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万見
- PDB-9r2v: De novo designed M16 protein fold -

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データを開く


IDまたはキーワード:

読み込み中...

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基本情報

登録情報
データベース: PDB / ID: 9r2v
タイトルDe novo designed M16 protein fold
要素M16
キーワードDE NOVO PROTEIN / dark fold / de novo / unnatural
機能・相同性FORMIC ACID
機能・相同性情報
生物種synthetic construct (人工物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.49 Å
データ登録者Pacesa, M. / Miao, Y. / Georgeon, S. / Schmidt, J. / Correia, B.E.
資金援助1件
組織認可番号国
Swiss National Science Foundation
引用
ジャーナル: To Be Published
タイトル: Reimagine accessibility of protein space with generative model
著者: Miao, Y. / Pacesa, M. / Georgeon, S. / Schmidt, J. / Lu, T. / Huang, P. / Correia, B.E.
#1: ジャーナル: Acta Crystallogr D Struct Biol / 年: 2019
タイトル: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
著者: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / ...著者: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
要旨: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
履歴
登録2025年5月1日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02025年5月14日Provider: repository / タイプ: Initial release

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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: M16
B: M16
C: M16
D: M16
E: M16
F: M16
G: M16
H: M16
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)159,06831
ポリマ－158,0178
非ポリマー1,05123
水21612
1
A: M16
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)20,0568
ポリマ－19,7521
非ポリマー3047
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: M16
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)19,7982
ポリマ－19,7521
非ポリマー461
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: M16
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)19,9143
ポリマ－19,7521
非ポリマー1622
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: M16


分子量 (理論値)分子数
合計 (水以外)19,7521
ポリマ－19,7521
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
5
E: M16
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)20,0398
ポリマ－19,7521
非ポリマー2867
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
6
F: M16
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)19,8383
ポリマ－19,7521
非ポリマー862
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
7
G: M16
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)19,7982
ポリマ－19,7521
非ポリマー461
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
8
H: M16
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)19,8724
ポリマ－19,7521
非ポリマー1203
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)61.250, 82.110, 111.420
Angle α, β, γ (deg.)90.000, 92.454, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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要素

#1: タンパク質
M16


分子量: 19752.111 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) synthetic construct (人工物) / 発現宿主: Escherichia coli (大腸菌)
#2: 化合物
ChemComp-FMT / FORMIC ACID / ギ酸


分子量: 46.025 Da / 分子数: 8 / 由来タイプ: 天然 / 式: CH2O2
#3: 化合物
ChemComp-CA / CALCIUM ION / カルシウムジカチオン


分子量: 40.078 Da / 分子数: 14 / 由来タイプ: 合成 / 式: Ca
#4: 化合物 ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / トリス(ヒドロキシメチル)メチルアンモニウム


分子量: 122.143 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C4H12NO3 / コメント: pH緩衝剤*YM
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 12 / 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N
Has protein modificationN

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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

結晶化温度: 291.15 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8
詳細: 0.04 M Calcium chloride dihydrate 0.04 M Sodium formate 0.1 M Tris 8.0 25 % v/v PEG Smear Low

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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: ESRF / ビームライン: MASSIF-3 / 波長: 0.9184 Å
検出器タイプ: DECTRIS EIGER X 4M / 検出器: PIXEL / 日付: 2024年9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: 0.9184 Å / 相対比: 1
反射解像度: 2.49→111.318 Å / Num. obs: 35326 / % possible obs: 91.2 % / 冗長度: 2.5 % / Biso Wilson estimate: 70.97 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Net I/σ(I): 12.8
反射 シェル解像度: 2.492→2.535 Å / Rmerge(I) obs: 0.677 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1724 / CC1/2: 0.554 / % possible all: 89.6

