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- PDB-8upp: Campylobacter jejuni ketol-acid reductoisomerase in complex with ... -

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基本情報

登録情報
データベース: PDB / ID: 8upp
タイトルCampylobacter jejuni ketol-acid reductoisomerase in complex with NADPH and Hoe704
要素Ketol-acid reductoisomerase
キーワードOXIDOREDUCTASE / Inhibitor / Biofuel / Enzyme
機能・相同性
機能・相同性情報


ketol-acid reductoisomerase (NADP+) / ketol-acid reductoisomerase activity / valine biosynthetic process / isoleucine biosynthetic process / isomerase activity / NADP binding / magnesium ion binding / cytosol
類似検索 - 分子機能
Ketol-acid reductoisomerase, prokaryotic / Ketol-acid reductoisomerase, C-terminal / Ketol-acid reductoisomerase / Ketol-acid reductoisomerase, N-terminal / Acetohydroxy acid isomeroreductase, catalytic domain / Acetohydroxy acid isomeroreductase, NADPH-binding domain / KARI N-terminal domain profile. / KARI C-terminal domain profile. / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
類似検索 - ドメイン・相同性
Chem-NDP / : / Ketol-acid reductoisomerase (NADP(+))
類似検索 - 構成要素
生物種Campylobacter jejuni (カンピロバクター)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.78 Å
データ登録者Lin, X. / Lv, Y. / Lonhienne, T. / Guddat, L.W.
資金援助 オーストラリア, 1件
組織認可番号
Australian Research Council (ARC)DP210101802 オーストラリア
引用ジャーナル: Acs Catalysis / : 2024
タイトル: Mapping of the Reaction Trajectory catalyzed by Class I Ketol-Acid Reductoisomerase
著者: Lin, X. / Lonhienne, T. / Lv, Y. / Kurz, J. / McGeary, R. / Schenk, G. / Guddat, L.W.
履歴
登録2023年10月23日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年4月24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

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集合体

登録構造単位
B: Ketol-acid reductoisomerase
H: Ketol-acid reductoisomerase
K: Ketol-acid reductoisomerase
I: Ketol-acid reductoisomerase
D: Ketol-acid reductoisomerase
G: Ketol-acid reductoisomerase
J: Ketol-acid reductoisomerase
E: Ketol-acid reductoisomerase
L: Ketol-acid reductoisomerase
C: Ketol-acid reductoisomerase
F: Ketol-acid reductoisomerase
A: Ketol-acid reductoisomerase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)441,77260
ポリマ-430,41912
非ポリマー11,35348
29,2921626
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area102070 Å2
ΔGint-972 kcal/mol
Surface area125630 Å2
手法PISA
単位格子
Length a, b, c (Å)111.947, 111.954, 111.944
Angle α, β, γ (deg.)110.910, 107.730, 109.760
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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要素

#1: タンパク質
Ketol-acid reductoisomerase


分子量: 35868.223 Da / 分子数: 12 / 由来タイプ: 組換発現
由来: (組換発現) Campylobacter jejuni (カンピロバクター)
遺伝子: ilvC, CW563_00670 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: A0A5T0UG45, ketol-acid reductoisomerase (NADP+)
#2: 化合物...
ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 24 / 由来タイプ: 合成 / : Mg
#3: 化合物
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NADPH


分子量: 745.421 Da / 分子数: 12 / 由来タイプ: 合成 / : C21H30N7O17P3 / タイプ: SUBJECT OF INVESTIGATION
#4: 化合物
ChemComp-X9W / (2R)-(dimethylphosphoryl)(hydroxy)acetic acid


分子量: 152.086 Da / 分子数: 12 / 由来タイプ: 合成 / : C4H9O4P / タイプ: SUBJECT OF INVESTIGATION
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1626 / 由来タイプ: 天然 / : 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: 2.51 Å3/Da / 溶媒含有率: 50.96 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 0.2 M NH4I, 20% PEG3350

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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: Australian Synchrotron / ビームライン: MX1 / 波長: 1 Å
検出器タイプ: ADSC QUANTUM 210r / 検出器: CCD / 日付: 2020年5月10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: 1.78→34.35 Å / Num. obs: 372120 / % possible obs: 93.29 % / 冗長度: 12.3 % / Biso Wilson estimate: 19.53 Å2 / CC1/2: 0.765 / Net I/σ(I): 20.3
反射 シェル解像度: 1.78→3.85 Å / Num. unique obs: 31881 / CC1/2: 0.794

