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- PDB-8e2s: Crystal structure of TadAC-1.19 -

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基本情報

登録情報
データベース: PDB / ID: 8e2s
タイトルCrystal structure of TadAC-1.19
要素tRNA-specific adenosine deaminase 1.19
キーワードDNA BINDING PROTEIN (DNA結合タンパク質) / deaminase (脱アミノ) / TadAC
機能・相同性
機能・相同性情報


tRNA(adenine34) deaminase / tRNA wobble adenosine to inosine editing / tRNA-specific adenosine-34 deaminase activity / zinc ion binding
類似検索 - 分子機能
MafB19-like deaminase / tRNA-specific adenosine deaminase / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like
類似検索 - ドメイン・相同性
tRNA-specific adenosine deaminase
類似検索 - 構成要素
生物種Escherichia coli (大腸菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.95 Å
データ登録者Feliciano, P.R. / Lee, S.J. / Ciaramella, G.
資金援助1件
組織認可番号国
Other private
引用ジャーナル: Nat.Biotechnol. / 年: 2023
タイトル: Improved cytosine base editors generated from TadA variants.
著者: Lam, D.K. / Feliciano, P.R. / Arif, A. / Bohnuud, T. / Fernandez, T.P. / Gehrke, J.M. / Grayson, P. / Lee, K.D. / Ortega, M.A. / Sawyer, C. / Schwaegerle, N.D. / Peraro, L. / Young, L. / Lee, ...著者: Lam, D.K. / Feliciano, P.R. / Arif, A. / Bohnuud, T. / Fernandez, T.P. / Gehrke, J.M. / Grayson, P. / Lee, K.D. / Ortega, M.A. / Sawyer, C. / Schwaegerle, N.D. / Peraro, L. / Young, L. / Lee, S.J. / Ciaramella, G. / Gaudelli, N.M.
履歴
登録2022年8月15日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02023年1月11日Provider: repository / タイプ: Initial release
改定 1.12023年2月8日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
改定 1.22023年5月31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
改定 1.32023年10月25日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: tRNA-specific adenosine deaminase 1.19
B: tRNA-specific adenosine deaminase 1.19
C: tRNA-specific adenosine deaminase 1.19
D: tRNA-specific adenosine deaminase 1.19
E: tRNA-specific adenosine deaminase 1.19
F: tRNA-specific adenosine deaminase 1.19
G: tRNA-specific adenosine deaminase 1.19
H: tRNA-specific adenosine deaminase 1.19
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)149,85616
ポリマ－149,3328
非ポリマー5238
水88349
1
A: tRNA-specific adenosine deaminase 1.19
B: tRNA-specific adenosine deaminase 1.19
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)37,4644
ポリマ－37,3332
非ポリマー1312
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-100 kcal/mol
Surface area13630 Å2
手法PISA
2
C: tRNA-specific adenosine deaminase 1.19
D: tRNA-specific adenosine deaminase 1.19
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)37,4644
ポリマ－37,3332
非ポリマー1312
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-102 kcal/mol
Surface area12810 Å2
手法PISA
3
E: tRNA-specific adenosine deaminase 1.19
F: tRNA-specific adenosine deaminase 1.19
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)37,4644
ポリマ－37,3332
非ポリマー1312
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-105 kcal/mol
Surface area13020 Å2
手法PISA
4
G: tRNA-specific adenosine deaminase 1.19
H: tRNA-specific adenosine deaminase 1.19