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解析

ソフトウェア
名称バージョン分類
PHENIX1.21.2_5419精密化
autoPROCデータ削減
XSCALE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 / 解像度: 2.49→61.19 Å / SU ML: 0.4443 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 35.047
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2904 1798 5.09 %
Rwork0.2345 33515 -
obs0.2374 35313 91.17 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 96.14 Å2
精密化ステップサイクル: LAST / 解像度: 2.49→61.19 Å
タンパク質核酸リガンド溶媒全体
原子数10201 0 46 12 10259
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.001710353
X-RAY DIFFRACTIONf_angle_d0.448513713
X-RAY DIFFRACTIONf_chiral_restr0.03811402
X-RAY DIFFRACTIONf_plane_restr0.00211733
X-RAY DIFFRACTIONf_dihedral_angle_d11.43454310
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.560.38131280.34352543X-RAY DIFFRACTION89.75
2.56-2.630.35371390.32182628X-RAY DIFFRACTION94.02
2.64-2.720.40231010.30211904X-RAY DIFFRACTION67.76
2.72-2.820.33641520.29542783X-RAY DIFFRACTION98.79
2.82-2.930.39891300.31422813X-RAY DIFFRACTION98.76
2.93-3.060.391420.30492759X-RAY DIFFRACTION98.57
3.06-3.220.34821470.28052771X-RAY DIFFRACTION98.35
3.22-3.420.33221430.25462640X-RAY DIFFRACTION96.16
3.46-3.690.37521050.25381968X-RAY DIFFRACTION79.49
3.69-4.060.26921410.21992498X-RAY DIFFRACTION88.53
4.06-4.650.26751500.20492763X-RAY DIFFRACTION96.91
4.65-5.860.26991500.20762720X-RAY DIFFRACTION95.73
5.86-61.190.23761700.21022725X-RAY DIFFRACTION94.42
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)
11.58895714638-1.807536755761.113635098483.85629441544-3.699395719194.438245402290.3199297532760.575973399002-0.346859841881-1.15274872079-0.06343643332880.5363199135771.11880320194-0.7596137456240.3783316057380.393086244212-0.1083460281610.06536491623251.09959383659-0.1576505493410.87059291533913.6562566688-1.7682846857828.6392925067
22.609904921760.3524045308331.055044592113.85736373167-1.903983449011.46078776378-0.418186923466-0.0223645999224-0.197173960317-0.2719803863980.283627353870.2320924711-0.0569503577741-1.12190940762-0.002434684335680.4413956428480.003811364766310.0878983787270.653544870919-0.06309737923990.56866608669224.8901752101-1.3310451522333.7630373041
30.70114794698-0.819815428071.491100114411.34417411238-2.33590365754.09138871556-0.02957502420890.508836304503-0.163451691912-1.14927851117-0.506487112598-0.6882658369052.053855377840.273133934438-0.05594928576880.63937660134-0.01479257244140.1792032215920.582793007948-0.006381800129670.90471998593234.9210754723-6.9002147726330.0864400336
42.32196096740.13773818456-0.4509225247521.850527327811.637762990491.88797206995-0.111386639065-0.0868987711354-0.104167150630.385186562155-0.463035961712-0.088048259795-0.8368249335280.330767058981-0.004866475708980.3074417657650.00527939037172-0.0008630740829970.432044655777-0.02056333392460.48933864714334.7364475835.0237665236134.5532696203
55.839707804224.63435940167-5.848284501593.71696060238-4.75445251176.654270398951.30200850877-0.2507603837390.793953065543-0.1007286553320.2784784098541.96298736033-0.919614094988-0.9992269501372.006185716520.4642375640190.163611613462-0.2527613266160.9771116487070.1511749651361.05764065672-5.73306296949-13.474674117856.9628783111
62.25370945205-0.1995226938650.4171410244024.417414319220.2147273615165.79388827451-0.311615699565-0.790227293838-0.497337469042-0.3907344595750.7240112287650.2405883251930.420589998549-1.734529605481.110388505360.618013273570.09476734619040.1082174208540.94636598070.2145688960810.916212430347-1.83276813345-18.193760488663.5459507622
70.302340497746-0.267495195613-0.564024632950.6910868418090.3422861769091.12434130298-0.4852970584921.09293560206-1.065295713670.928083831812-0.477616909011.23726213880.632451422315-1.90869288451-0.02187860898161.54474522362-0.3261875084390.3008976222991.10310554769-0.01071586219990.9273638419375.95807358221-31.35307927447.2365479954