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
XDSデータ削減
XDSデータスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換 / 解像度: 1.78→34.35 Å / SU ML: 0.2925 / 交差検証法: FREE R-VALUE / σ(F): 0.09 / 位相誤差: 33.21
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2984 1907 0.51 %
Rwork0.2644 370213 -
obs0.2646 372120 93.29 %
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: 25.65 Å2
精密化ステップサイクル: LAST / 解像度: 1.78→34.35 Å
タンパク質核酸リガンド溶媒全体
原子数29916 0 708 1626 32250
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.008731176
X-RAY DIFFRACTIONf_angle_d0.974842180
X-RAY DIFFRACTIONf_chiral_restr0.05694752
X-RAY DIFFRACTIONf_plane_restr0.0075400
X-RAY DIFFRACTIONf_dihedral_angle_d9.17654320
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.830.39391180.328322282X-RAY DIFFRACTION78.57
1.83-1.880.30371260.315523937X-RAY DIFFRACTION84.71
1.88-1.930.41471110.295324887X-RAY DIFFRACTION87.52
1.93-1.990.3211290.292425397X-RAY DIFFRACTION89.61
1.99-2.070.3111290.280726194X-RAY DIFFRACTION92.43
2.07-2.150.29471420.27426763X-RAY DIFFRACTION94.26
2.15-2.250.34781350.271726983X-RAY DIFFRACTION95.25
2.25-2.360.31861430.269827128X-RAY DIFFRACTION95.91
2.36-2.510.30591300.270327379X-RAY DIFFRACTION96.51
2.51-2.710.28621390.264427527X-RAY DIFFRACTION97.06
2.71-2.980.34121450.273827680X-RAY DIFFRACTION97.71
2.98-3.410.31761360.268327960X-RAY DIFFRACTION98.37
3.41-4.290.30321610.240728057X-RAY DIFFRACTION98.95
4.29-34.350.22671630.241928039X-RAY DIFFRACTION99.18
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.791927256595-0.142804448912-0.06874520064280.4504991773420.02755503933591.82198768477-0.0456824424034-0.118642378614-0.126241555180.15304880582-0.03842050500020.3586090991780.28149248292-0.7864488829790.1205366644410.184218199327-0.0364010927951-0.004223827794920.47077181608-0.009962697243750.343320770785-45.494-32.311-17.745
20.608137915592-0.5221160428650.6992094034961.94976329419-0.1990900404361.88209565313-0.0806808718880.00664409164063-0.1013320024030.03376572784890.258955586209-0.02150839677070.4599238862120.322146556603-0.04168367900380.376132304399-0.0476581592454-0.01185347037520.26318605178-0.07064736908030.278979992868-33.534-41.57-25.033
31.21215431591-0.1020924091640.3324313143370.826579389839-0.3009227387232.004455666930.0520236238279-0.0297231553752-0.0623022566297-0.2083142348440.006908321348350.1150738151410.152437414999-0.145306934479-0.009059883620270.18979379733-0.0190885135192-0.0346910322650.24940826023-0.0354178148080.219352855347-37.57-28.611-23.993
40.661044078763-0.173959807980.4687283443110.458685716402-0.2970448750061.29036358731-0.02639179860840.0576802940507-0.00194769842460.00716913266647-0.044745443717-0.00227080054030.0266279825782-0.003150887849060.0472337337980.1573672451590.005965075226620.01396481038510.11491310348-0.01751378874760.111030226401-18.75-25.8040.56
52.19550577811-1.26859132399-0.0001627930296192.36461587492-0.2917855429871.33415468834-0.03130937977440.246209678978-0.09290499246160.0274746578164-0.1139516190160.1913535306070.2617863521910.1199280533460.09257641675930.167231466413-0.04233705868510.01282241103110.1859355074290.007496173078260.130023678961-12.995-24.999-21.841
62.165632519514.26370911851-0.6196973469659.16077184128-2.658774411652.83732228506-0.09467763190080.1498994422660.07718269821950.3022972195860.4392122799030.1115164206610.2968515499750.103619959409-0.2452572907860.342759868660.08312754341680.02709808234750.156872411603-0.01892562938960.219437913259-11.041-44.771-4.722
