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- PDB-7f35: Crystal structure of anti S-gatifloxacin antibody Fab fragment in... -

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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: 7f35
タイトルCrystal structure of anti S-gatifloxacin antibody Fab fragment in complex with S-gatifloxacin
要素(Antibody Fab fragment ...) x 2
キーワードIMMUNE SYSTEM / antibody / gatifloxacin / Fab fragment / enantioselectivity
機能・相同性Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / CITRIC ACID / Chem-GFN
機能・相同性情報
生物種Mus musculus (ハツカネズミ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.6 Å
データ登録者Wang, L.T. / Jiao, W.Y. / Shen, X. / Lei, H.T.
資金援助 中国, 1件
組織認可番号国
National Basic Research Program of China (973 Program)2017YFC1601700 中国
引用ジャーナル: Rsc Adv / 年: 2021
タイトル: Conformational adaptability determining antibody recognition to distomer: structure analysis of enantioselective antibody against chiral drug gatifloxacin
著者: Wang, L.T. / Xie, W. / Jiao, W.Y. / Zhang, C. / Li, X. / Xu, Z. / Huang, X. / Lei, H.T. / Shen, X.
履歴
登録2021年6月15日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02021年12月29日Provider: repository / タイプ: Initial release
改定 1.12023年11月29日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.22024年10月16日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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: Antibody Fab fragment light chain
B: Antibody Fab fragment heavy chain
C: Antibody Fab fragment light chain
D: Antibody Fab fragment heavy chain
E: Antibody Fab fragment light chain
F: Antibody Fab fragment heavy chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)145,69736
ポリマ－142,8066
非ポリマー2,89130
水81145
1
A: Antibody Fab fragment light chain
B: Antibody Fab fragment heavy chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)48,45312
ポリマ－47,6022
非ポリマー85110
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-40 kcal/mol
Surface area20820 Å2
手法PISA
2
C: Antibody Fab fragment light chain
D: Antibody Fab fragment heavy chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)48,66215
ポリマ－47,6022
非ポリマー1,06013
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-96 kcal/mol
Surface area20440 Å2
手法PISA
3
E: Antibody Fab fragment light chain
F: Antibody Fab fragment heavy chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)48,5829
ポリマ－47,6022
非ポリマー9807
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-30 kcal/mol
Surface area20110 Å2
手法PISA
単位格子
Length a, b, c (Å)184.071, 184.071, 100.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDモデル要素
11F-301-