80.383205874943-0.64314933434-0.2906936128491.21517461870.2947833848040.7511236053350.3462937236120.3485050466340.0678147550401-1.78947607044-0.9313338218651.37567192044-0.775618578107-0.971544613161-0.01018668110310.6824295769190.000963522442798-0.1444120900190.622893843532-0.03229735346630.6240077025894.44809739593-11.436304308155.9834157446
92.62100469508-2.346754701520.09802712812778.11125022039-1.032343520914.18977660579-0.197096993076-0.5106505028310.6897238901621.450605649680.7194970389170.314513325499-1.15209740377-1.013601253140.723280903755-0.216638211972-0.3660031141120.2546241801830.5479410318260.2608022958580.5409378145025.20211927531-21.794690221161.7117217596
100.619121674725-0.717928677634-0.3609290109580.9341202880810.07976380709680.651847350748-0.353230354625-0.1656118578240.3837819933750.7087006989190.1682030257561.44228878355-1.22152527047-0.2059489641120.004812171876981.195482361870.08764433196020.04278220861860.752514472356-0.003654833928970.6850486995629.95782735596-12.277040607565.1077730375
110.796934357847-0.1663383307350.1831455701080.481615836784-0.1716490553470.0765689380660.0355654385354-0.2464208247290.40083866606-0.9092453100780.562666559828-0.155742325258-0.5626187258480.8073114254950.00424384825070.62860786103-0.132542745995-0.02727235840410.7717693631650.1143943035330.53049671790815.510094505-14.911731733952.57175196
120.7355865156440.425266128853-0.2423016241691.21413265499-1.070518674920.948608523191-0.186550815543-0.602582891087-0.123914329583-0.05044686645290.02841552876360.2993321709140.4159561918320.5780194375830.0003971519427870.5964906325770.00471045207177-0.004628769519530.7343501089270.02392268363420.58802777336518.5973687154-23.094717161761.632257158
130.549451288346-0.501722474091-0.2531795016951.75913819088-0.9223113189461.08838695799-0.262525295932-0.2284222241670.08123564186040.9832910453510.6364153256530.379620618861-0.385332999389-0.1399643811820.1356725305930.724733583302-0.12250862559-0.02664637062450.748202986710.0255158271660.72367781021714.7333432518-19.320599640865.649344296
140.6577047973590.643414133119-0.1382810935243.98641666043-0.9268379687380.8863798616550.629938260523-0.6265758230880.4434046713381.08253801237-0.04413761548971.524545608720.00418896875545-0.938770663795-0.008640404408430.6798783278750.0132228424714-0.1915441935311.17939752239-0.1058291249771.098140848336.4174858168814.729470619847.9135317295
150.804335879975-0.5944426531060.1473736697640.421338111017-0.113831832050.0313061518255-0.4253706541270.49725028783-1.403186954560.2675298177210.10499706489-0.6948558757220.488721854778-0.400972345593-0.002218250838360.935355244031-0.0816167513968-0.1860214474220.61835465294-0.08710206090120.7496855669512.87379353257.5428776166350.9459760154
164.865354805551.585447498440.07856837829923.469206832010.1623357294111.313475465720.0302412032960.3775971076350.0973492812465-0.269990806593-0.2456053388710.060816958670.0200785602041-0.455351795561-0.001420737456160.5105661625810.05223053139920.02043506820870.560012315657-0.04146145476350.47302397248719.305216735918.096150066846.2882874098
170.4018626424020.0371311358298-0.156961888262-0.0132818952862-0.03603079005450.660208902065-0.1284086998390.1570766319770.518701663059-0.220997863235-0.54589677511-0.109364053336-1.057943156520.334175445625-0.004149939576621.143571140640.0648048247107-0.02124014630970.615880542955-0.03688983167670.79925304029224.896200811627.531880827650.611453485
181.62694728555-0.63487236998-0.3685584520682.947863937352.338729677551.84212283729-0.7858798005140.247274641666-0.528157218435-0.295162872634-0.160102333305-1.27288798546-0.145781912719-0.427504267414-0.0009684608354320.3839095023470.0233403646441-0.03191193199480.602962969517-0.06349566376170.68530684087530.895173045416.202194289748.4383392245