70.752454308817-0.523582379243-0.4848743985170.6736098934390.08884247669260.8523338596930.1515201282620.08856654313380.234320634687-0.290933630450.0482849285377-0.353498640688-0.2841395907490.229642664892-0.1372724271790.347587539442-0.02259053259710.09834382846210.248112761750.05192401432380.28934569174213.34453.233-16.62
81.50443981642-0.1708978935340.675983038731.91546916468-0.113246112421.30640451806-0.300748003942-0.1783823866840.08765742074060.5554967767150.2061756573370.1566129141870.0980589584408-0.0121900452092-0.0258675234120.3710153518930.0375529714623-0.02734654061910.233467700411-0.09919136274580.4126940317988.3757.648-1.243
92.02007007126-0.7007151111510.0845491719881.09589157124-0.3667825621480.9679044299790.00748376263240.05328989648540.293620393311-0.0331807157171-0.06771886651040.0163579286985-0.102050796442-0.0409324743280.04477473016620.2133805073570.01852804210930.004703596012260.1384647622080.008588204015340.2143657739194.03850.554-12.037
100.769394159719-0.05083709827110.1223149068010.679323492843-0.2395416270580.477345218107-0.0226832140748-0.09025175854890.06761891025670.01385187293420.031268696859-0.0994294486363-0.1151646864470.0144365197635-0.008144623427430.1605609811490.01724267771590.006466778277060.121463183874-0.04504648325520.17660696842217.88328.6813.184
111.56927473609-0.6987161343190.2803679887540.604590838714-0.04537864043860.1324216888060.01895554470850.001425618046630.0724135941105-0.01757926767870.04574361243840.03948385948760.001004532425810.0204361741755-0.05291193503780.143274275467-0.005641534287190.01251725865070.1476876831660.0315508748020.1897102902766.17726.5070.732
127.479285142764.016551732751.506885297055.415575097751.077828469921.77020326953-0.1326865723960.02996241975870.2985189562040.05688680125780.1423905420980.2287714566-0.001940153470580.151585725928-0.03364951203250.2630017846730.0522401121104-0.05974499832560.265918582617-0.09526989933330.2336424822519.75537.39618.315
132.35192966212-0.358985979612-0.7359638926430.788494228827-0.07007462940852.2839672492-0.001462525841970.05398816716870.2941503291730.0888031356767-0.0541657810956-0.353061457791-0.244991248772-0.104484311949-0.00254718467190.15343762003-0.0227214517881-0.06003130932750.202646863605-0.001108436540870.37303616426644.46531.8713.734
141.11431306944-0.4532336020180.1314190061831.72200526324-0.1359007980860.8558651062470.0725829587851-0.05276813894330.1302554308040.071246281731-0.0475163812877-0.209142697670.01692571569120.1279186193370.0004762088281610.155495898669-0.00399605351732-0.0267774932630.219548030197-0.01637603196470.20395108697443.35523.98214.381
151.26698108007-0.5983366612410.619775020870.492176298211-0.3948061394830.3818115475720.02269609518040.01583349106440.046761857458-0.0200205726987-0.01995208664410.01711967928210.0171801884230.0277429650051-0.0008657065277590.1357295290990.01197820572520.003937805706720.11412265485-0.01252579028790.15070520120315.25626.5391.505
160.880897901112-0.585917127646-0.02673166600831.32597306923-1.253844335831.543670529450.02333428030070.1438791504170.1025740561450.0944774930186-0.061948306594-0.277375015417-0.193329123575-0.0578280633970.05508282329990.1900404620710.000265524628095-0.01720026653810.17108785628-0.03040591140230.20072738811729.92320.137-7.916