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)37,4644
ポリマ－37,3332
非ポリマー1312
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-103 kcal/mol
Surface area12840 Å2
手法PISA
単位格子
Length a, b, c (Å)59.495, 63.396, 95.169
Angle α, β, γ (deg.)87.890, 82.820, 77.140
Int Tables number1
Space group name H-MP1
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and ((resid 6 and (name N or name...
21(chain B and ((resid 6 and (name N or name...
31(chain C and ((resid 6 and (name N or name...
41(chain D and ((resid 6 and (name N or name...
51(chain G and ((resid 6 and (name N or name...
61(chain H and ((resid 6 and (name N or name...
71(chain E and (resid 6 through 20 or (resid 22...
81(chain F and ((resid 6 and (name N or name...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and ((resid 6 and (name N or name...A6
121(chain A and ((resid 6 and (name N or name...A3 - 155
131(chain A and ((resid 6 and (name N or name...A3 - 155
141(chain A and ((resid 6 and (name N or name...A3 - 155
151(chain A and ((resid 6 and (name N or name...A3 - 155
211(chain B and ((resid 6 and (name N or name...B6
221(chain B and ((resid 6 and (name N or name...B1 - 151
231(chain B and ((resid 6 and (name N or name...B1 - 151
241(chain B and ((resid 6 and (name N or name...B1 - 151
251(chain B and ((resid 6 and (name N or name...B1 - 151
311(chain C and ((resid 6 and (name N or name...C6
321(chain C and ((resid 6 and (name N or name...C6 - 155
331(chain C and ((resid 6 and (name N or name...C6 - 155
341(chain C and ((resid 6 and (name N or name...C6 - 155
351(chain C and ((resid 6 and (name N or name...C6 - 155
411(chain D and ((resid 6 and (name N or name...D6
421(chain D and ((resid 6 and (name N or name...D6 - 151
431(chain D and ((resid 6 and (name N or name...D6 - 151
441(chain D and ((resid 6 and (name N or name...D6 - 151
451(chain D and ((resid 6 and (name N or name...D6 - 151
511(chain G and ((resid 6 and (name N or name...G6
521(chain G and ((resid 6 and (name N or name...G6 - 151
531(chain G and ((resid 6 and (name N or name...G6 - 151
541(chain G and ((resid 6 and (name N or name...G6 - 151
551(chain G and ((resid 6 and (name N or name...G6 - 151
611(chain H and ((resid 6 and (name N or name...H6
621(chain H and ((resid 6 and (name N or name...H4 - 155
631(chain H and ((resid 6 and (name N or name...H4 - 155
641(chain H and ((resid 6 and (name N or name...H4 - 155
651(chain H and ((resid 6 and (name N or name...H4 - 155
711(chain J and (resid 6 through 20 or (resid 22...E6 - 20
721(chain J and (resid 6 through 20 or (resid 22...E22 - 26
731(chain J and (resid 6 through 20 or (resid 22...E0
741(chain J and (resid 6 through 20 or (resid 22...E0
751(chain J and (resid 6 through 20 or (resid 22...E0
761(chain J and (resid 6 through 20 or (resid 22...E0
811(chain K and ((resid 6 and (name N or name...F6
821(chain K and ((resid 6 and (name N or name...F0
831(chain K and ((resid 6 and (name N or name...F0
841(chain K and ((resid 6 and (name N or name...F0
851(chain K and ((resid 6 and (name N or name...F0

