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- PDB-6et0: Crystal structure of PqsBC (C129A) mutant from Pseudomonas aerugi... -

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IDまたはキーワード:

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基本情報

登録情報
データベース: PDB / ID: 6et0
タイトルCrystal structure of PqsBC (C129A) mutant from Pseudomonas aeruginosa (crystal form 1)
要素
  • PqsB
  • PqsC
キーワードTRANSFERASE / Pseudomonas Quinolone Signal / FabH / HHQ
機能・相同性
機能・相同性情報


2-heptyl-4(1H)-quinolone synthase / secondary metabolite biosynthetic process / acyltransferase activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytoplasm
類似検索 - 分子機能
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
DI(HYDROXYETHYL)ETHER / 2-heptyl-4(1H)-quinolone synthase subunit PqsC / 2-heptyl-4(1H)-quinolone synthase subunit PqsB
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 / フーリエ合成 / 解像度: 1.53 Å
データ登録者Witzgall, F. / Blankenfeldt, W.
引用ジャーナル: Chembiochem / 年: 2018
タイトル: The Alkylquinolone Repertoire of Pseudomonas aeruginosa is Linked to Structural Flexibility of the FabH-like 2-Heptyl-3-hydroxy-4(1H)-quinolone (PQS) Biosynthesis Enzyme PqsBC.
著者: Witzgall, F. / Depke, T. / Hoffmann, M. / Empting, M. / Bronstrup, M. / Muller, R. / Blankenfeldt, W.
履歴
登録2017年10月25日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02018年7月4日Provider: repository / タイプ: Initial release
改定 1.12018年10月24日Group: Data collection / Database references / カテゴリ: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.22024年1月17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 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.32024年11月13日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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: PqsC
B: PqsB
C: PqsC
D: PqsB
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)143,82125
ポリマ－141,7394
非ポリマー2,08221
水27,3471518
1
A: PqsC
B: PqsB
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)71,98113
ポリマ－70,8702
非ポリマー1,11111
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-122 kcal/mol
Surface area23170 Å2
手法PISA
2
C: PqsC
D: PqsB
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)71,84012
ポリマ－70,8702
非ポリマー97110
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-112 kcal/mol
Surface area22970 Å2
手法PISA
単位格子
Length a, b, c (Å)61.666, 141.356, 170.662
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain B and (resid 1 or resid 3 through 5...
21(chain D and (resid 1 or resid 3 through 5...
12(chain A and ((resid -6 and (name N or name...
22(chain C and (resid -6 through -3 or resid -1...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain B and (resid 1 or resid 3 through 5...B1
121(chain B and (resid 1 or resid 3 through 5...B3 - 5
131(chain B and (resid 1 or resid 3 through 5...B7 - 15
141(chain B and (resid 1 or resid 3 through 5...B17 - 25
151(chain B and (resid 1 or resid 3 through 5...B28 - 31
161(chain B and (resid 1 or resid 3 through 5...B33 - 35
171(chain B and (resid 1 or resid 3 through 5...B38 - 42
181(chain B and (resid 1 or resid 3 through 5...B44 - 45