SO4

非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid -1 through 14 or resid 16...
21(chain C and (resid -1 through 14 or resid 16...
31(chain E and (resid -1 through 14 or resid 16...
12(chain B and (resid 2 through 26 or resid 30...
22(chain D and (resid 2 through 26 or resid 30...
32(chain F and (resid 2 through 26 or resid 30...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid -1 through 14 or resid 16...A-1 - 14
121(chain A and (resid -1 through 14 or resid 16...A16 - 21
131(chain A and (resid -1 through 14 or resid 16...A23 - 24
141(chain A and (resid -1 through 14 or resid 16...A26 - 27
151(chain A and (resid -1 through 14 or resid 16...A67
161(chain A and (resid -1 through 14 or resid 16...A-1 - 213
171(chain A and (resid -1 through 14 or resid 16...A-1 - 213
181(chain A and (resid -1 through 14 or resid 16...A-1 - 213
191(chain A and (resid -1 through 14 or resid 16...A-1 - 213
1101(chain A and (resid -1 through 14 or resid 16...A-1 - 213
211(chain C and (resid -1 through 14 or resid 16...C-1 - 14
221(chain C and (resid -1 through 14 or resid 16...C16 - 21
231(chain C and (resid -1 through 14 or resid 16...C23 - 24
241(chain C and (resid -1 through 14 or resid 16...C26 - 27
251(chain C and (resid -1 through 14 or resid 16...C67
261(chain C and (resid -1 through 14 or resid 16...C-1 - 213
271(chain C and (resid -1 through 14 or resid 16...C-1 - 213
281(chain C and (resid -1 through 14 or resid 16...C-1 - 213
291(chain C and (resid -1 through 14 or resid 16...C-1 - 213
2101(chain C and (resid -1 through 14 or resid 16...C-1 - 213
311(chain E and (resid -1 through 14 or resid 16...E-1 - 14
321(chain E and (resid -1 through 14 or resid 16...E16 - 21
331(chain E and (resid -1 through 14 or resid 16...E23 - 24
341(chain E and (resid -1 through 14 or resid 16...E-1 - 213
351(chain E and (resid -1 through 14 or resid 16...E-1 - 213
361(chain E and (resid -1 through 14 or resid 16...E63 - 69
371(chain E and (resid -1 through 14 or resid 16...E71 - 106
381(chain E and (resid -1 through 14 or resid 16...E0
391(chain E and (resid -1 through 14 or resid 16...E-1 - 213
3101(chain E and (resid -1 through 14 or resid 16...E-1 - 213
3111(chain E and (resid -1 through 14 or resid 16...E-1 - 213
3121(chain E and (resid -1 through 14 or resid 16...E-1 - 213
3131(chain E and (resid -1 through 14 or resid 16...E-1 - 213
112(chain B and (resid 2 through 26 or resid 30...B2 - 26
122(chain B and (resid 2 through 26 or resid 30...B30 - 61
132(chain B and (resid 2 through 26 or resid 30...B63 - 81
142(chain B and (resid 2 through 26 or resid 30...B0
152(chain B and (resid 2 through 26 or resid 30...B90 - 100
162(chain B and (resid 2 through 26 or resid 30...B0
172(chain B and (resid 2 through 26 or resid 30...B1 - 216
182(chain B and (resid 2 through 26 or resid 30...B137 - 156
192(chain B and (resid 2 through 26 or resid 30...B192 - 194
1102(chain B and (resid 2 through 26 or resid 30...B196 - 215
212(chain D and (resid 2 through 26 or resid 30...D2 - 26
222(chain D and (resid 2 through 26 or resid 30...D30 - 61
232(chain D and (resid 2 through 26 or resid 30...D85
242(chain D and (resid 2 through 26 or resid 30...D90 - 100
252(chain D and (resid 2 through 26 or resid 30...D119 - 129
262(chain D and (resid 2 through 26 or resid 30...D119 - 129
272(chain D and (resid 2 through 26 or resid 30...D137 - 190
282(chain D and (resid 2 through 26 or resid 30...D192 - 194
292(chain D and (resid 2 through 26 or resid 30...D215
2102(chain D and (resid 2 through 26 or resid 30...D1 - 215
2112(chain D and (resid 2 through 26 or resid 30...D1 - 215
2122(chain D and (resid 2 through 26 or resid 30...D1 - 215
2132(chain D and (resid 2 through 26 or resid 30...D1 - 215
2142(chain D and (resid 2 through 26 or resid 30...D1 - 215
2152(chain D and (resid 2 through 26 or resid 30...D1 - 215
2162(chain D and (resid 2 through 26 or resid 30...D1 - 215
2172(chain D and (resid 2 through 26 or resid 30...D1 - 215
312(chain F and (resid 2 through 26 or resid 30...F2 - 26
322(chain F and (resid 2 through 26 or resid 30...F30 - 61
332(chain F and (resid 2 through 26 or resid 30...F63 - 81
342(chain F and (resid 2 through 26 or resid 30...F83
352(chain F and (resid 2 through 26 or resid 30...F90 - 100
362(chain F and (resid 2 through 26 or resid 30...F1 - 215
372(chain F and (resid 2 through 26 or resid 30...F1 - 215
382(chain F and (resid 2 through 26 or resid 30...F137 - 156
392(chain F and (resid 2 through 26 or resid 30...F1 - 215
3102(chain F and (resid 2 through 26 or resid 30...F215 - 4
3112(chain F and (resid 2 through 26 or resid 30...F215 - 4
3122(chain F and (resid 2 through 26 or resid 30...F215
3132(chain F and (resid 2 through 26 or resid 30...F1 - 215
3142(chain F and (resid 2 through 26 or resid 30...F1 - 215
3152(chain F and (resid 2 through 26 or resid 30...F1 - 215
3162(chain F and (resid 2 through 26 or resid 30...F1 - 215
3172(chain F and (resid 2 through 26 or resid 30...F1 - 215