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要素

#1: タンパク質
tRNA-specific adenosine deaminase 1.19


分子量: 18666.555 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) / 遺伝子: tadA / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: W8T8U5, tRNA(adenine34) deaminase
#2: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 8 / 由来タイプ: 合成 / 式: Zn / タイプ: SUBJECT OF INVESTIGATION
#3: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 49 / 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: 2.32 Å3/Da / 溶媒含有率: 47.1 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: PEG 3,350, ammonium citrate tribasic pH 7.0)

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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: PETRA III, EMBL c/o DESY / ビームライン: P13 (MX1) / 波長: 0.97626 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2021年8月21日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.97626 Å / 相対比: 1
反射解像度: 2.95→51.88 Å / Num. obs: 27706 / % possible obs: 98 % / 冗長度: 2 % / CC1/2: 0.918 / Net I/σ(I): 2.9
反射 シェル解像度: 2.95→3.03 Å / Num. unique obs: 2043 / CC1/2: 0.771

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19.2_4158精密化
PDB_EXTRACT3.27データ抽出
XDSデータ削減
Aimlessデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 8E2P

8e2p


解像度: 2.95→51.49 Å / SU ML: 0.32 / 交差検証法: THROUGHOUT / σ(F): 1.96 / 位相誤差: 28.39 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2607 1363 4.96 %
Rwork0.2186 26130 -
obs0.2207 27493 96.98 %
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 max: 97.87 Å2 / Biso mean: 32.6496 Å2 / Biso min: 16.55 Å2
精密化ステップサイクル: final / 解像度: 2.95→51.49 Å
タンパク質核酸リガンド溶媒全体
原子数8995 0 8 49 9052
Biso mean--27.7 23.57 -
残基数----1199
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A3272X-RAY DIFFRACTION3.092TORSIONAL
12B3272X-RAY DIFFRACTION3.092TORSIONAL
13C3272X-RAY DIFFRACTION3.092TORSIONAL
14D3272X-RAY DIFFRACTION3.092TORSIONAL
15G3272X-RAY DIFFRACTION3.092TORSIONAL
16H3272X-RAY DIFFRACTION3.092TORSIONAL
17E3272X-RAY DIFFRACTION3.092TORSIONAL
18F3272X-RAY DIFFRACTION3.092TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.95-3.050.36981430.29982488263193
3.05-3.180.32411500.27062565271595
3.18-3.320.3261290.25552606273596
3.32-3.50.27891430.23452590273396
3.5-3.710.27891390.21322611275097
3.71-40.23481240.19752663278799
4-4.40.21841360.19292627276399
4.4-5.040.23331300.18792699282999
5.04-6.350.24941450.21832645279098
6.35-51.490.18441240.20392636276098
精密化 TLS手法: refined / Origin x: -23.276 Å / Origin y: -47.803 Å / Origin z: 12.466 Å
111213212223313233
T0.038 Å20.0551 Å2-0.0137 Å2-0.2938 Å20.1383 Å2--0.3167 Å2
L0.1976 °2-0.0663 °20.0209 °2-0.0828 °2-0.01 °2--0.0714 °2
S0.0054 Å °0.0214 Å °-0.0117 Å °-0.0061 Å °0.029 Å °0.0056 Å °0.04 Å °-0.0385 Å °-0.0373 Å °
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:155 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN B AND ( RESID 1:151 OR RESID 201:201 OR RESID 301:313 ) ) OR ( CHAIN C AND ( RESID 6:155 OR RESID 201:201 OR RESID 301:304 ) ) OR ( CHAIN D AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:306 ) ) OR ( CHAIN E AND ( RESID 6:160 OR RESID 201:201 OR RESID 301:302 ) ) OR ( CHAIN F AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN G AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:309 ) ) OR ( CHAIN H AND ( RESID 4:155 OR RESID 201:201 OR RESID 301:305 ) )A3 - 155
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:155 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN B AND ( RESID 1:151 OR RESID 201:201 OR RESID 301:313 ) ) OR ( CHAIN C AND ( RESID 6:155 OR RESID 201:201 OR RESID 301:304 ) ) OR ( CHAIN D AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:306 ) ) OR ( CHAIN E AND ( RESID 6:160 OR RESID 201:201 OR RESID 301:302 ) ) OR ( CHAIN F AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN G AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:309 ) ) OR ( CHAIN H AND ( RESID 4:155 OR RESID 201:201 OR RESID 301:305 ) )A201
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:155 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN B AND ( RESID 1:151 OR RESID 201:201 OR RESID 301:313 ) ) OR ( CHAIN C AND ( RESID 6:155 OR RESID 201:201 OR RESID 301:304 ) ) OR ( CHAIN D AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:306 ) ) OR ( CHAIN E AND ( RESID 6:160 OR RESID 201:201 OR RESID 301:302 ) ) OR ( CHAIN F AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN G AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:309 ) ) OR ( CHAIN H AND ( RESID 4:155 OR RESID 201:201 OR RESID 301:305 ) )A301 - 305
