 'C' and (resid 2 through 19 or resid 21...CC21 - 4021 - 40
33ARGARGILEILE(chain 'C' and (resid 2 through 19 or resid 21...CC42 - 10442 - 104
34SERSERASNASN(chain 'C' and (resid 2 through 19 or resid 21...CC106 - 119106 - 119
35ASPASPLEULEU(chain 'C' and (resid 2 through 19 or resid 21...CC121 - 126121 - 126
36PROPROPROPRO(chain 'C' and (resid 2 through 19 or resid 21...CC128128
37LEULEUARGARG(chain 'C' and (resid 2 through 19 or resid 21...CC130 - 135130 - 135
38GLYGLYSERSER(chain 'C' and (resid 2 through 19 or resid 21...CC137 - 155137 - 155
39GLNGLNARGARG(chain 'C' and (resid 2 through 19 or resid 21...CC157 - 174157 - 174
310ALAALAASPASP(chain 'C' and (resid 2 through 19 or resid 21...CC176 - 178176 - 178
311PHEPHETHRTHR(chain 'C' and (resid 2 through 19 or resid 21...CC180 - 183180 - 183
312GLNGLNGLNGLN(chain 'C' and (resid 2 through 19 or resid 21...CC185185
313ARGARGPROPRO(chain 'C' and (resid 2 through 19 or resid 21...CC187 - 203187 - 203
314THRTHRPROPRO(chain 'C' and (resid 2 through 19 or resid 21...CC205 - 223205 - 223
315THRTHRARGARG(chain 'C' and (resid 2 through 19 or resid 21...CC225 - 238225 - 238
316GLYGLYLEULEU(chain 'C' and (resid 2 through 19 or resid 21...CC241 - 271241 - 271
317PROPROLEULEU(chain 'C' and (resid 2 through 19 or resid 21...CC273 - 275273 - 275
318ILEILELEULEU(chain 'C' and (resid 2 through 19 or resid 21...CC277 - 302277 - 302
319ALAALATRPTRP(chain 'C' and (resid 2 through 19 or resid 21...CC305 - 307305 - 307
320VALVALASPASP(chain 'C' and (resid 2 through 19 or resid 21...CC309 - 330309 - 330
321LEULEUPROPRO(chain 'C' and (resid 2 through 19 or resid 21...CC332 - 336332 - 336
322ARGARGGLYGLY(chain 'C' and (resid 2 through 19 or resid 21...CC338 - 353338 - 353
323GLYGLYTHRTHR(chain 'C' and (resid 2 through 19 or resid 21...CC356 - 361356 - 361
324VALVALGLUGLU(chain 'C' and (resid 2 through 19 or resid 21...CC363 - 372363 - 372
325ARGARGLEULEU(chain 'C' and (resid 2 through 19 or resid 21...CC374 - 379374 - 379
326GLYGLYLEULEU(chain 'C' and (resid 2 through 19 or resid 21...CC383 - 396383 - 396
3273KI3KI3KI3KI(chain 'C' and (resid 2 through 19 or resid 21...CG501
41VALVALPHEPHE(chain 'D' and (resid 2 through 19 or resid 21...DD2 - 192 - 19
42GLYGLYLEULEU(chain 'D' and (resid 2 through 19 or resid 21...DD21 - 4021 - 40
43ARGARGILEILE(chain 'D' and (resid 2 through 19 or resid 21...DD42 - 10442 - 104
44SERSERASNASN(chain 'D' and (resid 2 through 19 or resid 21...DD106 - 119106 - 119
45ASPASPLEULEU(chain 'D' and (resid 2 through 19 or resid 21...DD121 - 126121 - 126
46PROPROPROPRO(chain 'D' and (resid 2 through 19 or resid 21...DD128128
47LEULEUARGARG(chain 'D' and (resid 2 through 19 or resid 21...DD130 - 135130 - 135
48GLYGLYSERSER(chain 'D' and (resid 2 through 19 or resid 21...DD137 - 155137 - 155
49GLNGLNARGARG(chain 'D' and (resid 2 through 19 or resid 21...DD157 - 174157 - 174
410ALAALAASPASP(chain 'D' and (resid 2 through 19 or resid 21...DD176 - 178176 - 178
411PHEPHETHRTHR(chain 'D' and (resid 2 through 19 or resid 21...DD180 - 183180 - 183
412GLNGLNGLNGLN(chain 'D' and (resid 2 through 19 or resid 21...DD185185
413ARGARGPROPRO(chain 'D' and (resid 2 through 19 or resid 21...DD187 - 203187 - 203
414THRTHRPROPRO(chain 'D' and (resid 2 through 19 or resid 21...DD205 - 223205 - 223
415THRTHRARGARG(chain 'D' and (resid 2 through 19 or resid 21...DD225 - 238225 - 238
416GLYGLYLEULEU(chain 'D' and (resid 2 through 19 or resid 21...DD241 - 271241 - 271
417PROPROLEULEU(chain 'D' and (resid 2 through 19 or resid 21...DD273 - 275273 - 275
418ILEILELEULEU(chain 'D' and (resid 2 through 19 or resid 21...DD277 - 302277 - 302
419ALAALATRPTRP(chain 'D' and (resid 2 through 19 or resid 21...DD305 - 307305 - 307
420VALVALASPASP(chain 'D' and (resid 2 through 19 or resid 21...DD309 - 330309 - 330
421LEULEUPROPRO(chain 'D' and (resid 2 through 19 or resid 21...DD332 - 336332 - 336
422ARGARGGLYGLY(chain 'D' and (resid 2 through 19 or resid 21...DD338 - 353338 - 353
423GLYGLYTHRTHR(chain 'D' and (resid 2 through 19 or resid 21...DD356 - 361356 - 361
424VALVALGLUGLU(chain 'D' and (resid 2 through 19 or resid 21...DD363 - 372363 - 372
425ARGARGLEULEU(chain 'D' and (resid 2 through 19 or resid 21...DD374 - 379374 - 379
426GLYGLYLEULEU(chain 'D' and (resid 2 through 19 or resid 21...DD383 - 396383 - 396
4273KI3KI3KI3KI(chain 'D' and (resid 2 through 19 or resid 21...DH501