NCSアンサンブル:
ID
1
2

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要素

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抗体 , 2種, 6分子 ACEBDF

#1: 抗体 Antibody Fab fragment light chain


分子量: 24128.709 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ)
#2: 抗体 Antibody Fab fragment heavy chain


分子量: 23473.174 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ)

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非ポリマー , 8種, 75分子

#3: 化合物 ChemComp-GFN / 1-cyclopropyl-6-fluoro-8-methoxy-7-[(3S)-3-methylpiperazin-1-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid / Gatifloxacin


分子量: 375.394 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C19H22FN3O4 / タイプ: SUBJECT OF INVESTIGATION / コメント: 抗生剤*YM
#4: 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: 8 / 由来タイプ: 合成 / 式: C2H6O2
#5: 化合物
ChemComp-NA / SODIUM ION / ナトリウムカチオン


分子量: 22.990 Da / 分子数: 8 / 由来タイプ: 合成 / 式: Na
#6: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 7 / 由来タイプ: 合成 / 式: SO4
#7: 化合物 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C3H8O3
#8: 化合物 ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Cl
#9: 化合物 ChemComp-CIT / CITRIC ACID / クエン酸


分子量: 192.124 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C6H8O7
#10: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 45 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかY
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: 2.99 Å3/Da / 溶媒含有率: 58.8 %
結晶化温度: 293.15 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 0.1 M sodium acetate pH 4.9, 0.2 M sodium chloride, 1.4 M ammonium sulfate

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データ収集

回折平均測定温度: 80 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: SSRF / ビームライン: BL19U1 / 波長: 0.9785 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2019年6月3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: 0.9785 Å / 相対比: 1
反射解像度: 2.6→48.55 Å / Num. obs: 53623 / % possible obs: 100 % / 冗長度: 26.4 % / Biso Wilson estimate: 70.72 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.028 / Rrim(I) all: 0.106 / Χ2: 1.14 / Net I/σ(I): 29.2
反射 シェル解像度: 2.6→2.68 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4571 / CC1/2: 0.715 / Χ2: 0.9

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19_4092精密化
Aimlessデータスケーリング
PDB_EXTRACT3.27データ抽出
XDSデータ削減
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 1EGJ

1egj


解像度: 2.6→44.64 Å / SU ML: 0.36 / 交差検証法: THROUGHOUT / σ(F): 0.56 / 位相誤差: 25.78 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2348 2700 5.03 %
Rwork0.2 96412 -
obs0.2018 53536 99.93 %
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: 176.48 Å2 / Biso mean: 85.2261 Å2 / Biso min: 33.53 Å2
精密化ステップサイクル: final / 解像度: 2.6→44.64 Å
タンパク質核酸リガンド溶媒全体
原子数9426 0 182 45 9653
Biso mean--76.59 68.83 -
残基数----1229
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A1840X-RAY DIFFRACTION16.924TORSIONAL
12C1840X-RAY DIFFRACTION16.924TORSIONAL
13E1840X-RAY DIFFRACTION16.924TORSIONAL
21B2513X-RAY DIFFRACTION16.924TORSIONAL
22D2513X-RAY DIFFRACTION16.924TORSIONAL
23F2513X-RAY DIFFRACTION16.924TORSIONAL
LS精密化 シェル