190.122454960297-0.683840562154-0.5479496901094.061362383983.17645453692.49612587463-0.09737665244470.4702233348160.5698684198710.2620498801370.661322013402-0.9210911371180.1979752562590.7065022091853.416490918590.577328845711-0.4324505451040.3926508887991.20745642051-0.04424599831241.427554716266.891977642068.0061164597633.8494108413
202.109938647620.846290179151-1.098294873041.390750404760.03650135954981.15167113229-0.479369323033-1.072232877850.4686228204860.458519197660.7278139836950.215186227128-0.42417938084-0.8276842222560.034371239570.394729455762-0.0275546838845-0.07194017382650.705686058581-0.02856958243971.05912919061-1.5951410966713.118913734636.2388443052
214.323168560470.4521243191120.8263848775671.320153931051.203218880341.86095018436-0.2399544418220.2563983997910.07241427549760.162690785936-0.0923000844317-1.09978684956-0.5645383349520.592070527247-0.01852251472070.438210970679-0.02878265278540.04563496620180.626578870332-0.0143088769950.67932864262-6.25279997756.1048653334734.6904075606
222.105589509961.173207210060.3411810089011.019104512910.1956199656521.46085888331-0.2991060225660.897220184396-0.116261016208-0.3775928208060.358533937408-0.0639335069545-0.208175736015-0.4433171131280.002412176628670.6566378200090.01280924950520.06562169709140.638533374943-0.1248316842980.631924664482-15.34117371853.7317861100829.4012833763
232.3905157396-0.7939060780151.80385458285.32079710395-4.094247209897.71697919636-0.6229263239820.05893629086410.3445324297840.2265914994350.645959917277-0.342267394338-0.949263113409-0.629658484912-0.1080012062990.168420791567-0.04550440010650.03201639000680.3809840281970.08746934514280.741801881922-15.20720323795.2307027974938.9555647425
242.505892265790.6766515991032.741723087892.50441930962.909187295954.78330825964-0.6177622263350.9850487921710.473136406481-0.951578703077-0.3787579388040.135565248518-0.4258343195821.25569478564-0.949125985440.6605952396750.1856384758730.2580003071271.014413626210.2593334453580.7700297339117.3982797393.95226371812-8.27324127071
252.225985550010.5468044184750.2433011919340.315287612188-0.2228401819550.307323069766-0.1309745262430.0559205384398-0.661329612879-0.4034750370180.27770369039-0.0682624357420.6065950946041.36594422826-0.001228214138360.8346676887490.2766857587350.01787722119140.803608019254-0.0009832006865490.54536757382710.7098641662-0.319024272459-5.08014851658
260.107225668848-0.0805301905585-0.005799701641470.1132285039960.01179144299260.01004223831890.7097920709610.5214927539240.455459629685-1.04915602650.1990887684370.05716233297110.211819952968-0.1057306744940.002942648334251.619161836070.0755973342446-0.3880819557611.40061965389-0.2083136028851.15653934058-0.400066799856-6.06779597976-29.3189213987
272.768844355641.56689651266-0.2159785073130.815216338691-0.1050653155312.291179661730.0756475214372-0.0260109921675-0.05547038629190.403067144423-0.1708786446080.04327841819250.6248111362750.01840290227970.000280763022840.8887867954670.2517257626920.04324243775920.6038105271330.0519317026430.6318554196072.82220868556-3.08509111591-2.7820553599
281.68190184699-0.8236794100441.432388197130.509907449951-0.7261608557381.18955514295-0.6421137670310.2042473313440.303825539051-0.598261147274-0.1359114607011.04969865025-0.5050948886110.544154122915-0.0005366095823020.696986723713-0.000313608529698-0.01539210165990.5875494308270.002135621548970.66114191757-4.322251234711.41832964865-6.98849421543
291.56923130923-0.52266461125-1.179641825810.6197748403950.05647845384761.10122687803-0.0834774469264-0.355598528396-0.4224022934480.565499491235-0.03939784171170.8322579423470.88223137129-0.0786989278086-0.001060383017850.747637972722-0.1839016205370.05061252165060.7835024643820.0988058506580.70466695036731.2368981848-7.81861447624-2.8690132332