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要素

#1: タンパク質
Acetyl-CoA C-acyltransferase


分子量: 42607.332 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Massilia sp. YMA4 (バクテリア) / 遺伝子: DPH57_23275 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: A0A7U5Y2I6
#2: 化合物
ChemComp-3KI / (6~{R},7~{R},9~{E})-6,7-bis(oxidanyl)hexadeca-9,15-dien-11,13-diynoic acid


分子量: 276.328 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C16H20O4 / タイプ: SUBJECT OF INVESTIGATION
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1671 / 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

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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: 2.64 Å3/Da / 溶媒含有率: 53.41 %
結晶化温度: 283 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.5
詳細: 0.2 M sodium malonate, 20% (w/v) polyethylene glycol 3350, 0.1 M Bis-tris propane pH 6.5

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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 MX300HE / 検出器: CCD / 日付: 2020年8月30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: 1.4→30 Å / Num. obs: 314912 / % possible obs: 94.8 % / 冗長度: 2.9 % / Biso Wilson estimate: 13.93 Å2 / CC1/2: 0.914 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.04 / Net I/σ(I): 16.3
反射 シェル解像度: 1.4→1.45 Å / 冗長度: 2.5 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 2 / Num. unique obs: 28574 / CC1/2: 0.727 / Rpim(I) all: 0.404 / % possible all: 86

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解析

ソフトウェア
名称バージョン分類
PHENIX1.17.1_3660精密化
PHASER位相決定
HKL-2000データ収集
HKL-2000データスケーリング
HKL-2000データ削減
精密化構造決定の手法: 分子置換
開始モデル: 4N44