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

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.630.35931840.333932043388100
2.63-2.660.29691660.316632213387100
2.66-2.690.36851620.311531943356100
2.69-2.730.36751580.302832513409100
2.73-2.760.34081800.285132153395100
2.76-2.80.30631710.27232193390100
2.8-2.840.31731680.267631893357100
2.84-2.880.29051580.263532423400100
2.88-2.930.3061700.271431813351100
2.93-2.980.31541670.264532383405100
2.98-3.030.28831710.286732333404100
3.03-3.080.36521720.270432053377100
3.08-3.140.27271530.253432633416100
3.14-3.210.3011720.234131883360100
3.21-3.280.27951580.232832383396100
3.28-3.350.261740.229132113385100
3.35-3.440.33271870.211731993386100
3.44-3.530.23531790.220831903369100
3.53-3.630.23621380.211932443382100
3.63-3.750.26731590.215732573416100
3.75-3.880.20291820.187232103392100
3.88-4.040.20081970.181631713368100
4.04-4.220.23871400.168532233363100
4.22-4.440.16191800.153132223402100
4.45-4.720.17671710.142432253396100
4.72-5.090.1851880.149531933381100
5.09-5.60.19211610.167332213382100
5.6-6.410.23771870.19331903377100
6.41-8.060.23011820.204932143396100
8.06-44.640.22311710.18513161333298
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)
12.7279-1.3919-1.1896.14031.1911.9728-0.1294-0.30540.35680.75010.15670.0469-0.44060.2454-0.03720.71370.043-0.08090.5812-0.06460.45146.1777-43.0133-29.5203
21.00080.87271.194.8265-2.54114.79070.51330.7964-0.5279-0.5727-0.6501-0.692-0.23250.6275-0.01030.54910.0595-0.00580.4967-0.07490.503249.5126-49.7638-41.6966
36.46-0.4047-1.15831.90693.35615.88520.93861.1291.21940.4304-0.19560.6115-1.4853-1.3456-0.71280.61510.17770.04150.4820.03830.565835.4052-42.8665-39.5704
42.50390.6988-1.11435.31880.58042.78420.1417-0.09210.4130.2902-0.1807-0.0149-0.6505-0.05370.10280.5810.0887-0.05610.42590.03610.352544.3937-45.573-36.4673
53.1506-0.2594-1.6637-0.0174-0.09112.0145-0.2944-1.34940.3030.50720.16290.50250.04640.11550.14551.01750.31410.25890.8212-0.12910.896417.884-41.7981-16.7462
62.64882.64440.83414.30620.24752.43771.2016-1.78381.50711.3344-0.03470.3949-1.5845-0.2212-1.3241.57560.11920.50711.855-0.24681.117313.3588-45.2236-1.5547
73.83061.9664-2.25111.7458-1.0964.0797-0.1707-0.4715-0.21930.50520.03110.41480.172-0.39690.26451.09190.32330.33721.0144-0.09191.036116.0236-47.0396-13.8969
86.31270.16110.02932.3095-0.37352.78060.0206-2.29531.04850.304-0.27940.4999-0.33130.44470.32011.39210.13170.40021.4137-0.33491.205311.7681-38.1178-5.8305
93.60943.5461-4.40376.4168-5.71229.7655-0.03280.5917-0.34610.28190.43261.0459-0.2081-0.9545-0.3450.39680.04220.00780.5833-0.01090.881125.4293-64.4599-40.237
108.98370.9256-1.57979.57590.34696.082-0.14530.52210.0829-0.4178-0.01910.6543-0.4014-0.69110.15090.32970.0916-0.0560.3248-0.03190.422236.0986-59.3452-42.8769