191(chain B and (resid 1 or resid 3 through 5...B48 - 51
1101(chain B and (resid 1 or resid 3 through 5...B53
1111(chain B and (resid 1 or resid 3 through 5...B55
1121(chain B and (resid 1 or resid 3 through 5...B57 - 70
1131(chain B and (resid 1 or resid 3 through 5...B72 - 77
1141(chain B and (resid 1 or resid 3 through 5...B79 - 86
1151(chain B and (resid 1 or resid 3 through 5...B88 - 90
1161(chain B and (resid 1 or resid 3 through 5...B92 - 102
1171(chain B and (resid 1 or resid 3 through 5...B104 - 121
1181(chain B and (resid 1 or resid 3 through 5...B124 - 125
1191(chain B and (resid 1 or resid 3 through 5...B127 - 136
1201(chain B and (resid 1 or resid 3 through 5...B139 - 156
1211(chain B and (resid 1 or resid 3 through 5...B158 - 178
1221(chain B and (resid 1 or resid 3 through 5...B180 - 194
1231(chain B and (resid 1 or resid 3 through 5...B196 - 206
1241(chain B and (resid 1 or resid 3 through 5...B208 - 210
1251(chain B and (resid 1 or resid 3 through 5...B212 - 218
1261(chain B and (resid 1 or resid 3 through 5...B220
1271(chain B and (resid 1 or resid 3 through 5...B222 - 223
1281(chain B and (resid 1 or resid 3 through 5...B225
1291(chain B and (resid 1 or resid 3 through 5...B227 - 239
1301(chain B and (resid 1 or resid 3 through 5...B241 - 251
1311(chain B and (resid 1 or resid 3 through 5...B253 - 276
1321(chain B and (resid 1 or resid 3 through 5...B278
1331(chain B and (resid 1 or resid 3 through 5...B1 - 278
1341(chain B and (resid 1 or resid 3 through 5...B1 - 278
1351(chain B and (resid 1 or resid 3 through 5...B1 - 278
1361(chain B and (resid 1 or resid 3 through 5...B1 - 278
211(chain D and (resid 1 or resid 3 through 5...D1
221(chain D and (resid 1 or resid 3 through 5...D3 - 5
231(chain D and (resid 1 or resid 3 through 5...D7 - 15
241(chain D and (resid 1 or resid 3 through 5...D17 - 25
251(chain D and (resid 1 or resid 3 through 5...D28 - 31
261(chain D and (resid 1 or resid 3 through 5...D33 - 35
271(chain D and (resid 1 or resid 3 through 5...D38 - 42
281(chain D and (resid 1 or resid 3 through 5...D44 - 45
291(chain D and (resid 1 or resid 3 through 5...D48 - 51
2101(chain D and (resid 1 or resid 3 through 5...D53
2111(chain D and (resid 1 or resid 3 through 5...D55
2121(chain D and (resid 1 or resid 3 through 5...D57 - 70
2131(chain D and (resid 1 or resid 3 through 5...D72 - 77
2141(chain D and (resid 1 or resid 3 through 5...D79 - 86
2151(chain D and (resid 1 or resid 3 through 5...D88 - 90
2161(chain D and (resid 1 or resid 3 through 5...D92 - 102
2171(chain D and (resid 1 or resid 3 through 5...D104 - 121
2181(chain D and (resid 1 or resid 3 through 5...D124 - 125
2191(chain D and (resid 1 or resid 3 through 5...D127 - 136
2201(chain D and (resid 1 or resid 3 through 5...D139 - 156
2211(chain D and (resid 1 or resid 3 through 5...D158 - 178
2221(chain D and (resid 1 or resid 3 through 5...D180 - 194
2231(chain D and (resid 1 or resid 3 through 5...D196 - 206
2241(chain D and (resid 1 or resid 3 through 5...D208 - 210
2251(chain D and (resid 1 or resid 3 through 5...D212 - 218