171.645950469690.88051080962-0.2737177743650.7789761209570.1452124252950.9563296737340.375668718601-0.6214666592140.03905388785410.183088405762-0.313055214241-0.142032733104-0.183941795280.181309448444-0.08847052176640.279402330726-0.0497190860072-0.04188627596610.3783044849580.03778157027960.15076321551615.168-11.37354.539
182.726407501360.129352554820.03270466977931.210653755230.4363209743572.06837722258-0.217043879115-0.091180948252-0.4678452147050.1712617731230.09538122482430.1405306342350.4401836122650.144462146120.01455679832290.321719268058-0.00821543921159-0.0198341872440.292316888810.1070814091790.29352537253710.62-27.07150.759
192.323625016580.222166894115-0.4634980261570.8695540440410.1275589786721.344387892980.178458208353-0.328811365022-0.07029242905270.23902525932-0.1274109617210.0844233347899-0.01952842148570.133218249848-0.01880028100330.225231284635-0.0291512891197-0.02448244800760.198923886955-0.0001186170857620.139973562535.855-14.31450.152
200.9961253289380.298879592762-0.7092874320020.59674564789-0.3711620936010.7792780875950.00376528812887-0.0940287026761-0.0893039706590.0261781197670.0223632543837-0.1396761416320.05890659551790.1162637156-0.01181679832570.1185821001120.0308644764961-0.01765668379460.1583385654060.004082955905480.14361805509320.796-14.21221.64
211.731236566280.664426183777-0.7030510780721.030614516970.4666407477630.7993696191380.009219022850670.03145360197930.02258404755480.107252821157-0.02625259573750.02306296647660.0308154259436-0.006935352544620.05409669405710.132388459250.0167734918702-0.0324969698410.1452180563150.0007586905632380.1059526168690.445-14.83926.091
220.3814703214350.434786120630.441824050860.912159090582-0.2097833660811.69539929312-0.4408942258950.187506679651-1.04988058499-0.2579760565060.140985743279-0.4659058476820.6850954403490.4940589966520.2237637192840.3804142632520.04392843795710.1526262455870.3234140595330.03889245744540.60672498921819.27-36.37617.104
231.09720571144-0.2155098807130.9433238981691.16262550659-0.2789339542280.914572702047-0.2750453106480.08853057674220.0082433907767-0.2718250511380.23716389056-0.0804542943892-0.1383779322740.209086350263-0.01554681912750.290340810512-0.07126168126510.07871997673710.2276507028-0.02931192088650.20112331482742.8692.036-37.083
242.003669590650.07094434457531.055220256241.908149745930.02765462517432.148255083960.20135181039-0.0592789141417-0.27448493334-0.1416859941980.385117590949-0.2722696602470.555976599942-0.0898034715561-0.1900526038770.2493322021840.02375249327270.09059351955350.281338947907-0.08479089952730.4272533009849.708-9.802-27.333
252.135124236730.410421879230.2906669394930.9771181241270.1356812606251.486443834030.147334015219-0.0572298073115-0.332993623568-0.07049621979090.064927551988-0.2429069986650.07689445770110.440484158065-0.1814108193440.203283634091-0.01313325553830.007549773742540.2836129408370.002291362565710.2573024964751.411-0.406-20.527
260.908760053484-0.107487083953-0.003367724576930.11903185845-0.1838665156151.35408701471-0.03869492809530.04254610699760.132365015859-0.117164440233-0.0300050363952-0.0836791230504-0.1143247666040.1393920928070.0151592433840.193553831482-0.02580632497980.04795496291320.1818445314420.01204281863310.17709599442941.844.152-27.815