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:155 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN B AND ( RESID 1:151 OR RESID 201:201 OR RESID 301:313 ) ) OR ( CHAIN C AND ( RESID 6:155 OR RESID 201:201 OR RESID 301:304 ) ) OR ( CHAIN D AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:306 ) ) OR ( CHAIN E AND ( RESID 6:160 OR RESID 201:201 OR RESID 301:302 ) ) OR ( CHAIN F AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN G AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:309 ) ) OR ( CHAIN H AND ( RESID 4:155 OR RESID 201:201 OR RESID 301:305 ) )B1 - 151
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:155 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN B AND ( RESID 1:151 OR RESID 201:201 OR RESID 301:313 ) ) OR ( CHAIN C AND ( RESID 6:155 OR RESID 201:201 OR RESID 301:304 ) ) OR ( CHAIN D AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:306 ) ) OR ( CHAIN E AND ( RESID 6:160 OR RESID 201:201 OR RESID 301:302 ) ) OR ( CHAIN F AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN G AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:309 ) ) OR ( CHAIN H AND ( RESID 4:155 OR RESID 201:201 OR RESID 301:305 ) )B201
6X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:155 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN B AND ( RESID 1:151 OR RESID 201:201 OR RESID 301:313 ) ) OR ( CHAIN C AND ( RESID 6:155 OR RESID 201:201 OR RESID 301:304 ) ) OR ( CHAIN D AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:306 ) ) OR ( CHAIN E AND ( RESID 6:160 OR RESID 201:201 OR RESID 301:302 ) ) OR ( CHAIN F AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN G AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:309 ) ) OR ( CHAIN H AND ( RESID 4:155 OR RESID 201:201 OR RESID 301:305 ) )B301 - 313
7X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:155 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN B AND ( RESID 1:151 OR RESID 201:201 OR RESID 301:313 ) ) OR ( CHAIN C AND ( RESID 6:155 OR RESID 201:201 OR RESID 301:304 ) ) OR ( CHAIN D AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:306 ) ) OR ( CHAIN E AND ( RESID 6:160 OR RESID 201:201 OR RESID 301:302 ) ) OR ( CHAIN F AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN G AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:309 ) ) OR ( CHAIN H AND ( RESID 4:155 OR RESID 201:201 OR RESID 301:305 ) )C6 - 155
8X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:155 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN B AND ( RESID 1:151 OR RESID 201:201 OR RESID 301:313 ) ) OR ( CHAIN C AND ( RESID 6:155 OR RESID 201:201 OR RESID 301:304 ) ) OR ( CHAIN D AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:306 ) ) OR ( CHAIN E AND ( RESID 6:160 OR RESID 201:201 OR RESID 301:302 ) ) OR ( CHAIN F AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN G AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:309 ) ) OR ( CHAIN H AND ( RESID 4:155 OR RESID 201:201 OR RESID 301:305 ) )C201
9X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:155 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN B AND ( RESID 1:151 OR RESID 201:201 OR RESID 301:313 ) ) OR ( CHAIN C AND ( RESID 6:155 OR RESID 201:201 OR RESID 301:304 ) ) OR ( CHAIN D AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:306 ) ) OR ( CHAIN E AND ( RESID 6:160 OR RESID 201:201 OR RESID 301:302 ) ) OR ( CHAIN F AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN G AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:309 ) ) OR ( CHAIN H AND ( RESID 4:155 OR RESID 201:201 OR RESID 301:305 ) )C301 - 304
10X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:155 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN B AND ( RESID 1:151 OR RESID 201:201 OR RESID 301:313 ) ) OR ( CHAIN C AND ( RESID 6:155 OR RESID 201:201 OR RESID 301:304 ) ) OR ( CHAIN D AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:306 ) ) OR ( CHAIN E AND ( RESID 6:160 OR RESID 201:201 OR RESID 301:302 ) ) OR ( CHAIN F AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN G AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:309 ) ) OR ( CHAIN H AND ( RESID 4:155 OR RESID 201:201 OR RESID 301:305 ) )D6 - 151