2261(chain D and (resid 1 or resid 3 through 5...D220
2271(chain D and (resid 1 or resid 3 through 5...D222 - 223
2281(chain D and (resid 1 or resid 3 through 5...D225
2291(chain D and (resid 1 or resid 3 through 5...D227 - 239
2301(chain D and (resid 1 or resid 3 through 5...D241 - 251
2311(chain D and (resid 1 or resid 3 through 5...D253 - 276
2321(chain D and (resid 1 or resid 3 through 5...D278
2331(chain D and (resid 1 or resid 3 through 5...D900 - 903
112(chain A and ((resid -6 and (name N or name...A-6
122(chain A and ((resid -6 and (name N or name...A-8 - 348
132(chain A and ((resid -6 and (name N or name...A-8 - 348
142(chain A and ((resid -6 and (name N or name...A-8 - 348
152(chain A and ((resid -6 and (name N or name...A-8 - 348
212(chain C and (resid -6 through -3 or resid -1...C-6 - -3
222(chain C and (resid -6 through -3 or resid -1...C-1 - 2
232(chain C and (resid -6 through -3 or resid -1...C4 - 5
242(chain C and (resid -6 through -3 or resid -1...C7 - 15
252(chain C and (resid -6 through -3 or resid -1...C17 - 18
262(chain C and (resid -6 through -3 or resid -1...C20 - 36
272(chain C and (resid -6 through -3 or resid -1...C38 - 48
282(chain C and (resid -6 through -3 or resid -1...C50 - 57
292(chain C and (resid -6 through -3 or resid -1...C59 - 67
2102(chain C and (resid -6 through -3 or resid -1...C70 - 74
2112(chain C and (resid -6 through -3 or resid -1...C77 - 90
2122(chain C and (resid -6 through -3 or resid -1...C92 - 96
2132(chain C and (resid -6 through -3 or resid -1...C98
2142(chain C and (resid -6 through -3 or resid -1...C100 - 109
2152(chain C and (resid -6 through -3 or resid -1...C111 - 124
2162(chain C and (resid -6 through -3 or resid -1...C127 - 135
2172(chain C and (resid -6 through -3 or resid -1...C137 - 141
2182(chain C and (resid -6 through -3 or resid -1...C143 - 148
2192(chain C and (resid -6 through -3 or resid -1...C150 - 156
2202(chain C and (resid -6 through -3 or resid -1...C158
2212(chain C and (resid -6 through -3 or resid -1...C160 - 161
2222(chain C and (resid -6 through -3 or resid -1...C163 - 176
2232(chain C and (resid -6 through -3 or resid -1...C178 - 181
2242(chain C and (resid -6 through -3 or resid -1...C183 - 191
2252(chain C and (resid -6 through -3 or resid -1...C193 - 203
2262(chain C and (resid -6 through -3 or resid -1...C205 - 228
2272(chain C and (resid -6 through -3 or resid -1...C230 - 231
2282(chain C and (resid -6 through -3 or resid -1...C237 - 242
2292(chain C and (resid -6 through -3 or resid -1...C244 - 253
2302(chain C and (resid -6 through -3 or resid -1...C256 - 257
2312(chain C and (resid -6 through -3 or resid -1...C259 - 287
2322(chain C and (resid -6 through -3 or resid -1...C289 - 295
2332(chain C and (resid -6 through -3 or resid -1...C297 - 310
2342(chain C and (resid -6 through -3 or resid -1...C312 - 313
2352(chain C and (resid -6 through -3 or resid -1...C315 - 322
2362(chain C and (resid -6 through -3 or resid -1...C324 - 348
2372(chain C and (resid -6 through -3 or resid -1...C900 - 901