4n44


解像度: 1.4→27.16 Å / SU ML: 0.1123 / 交差検証法: FREE R-VALUE / σ(F): 1.67 / 位相誤差: 17.1931
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.1627 1296 -
Rwork0.1463 290747 -
obs0.1464 292742 88.03 %
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Biso mean: 21.53 Å2
精密化ステップサイクル: LAST / 解像度: 1.4→27.16 Å
タンパク質核酸リガンド溶媒全体
原子数11679 0 0 1671 13350
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONbond angles1.53
X-RAY DIFFRACTIONbond lengths0.0153
LS精密化 シェル解像度: 1.4→1.45 Å
Rfactor反射数%反射
Rfree0.254 116 -
Rwork0.212 17072 -
obs--51.3 %
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)
1-0.01288235758560.04983656155570.1140220571260.3806767764730.01018932887510.243523542606-0.005316189740860.0038893251993-0.0193047223829-0.004493579319970.0266839335257-0.0256357309389-0.01047798928770.0527114104750.0276878861830.06803430515690.005788026922930.01441420173750.100442559157-0.007612997394760.10674604939-54.165736438-57.0986763863-105.058191786
20.02405600487820.0734561394274-0.02869428836930.222087514267-0.1258095916220.261295154544-0.00371464265903-0.14169296486-0.04708841979410.134178685550.0202339182185-0.03450852181840.06914512209660.02353362252336.78687984216E-60.1161613531410.0315747673697-0.009952970573060.132059808584-0.01036381971320.138653479473-57.301643768-69.0344306136-93.0329736428
30.1860341554860.2386583790060.07719539783790.41491425280.01627612477790.486790286463-0.0184772689366-0.00483800903522-0.0392412856474-0.0515040695810.062825603175-0.03830868769420.08286964740420.03702727560760.02647928001540.08547616618430.02164334562960.01412578957370.0919658419964-0.01704232638410.109482772757-56.1148853171-69.7775320538-113.624391586
40.379747996524-0.1247618804110.2935681519560.297706265325-0.1585880805160.2344596359550.0354731398666-1.90161109768E-5-0.0351915193717-0.00389256202202-0.000469926240210.04751536456840.0387248116072-0.0776112258484-6.05400026844E-50.107318292661-0.008540312158550.01644828414960.1242667626490.009344752817820.10078882598-75.4971098828-44.0227567647-58.94877482
5-0.0944917168438-0.01190425456730.06086097288040.246172890413-0.1310706881290.3039109830830.00537450561624-0.00631326049587-0.00409757070883-0.00845357382607-0.0330519363629-0.0302070162572-0.0193134838520.0432084312312-3.64393803594E-50.08733853864220.0002720941334620.005501675586440.1249596538380.001821185306110.102212500031-62.8422821809-34.1138672638-66.366753332
60.0632383097082-0.131638681784-0.009231750686720.222946244258-0.0498044014320.151164287879-0.01391764799010.0503423229181-0.1428189218010.03096038488720.0229367234797-0.05889234177170.2073087148210.0502900304160.0008079096591890.1844290561980.00312121638562-0.02389640225210.137080875940.002526859770530.15372134323-58.8014982511-54.8769597924-56.4807032821
70.00522055496804-0.008701503735020.03508951321980.0241785688682-0.01681930499590.1127641383390.03835107553620.202904128347-0.145227427804-0.02193908208810.0407934346791-0.1205557247330.2860631420460.1027097417450.003119982492340.1330113026660.06642125167010.004144642779850.229464716269-0.009269219681880.216034665101-44.9301210096-49.2346486075-62.1861477768
80.307561758315-0.1613920204850.2056021216780.3352572451720.01405697338130.430065498553-0.00464065681753-0.00307437486442-0.01191564114450.1223020463460.00816944040379-0.0721047436376-0.0006680246666960.02040021858110.0004730256004970.147702614313-0.00949151346556-0.01172973310730.1246264663190.01126282637590.0993029463798-60.7128922025-38.9955658944-47.3697789671
90.080882990339-0.1003172390390.04345362237910.235391685915-0.1936181825690.116359542202-0.0181470761475-0.005814401557690.02158030417681.18333383725E-5-0.00261748065837-0.00610180280016-0.04443948789060.0109532133931-7.70316338128E-60.100922865550.00504591945099-0.006458197361530.101981964467-0.01036913766160.101301539862-72.2600961613-24.9266821862-69.8968787871
100.292737519848-0.03606859591070.3648018614950.389052975023-0.1967069304670.674189228354-0.0429297000007-0.04534495817670.05906710910940.0007424382169670.03475898719780.0633920702873-0.102742564496-0.1233713703620.003071144075630.1190186534490.0366663501813-0.003587409239270.119776817273-0.01068051414490.135829613027-85.7775760776-15.7305177679-71.8507466188
110.04841725201430.008579117327350.01019759012990.344215125259-0.00398520769837-0.0705059634217-0.04449946146760.01429588330860.00679215756905-0.06037015864280.02925050371770.0262944785238-0.05541367809480.014091959322-0.00643285065930.0955508282641-0.0221846951021-0.0006538642416440.08817380480560.00368996224640.0814180808682-56.5421329377-40.8828315156-112.135646509
120.3843320480340.2541832480660.1385777431540.623077408420.2409311791540.20367641806-0.09829187847290.05719379800710.0615549971435-0.1424751958050.0861842282389-0.00487807303919-0.08281797103090.0454515338659-0.009948222468960.150247751434-0.053020381593-0.004649081067880.1111669584030.02217030936580.0874792885588-49.1015102426-28.9354112213-120.836953595
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 193 )
2X-RAY DIFFRACTION2chain 'A' and (resid 194 through 242 )
3X-RAY DIFFRACTION3chain 'A' and (resid 243 through 396 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 74 )
5X-RAY DIFFRACTION5chain 'B' and (resid 75 through 173 )
6X-RAY DIFFRACTION6chain 'B' and (resid 174 through 215 )
7X-RAY DIFFRACTION7chain 'B' and (resid 216 through 242 )
8X-RAY DIFFRACTION8chain 'B' and (resid 243 through 397 )
9X-RAY DIFFRACTION9chain 'C' and (resid 2 through 173 )
10X-RAY DIFFRACTION10chain 'C' and (resid 174 through 397 )
11X-RAY DIFFRACTION11chain 'D' and (resid 2 through 173 )
12X-RAY DIFFRACTION12chain 'D' and (resid 174 through 397 )

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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://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

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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