305.708730572820.9180232788357.14280030542.44456108816-1.220963573952.00071229677-0.362563737509-0.8368070504671.066771991430.0176849626303-1.829270527751.35285439428-1.387046771-1.71622157508-0.3457485788760.6253428768180.162852321173-0.00137583314711.54785637548-0.2304377190261.6791153141840.051124615514.17160082134.29006556691
311.776568648231.211212663850.5716780706740.9057993114370.8747177179781.81669940987-0.3334816693980.251476701968-0.241605987224-0.1136873431020.579492660165-0.2503778192340.5400614771720.06519144063780.0008424984678250.82138454661-0.0709604923328-0.09860688531940.6685443614020.08573641772920.5052709708643.8124162773-8.89244921455-2.48978318741
320.770805989876-0.2334303618640.933710012920.462571143614-0.5989876172651.57585264817-0.2294879711290.315421903291-0.00978545026821-0.3740784202770.372833733413-0.02233276566970.5840330564920.02182395443137.50978960048E-50.9324465044870.02453585381250.1145976281950.685183386153-0.00394727959450.69941466425147.6568784335-1.60927715647-7.51489376082
330.4103043592870.06341979729490.3721526884712.40654253495-2.155523330522.410985316010.1677577603930.08593195159160.225151502324-0.02081904577040.85956843590.4772766684830.28277370069-0.8219557681380.2404562646241.435343563220.3318062997610.2092250525210.984176000377-0.1116527329410.798546846485-17.1274286003-16.740998951225.541081192
341.70672708125-0.6970527409890.4244986484670.715456036256-0.636380533420.4210361117510.154602311974-0.5214681947770.5749647704110.322139387953-0.04862195515010.760299937981-0.906126435522-1.13165387114-0.03174862163151.129312654190.149901919441-0.0001846826413710.78365263901-0.1366904822130.831527083186-8.85746018438-20.747432611523.5087882478
352.993827274610.2629958185382.111497784292.602643147683.587134536495.981921132130.7096315829330.6122843668040.880662420122-2.40073320005-0.3099729781790.6274902165280.959814851427-0.801462193201-0.5400378276161.50566492139-0.2972105680470.1853123474431.257291648650.3942816424320.846223735420.134805545711-20.0470118568-0.463097677104
361.5868045235-0.5268435584880.7774017509470.101315078029-0.2628918395780.388313371619-0.824716036459-0.915874805534-0.323583863004-0.316432425548-0.6521009830870.3401592566960.20578930328-0.775112475734-0.5099930120271.294158027740.117773356756-0.01492941593640.8744409419820.01475690704040.612721560241-2.99309819449-26.926367209329.4275064113
372.90973444565-0.218245291184-0.1049015739970.708868574026-1.794044620915.37478306005-0.0178325859044-1.275985077850.959715304621.77265281714-0.173438428703-0.585209125965-0.4737026682691.11176635575-1.311825357261.185448850740.201135739034-0.1848585222880.345546383106-0.2827789401060.7944943409034.94495738587-16.075144622625.5281612632
382.245749647630.2317295984761.300483688090.3715524414150.05027438251740.7427034577290.3894679936510.3773050391210.005870717887810.8303468168840.8104264646621.07261274112-1.16209746028-0.7683275812280.0005761877430251.14154115817-0.0428223830555-0.05840996785310.504337906167-0.01678002429340.7508670095366.85107624315-26.600263346119.2796027947
391.00728658864-0.10857892951-0.1774048537421.05067365003-0.389113132670.142009250728-0.4659026694430.096189282443-0.274449976691-0.496997082657-0.501430848826-0.2389514322250.697242642511-0.137298362187-0.01174107250070.9182983026730.0479434539857-0.05323782462990.741050985456-0.0879474542770.4770636123082.09215300903-29.235066170523.2438824946
404.37309707157-1.49838845697-1.150349103560.6984294598260.345038944912.27722865136-0.07772552645990.0695073223928-0.329495467625-0.3060422044730.313888854424-0.5564002191161.07156004470.7414345342060.1039763944060.5882819531550.0658868375955-0.1177304407590.8326668746720.09822070958310.85796893916230.9093118139-30.823236398721.631197144
414.207881567271.797671606095.176692833230.8205029379872.310660020836.558581642981.806472389180.249226285561-0.8415613507170.362620930604-0.2293491683171.258541501281.65684084487-1.71921228413-0.03290288874251.85646495040.129924600675-0.3310771204270.7782115091060.2126445036692.1519878778213.1680881684-48.936048791830.5486077707