NCSアンサンブル:
ID
1
2

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要素

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タンパク質 , 2種, 4分子 ACBD

#1: タンパク質 PqsC


分子量: 40321.777 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Pseudomonas aeruginosa PAO1 (緑膿菌)
遺伝子: pqsC, PA0998 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9I4X1
#2: タンパク質 PqsB


分子量: 30547.760 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Pseudomonas aeruginosa PAO1 (緑膿菌)
遺伝子: pqsB, PA0997 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9I4X2

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非ポリマー , 6種, 1539分子

#3: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 15 / 由来タイプ: 合成 / 式: SO4
#4: 化合物 ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / (4R)-2-メチル-2,4-ペンタンジオ-ル


分子量: 118.174 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C6H14O2 / コメント: 沈殿剤*YM
#5: 化合物 ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / (S)-2-メチル-2,4-ペンタンジオ-ル


分子量: 118.174 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C6H14O2 / コメント: 沈殿剤*YM
#6: 化合物 ChemComp-PEG / DI(HYDROXYETHYL)ETHER / ジエチレングリコ-ル


分子量: 106.120 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C4H10O3
#7: 化合物 ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C2H6O2
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1518 / 由来タイプ: 天然 / 式: H2O

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詳細

Has protein modificationY

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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: 2.66 Å3/Da / 溶媒含有率: 53.81 %
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: 6.7
詳細: 0.1 M Bis-Tris (pH 6.7), 0.2 M Lithium sulfate, 14% PEG 3350, 5% MPD

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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6月18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: 1.53→47.122 Å / Num. obs: 224695 / % possible obs: 100 % / 冗長度: 7.4 % / Biso Wilson estimate: 17.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.029 / Rrim(I) all: 0.081 / Net I/σ(I): 14.1
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.53-1.567.61.13783877110310.7410.4361.219299.8
8.38-47.126.90.0261071515620.9990.010.02846.799.3

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解析

ソフトウェア
名称バージョン分類
PHENIXdev_2875精密化
Aimless0.5.26データスケーリング
PDB_EXTRACT3.22データ抽出
Cootモデル構築
PHENIX位相決定
XDSデータ削減
精密化構造決定の手法: フーリエ合成
開始モデル: 6ESZ