11X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:155 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN B AND ( RESID 1:151 OR RESID 201:201 OR RESID 301:313 ) ) OR ( CHAIN C AND ( RESID 6:155 OR RESID 201:201 OR RESID 301:304 ) ) OR ( CHAIN D AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:306 ) ) OR ( CHAIN E AND ( RESID 6:160 OR RESID 201:201 OR RESID 301:302 ) ) OR ( CHAIN F AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN G AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:309 ) ) OR ( CHAIN H AND ( RESID 4:155 OR RESID 201:201 OR RESID 301:305 ) )D201
12X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:155 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN B AND ( RESID 1:151 OR RESID 201:201 OR RESID 301:313 ) ) OR ( CHAIN C AND ( RESID 6:155 OR RESID 201:201 OR RESID 301:304 ) ) OR ( CHAIN D AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:306 ) ) OR ( CHAIN E AND ( RESID 6:160 OR RESID 201:201 OR RESID 301:302 ) ) OR ( CHAIN F AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN G AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:309 ) ) OR ( CHAIN H AND ( RESID 4:155 OR RESID 201:201 OR RESID 301:305 ) )D301 - 306
13X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:155 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN B AND ( RESID 1:151 OR RESID 201:201 OR RESID 301:313 ) ) OR ( CHAIN C AND ( RESID 6:155 OR RESID 201:201 OR RESID 301:304 ) ) OR ( CHAIN D AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:306 ) ) OR ( CHAIN E AND ( RESID 6:160 OR RESID 201:201 OR RESID 301:302 ) ) OR ( CHAIN F AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN G AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:309 ) ) OR ( CHAIN H AND ( RESID 4:155 OR RESID 201:201 OR RESID 301:305 ) )E6 - 160
14X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:155 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN B AND ( RESID 1:151 OR RESID 201:201 OR RESID 301:313 ) ) OR ( CHAIN C AND ( RESID 6:155 OR RESID 201:201 OR RESID 301:304 ) ) OR ( CHAIN D AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:306 ) ) OR ( CHAIN E AND ( RESID 6:160 OR RESID 201:201 OR RESID 301:302 ) ) OR ( CHAIN F AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN G AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:309 ) ) OR ( CHAIN H AND ( RESID 4:155 OR RESID 201:201 OR RESID 301:305 ) )E201
15X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:155 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN B AND ( RESID 1:151 OR RESID 201:201 OR RESID 301:313 ) ) OR ( CHAIN C AND ( RESID 6:155 OR RESID 201:201 OR RESID 301:304 ) ) OR ( CHAIN D AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:306 ) ) OR ( CHAIN E AND ( RESID 6:160 OR RESID 201:201 OR RESID 301:302 ) ) OR ( CHAIN F AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN G AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:309 ) ) OR ( CHAIN H AND ( RESID 4:155 OR RESID 201:201 OR RESID 301:305 ) )E301 - 302
16X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:155 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN B AND ( RESID 1:151 OR RESID 201:201 OR RESID 301:313 ) ) OR ( CHAIN C AND ( RESID 6:155 OR RESID 201:201 OR RESID 301:304 ) ) OR ( CHAIN D AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:306 ) ) OR ( CHAIN E AND ( RESID 6:160 OR RESID 201:201 OR RESID 301:302 ) ) OR ( CHAIN F AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN G AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:309 ) ) OR ( CHAIN H AND ( RESID 4:155 OR RESID 201:201 OR RESID 301:305 ) )F6 - 151
17X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:155 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN B AND ( RESID 1:151 OR RESID 201:201 OR RESID 301:313 ) ) OR ( CHAIN C AND ( RESID 6:155 OR RESID 201:201 OR RESID 301:304 ) ) OR ( CHAIN D AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:306 ) ) OR ( CHAIN E AND ( RESID 6:160 OR RESID 201:201 OR RESID 301:302 ) ) OR ( CHAIN F AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN G AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:309 ) ) OR ( CHAIN H AND ( RESID 4:155 OR RESID 201:201 OR RESID 301:305 ) )F201