115.096-0.04641.34655.7815-0.77436.98010.15690.4138-0.8707-0.5609-0.04880.24580.58890.5249-0.13950.520.1023-0.00220.4286-0.0680.617542.8214-67.5072-43.0713
125.0454-1.00240.77977.2003-2.01152.1935-0.13610.7521-0.7685-1.0531-0.2412-0.11751.7065-0.33680.39570.5083-0.01120.06660.5932-0.14590.70132.4527-69.283-45.4189
134.38110.2479-3.05274.4174-1.31083.7078-0.06390.2435-0.23870.13820.16090.64720.0379-0.2821-0.09730.46520.0509-0.04770.4836-0.09020.549333.0655-59.7067-39.4839
145.0093-0.09890.0965-0.0303-0.2221.9291-0.5654-0.3883-0.04811.06470.45311.0591-0.1805-0.17810.09190.89110.26980.36480.75890.15640.878210.176-53.4255-22.3623
153.1124-0.6485-0.02531.40190.3342.8483-0.2279-0.2116-0.1363-0.17420.16560.3749-0.2075-0.03250.06581.03340.11360.30890.5456-0.00050.961711.9239-49.9328-26.7029
165.1657-0.4565-0.011.89891.45463.1515-0.1056-0.6924-0.18050.09090.17770.7556-0.45890.5011-0.11290.92880.22330.25240.665-0.10030.916715.4764-48.3092-23.7459
173.49510.4165-0.80770.2194-0.09842.5853-0.3160.11860.389-0.30440.14950.308-0.1681-0.02430.11320.95680.17560.08760.6874-0.10220.92724.1847-46.9606-29.3431
186.46963.4117-0.75942.18961.42023.77340.2844-0.4081-0.67280.4583-0.2598-0.29970.56310.3061-0.13580.52220.08390.01880.42080.03240.499236.38616.8042-3.9358
195.1942-2.2394-2.7621.5588-0.53475.48980.0231-0.57020.9524-0.00610.0285-0.1218-0.83630.7801-0.11830.5771-0.03010.03760.3799-0.01540.51732.450820.4212-2.7894
203.0771-0.30942.30657.82122.49314.4022-0.1907-0.0815-0.4620.3348-0.35531.45161.5511-0.90630.59460.5805-0.08390.02690.4146-0.01060.518821.80319.5396-8.4961
213.9671.452-1.66172.6612-1.8164.80740.1335-0.4366-0.28781.08-0.30380.38860.38140.2160.09240.6150.05890.07280.39770.04340.434829.74048.6435-3.0435
221.00660.07131.21125.47261.54862.26010.10770.3197-0.4175-0.40810.2290.31840.65470.2142-0.29350.6511-0.0630.04290.4418-0.05720.559129.8801-2.9976-22.4428
231.9656-0.2204-0.86093.60761.68746.6711-0.3456-0.0477-0.1482-0.50310.05750.2319-0.23650.80490.37681.01340.05730.09940.4829-0.06150.678934.8944-16.0376-29.0172
242.0941.04190.96173.159-0.28153.96450.09330.3502-0.0731-1.01510.13050.09540.11830.7255-0.23211.08260.081-0.02320.4881-0.08270.669233.1369-13.5634-32.1723
255.9423-0.7794-2.43145.8838-1.94943.8356-0.3631-0.18570.01960.30980.00510.26180.9995-0.0170.40891.20430.0285-0.05480.4143-0.10610.764533.6492-24.365-28.5287
264.77610.87240.90135.52540.38249.5969-0.03970.16780.1393-0.3534-0.04660.4179-0.4121-0.30290.06840.4274-0.0234-0.00950.27360.02210.285126.032523.8876-22.4871
271.86660.12980.37334.57631.81313.24710.00390.1766-0.5058-0.831-0.04190.73480.392-0.33960.07340.730.0036-0.1760.48050.02150.61821.65692.8471-31.4339
284.0721.45030.17472.1298-1.56131.9311-0.0488-0.26381.26510.72370.2923-0.5283-0.7122-0.1134-0.04051.28690.3084-0.30040.7724-0.36871.179152.4108-27.1588-6.4064