6esz


解像度: 1.53→47.122 Å / SU ML: 0.13 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 15.93
Rfactor反射数%反射
Rfree0.1579 10962 4.88 %
Rwork0.1395 --
obs0.1404 224558 99.92 %
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: 158.77 Å2 / Biso mean: 29.2113 Å2 / Biso min: 9.8 Å2
精密化ステップサイクル: final / 解像度: 1.53→47.122 Å
タンパク質核酸リガンド溶媒全体
原子数9681 0 256 1518 11455
Biso mean--53.62 40.33 -
残基数----1265
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00510672
X-RAY DIFFRACTIONf_angle_d0.90214670
X-RAY DIFFRACTIONf_chiral_restr0.0521637
X-RAY DIFFRACTIONf_plane_restr0.0071936
X-RAY DIFFRACTIONf_dihedral_angle_d15.0146638
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11B2616X-RAY DIFFRACTION4.313TORSIONAL
12D2616X-RAY DIFFRACTION4.313TORSIONAL
21A3466X-RAY DIFFRACTION4.313TORSIONAL
22C3466X-RAY DIFFRACTION4.313TORSIONAL
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
1.53-1.54740.27983520.245770827434
1.5474-1.56560.24153680.236670107378
1.5656-1.58470.25073680.221970497417
1.5847-1.60470.22613560.214770537409
1.6047-1.62590.22393830.207870417424
1.6259-1.64810.23693270.205370307357
1.6481-1.67170.22053450.200171197464
1.6717-1.69660.22173820.195570087390
1.6966-1.72320.18933370.188471117448
1.7232-1.75140.19783740.182870497423
1.7514-1.78160.18923780.174770367414
1.7816-1.8140.20793600.169271497509
1.814-1.84890.17423730.156969857358
1.8489-1.88660.16293760.153170937469
1.8866-1.92770.17233660.146671217487
1.9277-1.97250.17383230.140471117434
1.9725-2.02180.15883610.138570667427
2.0218-2.07650.14133550.136471297484
2.0765-2.13760.14843730.12871157488
2.1376-2.20660.15513900.131370847474
2.2066-2.28550.15393960.124470907486
2.2855-2.3770.14183710.120971197490
2.377-2.48510.15583680.124971277495
2.4851-2.61610.14693600.124671317491
2.6161-2.780.14283570.124971827539
2.78-2.99470.13873700.126371747544
2.9947-3.29590.16543600.129272227582
3.2959-3.77270.13653550.118872387593
3.7727-4.75250.11974000.105572987698
4.7525-47.14430.15833780.156575747952
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)
10.0648-0.06370.20867.1623-6.48425.0574-0.09490.12530.0837-0.13680.29540.42640.1149-0.1797-0.1380.246-0.0995-0.02460.30060.01480.225-26.0759-15.0141-0.7997
23.0754-1.07580.05934.7384-1.02084.5620.0229-0.1823-0.45770.25850.09860.3890.4331-0.554-0.10430.358-0.10250.00630.18650.00190.2459-36.6049-46.858427.3182
35.25530.9877-2.07970.87290.90226.5198-0.0986-0.0766-0.4415-0.08310.0264-0.25060.34150.40550.14580.20580.03530.02070.1226-0.06010.1944-16.2779-38.525217.8295
40.57140.07540.08570.8985-0.09821.4335-0.06170.0862-0.049-0.04450.0685-0.06790.12470.13620.00250.1459-0.02930.01690.1522-0.03080.1173-20.0087-26.883620.2308
51.04820.01810.23391.1953-0.18421.5293-0.06760.15220.0213-0.12440.06130.050.0137-0.039-0.00710.1384-0.0772-0.01090.1313-0.01570.1237-31.2778-22.891917.7321
66.84950.20281.78948.7075-1.58957.4418-0.1089-0.3198-0.45430.62620.19110.44670.5532-0.3357-0.19460.3478-0.06690.07170.1638-0.0020.1762-32.8691-35.110741.0129
72.211-0.3560.69262.00840.10181.9622-0.05380.1501-0.0509-0.1550.01230.21270.1008-0.1940.04960.1719-0.0813-0.01190.1929-0.02540.1468-41.0404-30.078112.0806
81.9597-0.5596-0.67361.62110.82932.3795-0.0680.3305-0.128-0.27990.05890.07720.05810.14090.01080.2127-0.0996-0.01670.2427-0.02790.1441-34.3284-28.0756.8052
91.17040.10270.48610.5725-0.16251.9806-0.0428-0.06440.1120.0210.01480.0415-0.19970.01090.04240.185-0.02660.00980.1507-0.02810.149-22.5489-5.691439.2813
100.8626-0.36370.99453.9573-3.52935.61340.0047-0.11550.04630.01080.19470.3286-0.0671-0.2676-0.20480.1055-0.03190.00880.1313-0.02490.1321-31.6236-13.889233.0721
111.23670.18350.74350.65970.02142.4274-0.0730.03090.0791-0.04970.02420.0563-0.14450.02760.04590.1275-0.04160.00360.099-0.01440.1145-24.8406-12.241228.2009
121.4740.1734-0.28291.5775-0.63672.2805-0.0685-0.0349-0.0618-0.0915-0.0064-0.20290.12790.28890.09240.1249-0.04320.0060.1501-0.06290.1075-12.281-16.81331.38