18X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:155 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN B AND ( RESID 1:151 OR RESID 201:201 OR RESID 301:313 ) ) OR ( CHAIN C AND ( RESID 6:155 OR RESID 201:201 OR RESID 301:304 ) ) OR ( CHAIN D AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:306 ) ) OR ( CHAIN E AND ( RESID 6:160 OR RESID 201:201 OR RESID 301:302 ) ) OR ( CHAIN F AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN G AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:309 ) ) OR ( CHAIN H AND ( RESID 4:155 OR RESID 201:201 OR RESID 301:305 ) )F301 - 305
19X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:155 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN B AND ( RESID 1:151 OR RESID 201:201 OR RESID 301:313 ) ) OR ( CHAIN C AND ( RESID 6:155 OR RESID 201:201 OR RESID 301:304 ) ) OR ( CHAIN D AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:306 ) ) OR ( CHAIN E AND ( RESID 6:160 OR RESID 201:201 OR RESID 301:302 ) ) OR ( CHAIN F AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN G AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:309 ) ) OR ( CHAIN H AND ( RESID 4:155 OR RESID 201:201 OR RESID 301:305 ) )G6 - 151
20X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:155 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN B AND ( RESID 1:151 OR RESID 201:201 OR RESID 301:313 ) ) OR ( CHAIN C AND ( RESID 6:155 OR RESID 201:201 OR RESID 301:304 ) ) OR ( CHAIN D AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:306 ) ) OR ( CHAIN E AND ( RESID 6:160 OR RESID 201:201 OR RESID 301:302 ) ) OR ( CHAIN F AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN G AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:309 ) ) OR ( CHAIN H AND ( RESID 4:155 OR RESID 201:201 OR RESID 301:305 ) )G201
21X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:155 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN B AND ( RESID 1:151 OR RESID 201:201 OR RESID 301:313 ) ) OR ( CHAIN C AND ( RESID 6:155 OR RESID 201:201 OR RESID 301:304 ) ) OR ( CHAIN D AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:306 ) ) OR ( CHAIN E AND ( RESID 6:160 OR RESID 201:201 OR RESID 301:302 ) ) OR ( CHAIN F AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN G AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:309 ) ) OR ( CHAIN H AND ( RESID 4:155 OR RESID 201:201 OR RESID 301:305 ) )G301 - 309
22X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:155 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN B AND ( RESID 1:151 OR RESID 201:201 OR RESID 301:313 ) ) OR ( CHAIN C AND ( RESID 6:155 OR RESID 201:201 OR RESID 301:304 ) ) OR ( CHAIN D AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:306 ) ) OR ( CHAIN E AND ( RESID 6:160 OR RESID 201:201 OR RESID 301:302 ) ) OR ( CHAIN F AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN G AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:309 ) ) OR ( CHAIN H AND ( RESID 4:155 OR RESID 201:201 OR RESID 301:305 ) )H4 - 155
23X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:155 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN B AND ( RESID 1:151 OR RESID 201:201 OR RESID 301:313 ) ) OR ( CHAIN C AND ( RESID 6:155 OR RESID 201:201 OR RESID 301:304 ) ) OR ( CHAIN D AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:306 ) ) OR ( CHAIN E AND ( RESID 6:160 OR RESID 201:201 OR RESID 301:302 ) ) OR ( CHAIN F AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN G AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:309 ) ) OR ( CHAIN H AND ( RESID 4:155 OR RESID 201:201 OR RESID 301:305 ) )H201
24X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:155 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN B AND ( RESID 1:151 OR RESID 201:201 OR RESID 301:313 ) ) OR ( CHAIN C AND ( RESID 6:155 OR RESID 201:201 OR RESID 301:304 ) ) OR ( CHAIN D AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:306 ) ) OR ( CHAIN E AND ( RESID 6:160 OR RESID 201:201 OR RESID 301:302 ) ) OR ( CHAIN F AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:305 ) ) OR ( CHAIN G AND ( RESID 6:151 OR RESID 201:201 OR RESID 301:309 ) ) OR ( CHAIN H AND ( RESID 4:155 OR RESID 201:201 OR RESID 301:305 ) )H301 - 305

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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