421.49491633697-0.2610181247390.237143708361.92533551047-0.8723196210760.673563600967-0.5456151528560.994580856217-0.31348016731-0.08627228643640.263148294854-1.408558030530.9336704455630.4255717046870.03100498509550.860242289047-0.0578171779808-0.0198496373330.9866382166590.05921681846230.5290675267822.809928958-24.419509715215.7291685462
435.63188134652-1.308490055884.374181231073.60601356909-0.7250037735833.45899068481-0.334505668435-2.179216164960.6317240484251.753811472140.927617617969-0.599369234885-0.695816751787-0.3191812057010.3321588438360.8685197322890.0872670879072-0.1188927280390.823469699532-0.1964245193740.94631455576418.6292956879-23.597672306229.1234808687
442.57844655784-0.901655056199-0.6015012748982.75742224622-1.22565888632.0347442944-0.4387999920360.424784572922-0.638607278834-1.46505097307-0.319023440675-1.051729328911.57732797417-0.554022163493-0.07599247887320.8868208449270.0777144715437-0.1062043512240.5598858058620.03585377429750.63443626883713.7399730964-29.040892276319.1745396691
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 31 )AA2 - 311 - 30
22chain 'A' and (resid 32 through 105 )AA32 - 10531 - 104
33chain 'A' and (resid 106 through 125 )AA106 - 125105 - 124
44chain 'A' and (resid 126 through 154 )AA126 - 154125 - 153
55chain 'B' and (resid 2 through 20 )BF2 - 201 - 19
66chain 'B' and (resid 21 through 36 )BF21 - 3620 - 35
77chain 'B' and (resid 37 through 42 )BF37 - 4236 - 41
88chain 'B' and (resid 43 through 64 )BF43 - 6442 - 63
99chain 'B' and (resid 65 through 86 )BF65 - 8664 - 82
1010chain 'B' and (resid 87 through 105 )BF87 - 10583 - 101
1111chain 'B' and (resid 106 through 125 )BF106 - 125102 - 121
1212chain 'B' and (resid 126 through 138 )BF126 - 138122 - 134
1313chain 'B' and (resid 139 through 154 )BF139 - 154135 - 150
1414chain 'C' and (resid 2 through 21 )CH2 - 211 - 20
1515chain 'C' and (resid 22 through 31 )CH22 - 3121 - 30
1616chain 'C' and (resid 32 through 105 )CH32 - 10531 - 104
1717chain 'C' and (resid 106 through 126 )CH106 - 126105 - 125
1818chain 'C' and (resid 127 through 153 )CH127 - 153126 - 152
1919chain 'D' and (resid 2 through 20 )DJ2 - 201 - 19
2020chain 'D' and (resid 21 through 40 )DJ21 - 4020 - 39
2121chain 'D' and (resid 41 through 105 )DJ41 - 10540 - 104
2222chain 'D' and (resid 106 through 138 )DJ106 - 138105 - 137
2323chain 'D' and (resid 139 through 154 )DJ139 - 154138 - 153
2424chain 'E' and (resid 3 through 41 )EK3 - 411 - 32
2525chain 'E' and (resid 42 through 78 )EK42 - 7833 - 69
2626chain 'E' and (resid 79 through 86 )EK79 - 8670 - 75
2727chain 'E' and (resid 87 through 125 )EK87 - 12576 - 114
2828chain 'E' and (resid 126 through 152 )EK126 - 152115 - 141
2929chain 'F' and (resid 2 through 77 )FM2 - 771 - 70
3030chain 'F' and (resid 78 through 86 )FM78 - 8671 - 76
3131chain 'F' and (resid 87 through 125 )FM87 - 12577 - 115
3232chain 'F' and (resid 126 through 154 )FM126 - 154116 - 144
3333chain 'G' and (resid 2 through 20 )GO2 - 201 - 19
3434chain 'G' and (resid 21 through 78 )GO21 - 7820 - 77
3535chain 'G' and (resid 79 through 86 )GO79 - 8678 - 85
3636chain 'G' and (resid 87 through 105 )GO87 - 10586 - 104
3737chain 'G' and (resid 106 through 125 )GO106 - 125105 - 124
3838chain 'G' and (resid 126 through 138 )GO126 - 138125 - 137
3939chain 'G' and (resid 139 through 154 )GO139 - 154138 - 153
4040chain 'H' and (resid 2 through 78 )HQ2 - 781 - 77
4141chain 'H' and (resid 79 through 86 )HQ79 - 8678 - 85
4242chain 'H' and (resid 87 through 105 )HQ87 - 10586 - 104
4343chain 'H' and (resid 106 through 125 )HQ106 - 125105 - 124
4444chain 'H' and (resid 126 through 153 )HQ126 - 153125 - 152

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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