132.024-0.0348-0.28282.3548-1.98972.8791-0.0533-0.06480.16380.02950.0986-0.0673-0.32870.2619-0.01140.1902-0.11310.00920.1872-0.03860.1612-9.247-1.063729.834
143.7521-1.97480.5999.2992-1.46683.2134-0.02220.17480.3368-0.17110.00740.1742-0.3550.0904-0.01420.162-0.10420.01430.1711-0.00780.1266-14.2802-2.432123.1235
154.44761.382-3.22050.8223-1.12412.9180.2175-0.3302-0.14610.1359-0.1893-0.0873-0.10240.25590.04060.1596-0.0599-0.05860.15280.01260.179714.32489.89272.6851
161.73230.32750.00070.65630.1880.88170.0718-0.014-0.17250.0299-0.0243-0.15370.0270.0913-0.03040.118-0.0089-0.02120.11070.00710.192113.74767.906-9.3982
171.65140.19490.26590.66010.20231.58670.067-0.20060.0950.1088-0.0402-0.105-0.17670.0909-0.01190.1652-0.0597-0.01070.1412-0.00520.190114.605320.4742-0.3844
180.85840.1304-0.09461.1998-0.37871.63190.00140.07490.0534-0.1510.0290.0661-0.1469-0.1624-0.00060.0996-0.0109-0.01920.13770.01020.1426-14.968911.2287-23.1229
191.83770.0016-0.59280.76340.74652.8640.0283-0.0120.28110.0045-0.0340.0737-0.2254-0.0868-0.02630.14720.0033-0.00420.079-0.00410.1832-8.202822.8627-13.1398
201.14230.22350.3660.63590.21061.85780.0345-0.10810.07820.0519-0.02510.0006-0.0994-0.114-0.02220.0861-0.01380.00510.0829-0.00290.1239-7.091612.325-10.1212
210.90370.84230.39521.9884-0.0441.57010.0113-0.099-0.2660.1387-0.1290.02610.3753-0.09550.10020.1163-0.009-0.02430.1060.03720.1729-7.7406-5.0041-8.1309
226.64545.0213-1.94157.5201-2.72163.2092-0.11880.2590.0644-0.44310.0083-0.14440.11230.1940.13850.12630.01160.01360.1424-0.02120.09831.9975.6328-29.4126
231.23780.7254-1.62652.599-1.2683.2678-0.0161-0.0073-0.0849-0.09150.10110.12640.1867-0.2482-0.09310.0818-0.0468-0.02520.14050.02070.1631-18.2381-2.8487-13.484
245.7282-2.6592-1.00783.65070.59591.7507-0.0001-0.25120.05050.0220.06160.1353-0.0644-0.1705-0.05670.0902-0.0382-0.01250.1393-0.00580.1205-20.77646.8178-8.0023
253.1386-0.3575-0.44893.57830.00013.9682-0.0596-0.39780.15650.36130.04190.3704-0.1597-0.33560.03020.0818-0.0291-0.01290.1475-0.00810.1727-15.54225.4661-3.4511
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -8 through 12 )A-8 - 12
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 45 )A13 - 45
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 69 )A46 - 69
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 175 )A70 - 175
5X-RAY DIFFRACTION5chain 'A' and (resid 176 through 212 )A176 - 212
6X-RAY DIFFRACTION6chain 'A' and (resid 213 through 237 )A213 - 237
7X-RAY DIFFRACTION7chain 'A' and (resid 238 through 314 )A238 - 314
8X-RAY DIFFRACTION8chain 'A' and (resid 315 through 348 )A315 - 348
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 49 )B1 - 49
10X-RAY DIFFRACTION10chain 'B' and (resid 50 through 80 )B50 - 80
11X-RAY DIFFRACTION11chain 'B' and (resid 81 through 145 )B81 - 145
12X-RAY DIFFRACTION12chain 'B' and (resid 146 through 201 )B146 - 201
13X-RAY DIFFRACTION13chain 'B' and (resid 202 through 252 )B202 - 252
14X-RAY DIFFRACTION14chain 'B' and (resid 253 through 278 )B253 - 278
15X-RAY DIFFRACTION15chain 'C' and (resid -6 through 25 )C-6 - 25
16X-RAY DIFFRACTION16chain 'C' and (resid 26 through 175 )C26 - 175
17X-RAY DIFFRACTION17chain 'C' and (resid 176 through 348 )C176 - 348
18X-RAY DIFFRACTION18chain 'D' and (resid 1 through 33 )D1 - 33
19X-RAY DIFFRACTION19chain 'D' and (resid 34 through 88 )D34 - 88
20X-RAY DIFFRACTION20chain 'D' and (resid 89 through 153 )D89 - 153
21X-RAY DIFFRACTION21chain 'D' and (resid 154 through 176 )D154 - 176
22X-RAY DIFFRACTION22chain 'D' and (resid 177 through 201 )D177 - 201
23X-RAY DIFFRACTION23chain 'D' and (resid 202 through 238 )D202 - 238
24X-RAY DIFFRACTION24chain 'D' and (resid 239 through 264 )D239 - 264
25X-RAY DIFFRACTION25chain 'D' and (resid 265 through 283 )D265 - 283

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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