294.41340.8167-2.74891.9451-1.8923.08310.0666-0.72320.5605-0.1093-0.14850.2199-0.1833-0.1657-0.0130.95730.2144-0.23190.7814-0.38760.876155.6896-39.0546-5.227
301.25073.4112-0.27318.595-0.74141.3921-0.2791-0.9798-0.44961.0171-0.5652-0.5368-1.0588-0.61740.63651.2417-0.0942-0.08791.31-0.33671.238857.214-37.07147.0177
312.7657-0.5022-0.93684.47760.22184.1089-0.1792-0.53331.03210.4738-0.04990.211-0.5802-0.36240.20991.00750.2683-0.36030.8391-0.40190.870955.2173-32.8172-5.3956
323.28980.372-0.81771.5901-1.39881.2305-0.0678-0.0341.5586-0.09380.3639-0.4485-0.69620.0422-0.18341.4375-0.2051-0.04830.5968-0.21631.86281.4589-15.3248-17.4685
330.5522-0.5454-1.37910.56791.16693.77360.26530.06511.3887-1.2591.1165-0.1304-1.82390.9879-1.01612.0695-0.93060.602-0.065-0.14433.088390.7838-6.5837-23.6678
342.73880.8731-1.35443.2167-5.18739.3062-0.2613-0.10720.21360.09080.0098-0.2878-0.8038-0.03730.29960.7584-0.0475-0.12560.4952-0.09080.639873.2779-48.2772-17.7754
357.2057-0.6896-0.19513.69120.79544.6849-0.4066-0.82670.89060.19060.4124-0.4398-0.9373-0.2184-0.00420.7290.0392-0.12280.6077-0.21140.539764.575-47.3293-10.8498
362.84330.7729-0.60865.4505-0.3862.0607-0.3429-0.02770.2861-0.40720.10860.3318-0.5192-0.65330.23180.78480.0251-0.16410.567-0.11280.425857.3349-51.6528-16.6203
374.57371.1188-0.63240.68741.02524.7102-0.51240.2760.3833-0.43790.23280.0516-0.738-0.35350.2570.7615-0.0787-0.11470.3625-0.04750.419666.392-52.0557-21.4244
383.72851.40760.20851.9972-0.02751.0265-0.4157-0.34240.5353-0.2246-0.0177-0.1392-0.4560.19080.26750.81840.0183-0.19090.4292-0.10.656169.633-43.6537-14.852
398.1387-0.48-3.42094.6571-3.05793.7531-0.9851-1.77070.4084-0.2635-0.206-0.3051-1.52450.6771.33251.2196-0.1828-0.37410.8116-0.01121.552693.1472-18.0831-13.9923
403.2964-0.6095-0.77351.9379-1.39491.4061-0.5653-0.56970.8140.01240.9261-0.3581-1.08750.1038-0.7531.4532-0.2069-0.33740.6484-0.18351.579188.2091-23.0628-15.5741
416.56750.85911.35625.79962.02053.909-0.2296-1.13621.70420.67930.3386-0.1067-0.42050.01790.01451.0519-0.1287-0.1180.7168-0.23021.082985.1967-31.7341-12.0096
423.3761-0.72390.52192.39620.67937.29460.1325-0.0851.2244-0.02950.04330.4155-0.66640.5047-0.24121.1083-0.146-0.2140.5717-0.1451.543679.0946-25.3889-20.7309
433.281-0.2152-1.10791.2762-0.79180.94180.0582-0.83531.4187-0.39110.14740.2572-0.60510.1368-0.25151.4-0.3054-0.04570.6953-0.35181.480484.7703-24.1698-14.9638
443.21720.9881-1.21774.61111.07753.63850.3891-0.82950.68490.9790.2826-0.57430.12390.7059-0.55171.0505-0.1068-0.20670.7271-0.24041.158694.1665-28.9485-12.0584
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 23 )A-1 - 23
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 40 )A24 - 40
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 63 )A41 - 63
4X-RAY DIFFRACTION4chain 'A' and (resid 64 through 103 )A64 - 103
5X-RAY DIFFRACTION5chain 'A' and (resid 104 through 147 )A104 - 147
6X-RAY DIFFRACTION6chain 'A' and (resid 148 through 157 )A148 - 157
7X-RAY DIFFRACTION7chain 'A' and (resid 158 through 190 )A158 - 190
8X-RAY DIFFRACTION8chain 'A' and (resid 191 through 213 )A191 - 213
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 23 )B1 - 23
10X-RAY DIFFRACTION10chain 'B' and (resid 24 through 52 )B24 - 52
11X-RAY DIFFRACTION11chain 'B' and (resid 53 through 64 )B53 - 64
12X-RAY DIFFRACTION12chain 'B' and (resid 65 through 83 )B65 - 83
13X-RAY DIFFRACTION13chain 'B' and (resid 84 through 112 )B84 - 112
14X-RAY DIFFRACTION14chain 'B' and (resid 113 through 137 )B113 - 137
15X-RAY DIFFRACTION15chain 'B' and (resid 138 through 160 )B138 - 160
16X-RAY DIFFRACTION16chain 'B' and (resid 161 through 187 )B161 - 187
17X-RAY DIFFRACTION17chain 'B' and (resid 188 through 216 )B188 - 216
18X-RAY DIFFRACTION18chain 'C' and (resid -1 through 23 )C-1 - 23
19X-RAY DIFFRACTION19chain 'C' and (resid 24 through 40 )C24 - 40
20X-RAY DIFFRACTION20chain 'C' and (resid 41 through 63 )C41 - 63
21X-RAY DIFFRACTION21chain 'C' and (resid 64 through 93 )C64 - 93
22X-RAY DIFFRACTION22chain 'C' and (resid 94 through 130 )C94 - 130
23X-RAY DIFFRACTION23chain 'C' and (resid 131 through 157 )C131 - 157
24X-RAY DIFFRACTION24chain 'C' and (resid 158 through 199 )C158 - 199
25X-RAY DIFFRACTION25chain 'C' and (resid 200 through 213 )C200 - 213
26X-RAY DIFFRACTION26chain 'D' and (resid 1 through 73 )D1 - 73
27X-RAY DIFFRACTION27chain 'D' and (resid 74 through 215 )D74 - 215
28X-RAY DIFFRACTION28chain 'E' and (resid -1 through 23 )E-1 - 23
29X-RAY DIFFRACTION29chain 'E' and (resid 24 through 50 )E24 - 50
30X-RAY DIFFRACTION30chain 'E' and (resid 51 through 66 )E51 - 66
31X-RAY DIFFRACTION31chain 'E' and (resid 67 through 109 )E67 - 109
32X-RAY DIFFRACTION32chain 'E' and (resid 110 through 188 )E110 - 188
33X-RAY DIFFRACTION33chain 'E' and (resid 189 through 213 )E189 - 213
34X-RAY DIFFRACTION34chain 'F' and (resid 1 through 23 )F1 - 23
35X-RAY DIFFRACTION35chain 'F' and (resid 24 through 44 )F24 - 44
36X-RAY DIFFRACTION36chain 'F' and (resid 45 through 64 )F45 - 64
37X-RAY DIFFRACTION37chain 'F' and (resid 65 through 91 )F65 - 91
38X-RAY DIFFRACTION38chain 'F' and (resid 92 through 122 )F92 - 122
39X-RAY DIFFRACTION39chain 'F' and (resid 123 through 137 )F123 - 137
40X-RAY DIFFRACTION40chain 'F' and (resid 138 through 148 )F138 - 148
41X-RAY DIFFRACTION41chain 'F' and (resid 149 through 165 )F149 - 165
42X-RAY DIFFRACTION42chain 'F' and (resid 166 through 176 )F166 - 176
43X-RAY DIFFRACTION43chain 'F' and (resid 177 through 187 )F177 - 187
44X-RAY DIFFRACTION44chain 'F' and (resid 188 through 215 )F188 - 215

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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