270.5415844447090.4447927448890.2439863216410.801179684535-0.04201512601970.176868577715-0.0398621248791-0.007510608042840.033497788069-0.1592039201870.0141206710478-0.02398768172410.05566934702340.0441536262268-0.004616712458990.1327479513840.007413229742830.007479242732760.1354257569520.00324337035150.11953581114822.526-11.319-21.419
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精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 3:27 )B3 - 27
2X-RAY DIFFRACTION2( CHAIN B AND RESID 28:60 )B28 - 60
3X-RAY DIFFRACTION3( CHAIN B AND RESID 61:184 )B61 - 184
4X-RAY DIFFRACTION4( CHAIN B AND RESID 185:284 )B185 - 284
5X-RAY DIFFRACTION5( CHAIN B AND RESID 285:313 )B285 - 313
6X-RAY DIFFRACTION6( CHAIN B AND RESID 314:329 )B314 - 329
7X-RAY DIFFRACTION7( CHAIN H AND RESID 3:27 )H3 - 27
8X-RAY DIFFRACTION8( CHAIN H AND RESID 28:60 )H28 - 60
9X-RAY DIFFRACTION9( CHAIN H AND RESID 61:184 )H61 - 184
10X-RAY DIFFRACTION10( CHAIN H AND RESID 185:251 )H185 - 251
11X-RAY DIFFRACTION11( CHAIN H AND RESID 252:313 )H252 - 313
12X-RAY DIFFRACTION12( CHAIN H AND RESID 314:329 )H314 - 329
13X-RAY DIFFRACTION13( CHAIN K AND RESID 3:53 )K3 - 53
14X-RAY DIFFRACTION14( CHAIN K AND RESID 54:184 )K54 - 184
15X-RAY DIFFRACTION15( CHAIN K AND RESID 185:284 )K185 - 284
16X-RAY DIFFRACTION16( CHAIN K AND RESID 285:329 )K285 - 329
17X-RAY DIFFRACTION17( CHAIN I AND RESID 3:27 )I3 - 27
18X-RAY DIFFRACTION18( CHAIN I AND RESID 28:60 )I28 - 60
19X-RAY DIFFRACTION19( CHAIN I AND RESID 61:184 )I61 - 184
20X-RAY DIFFRACTION20( CHAIN I AND RESID 185:267 )I185 - 267
21X-RAY DIFFRACTION21( CHAIN I AND RESID 268:311 )I268 - 311
22X-RAY DIFFRACTION22( CHAIN I AND RESID 312:329 )I312 - 329
23X-RAY DIFFRACTION23( CHAIN D AND RESID 3:27 )D3 - 27
24X-RAY DIFFRACTION24( CHAIN D AND RESID 28:61 )D28 - 61
25X-RAY DIFFRACTION25( CHAIN D AND RESID 62:94 )D62 - 94
26X-RAY DIFFRACTION26( CHAIN D AND RESID 95:173 )D95 - 173
27X-RAY DIFFRACTION27( CHAIN D AND RESID 174:230 )D174 - 230
28X-RAY DIFFRACTION28( CHAIN D AND RESID 231:251 )D231 - 251
29X-RAY DIFFRACTION29( CHAIN D AND RESID 252:313 )D252 - 313
30X-RAY DIFFRACTION30( CHAIN D AND RESID 314:329 )D314 - 329
31X-RAY DIFFRACTION31( CHAIN G AND RESID 3:52 )G3 - 52
32X-RAY DIFFRACTION32( CHAIN G AND RESID 53:201 )G53 - 201
33X-RAY DIFFRACTION33( CHAIN G AND RESID 202:284 )G202 - 284
34X-RAY DIFFRACTION34( CHAIN G AND RESID 285:329 )G285 - 329
35X-RAY DIFFRACTION35( CHAIN J AND RESID 3:27 )J3 - 27
36X-RAY DIFFRACTION36( CHAIN J AND RESID 28:60 )J28 - 60
37X-RAY DIFFRACTION37( CHAIN J AND RESID 61:161 )J61 - 161
38X-RAY DIFFRACTION38( CHAIN J AND RESID 162:251 )J162 - 251
39X-RAY DIFFRACTION39( CHAIN J AND RESID 252:313 )J252 - 313
40X-RAY DIFFRACTION40( CHAIN J AND RESID 314:329 )J314 - 329
41X-RAY DIFFRACTION41( CHAIN E AND RESID 3:27 )E3 - 27
42X-RAY DIFFRACTION42( CHAIN E AND RESID 28:59 )E28 - 59
43X-RAY DIFFRACTION43( CHAIN E AND RESID 60:134 )E60 - 134
44X-RAY DIFFRACTION44( CHAIN E AND RESID 135:184 )E135 - 184
45X-RAY DIFFRACTION45( CHAIN E AND RESID 185:230 )E185 - 230
46X-RAY DIFFRACTION46( CHAIN E AND RESID 231:251 )E231 - 251
47X-RAY DIFFRACTION47( CHAIN E AND RESID 252:313 )E252 - 313
48X-RAY DIFFRACTION48( CHAIN E AND RESID 314:329 )E314 - 329
49X-RAY DIFFRACTION49( CHAIN L AND RESID 3:27 )L3 - 27
50X-RAY DIFFRACTION50( CHAIN L AND RESID 28:47 )L28 - 47
51X-RAY DIFFRACTION51( CHAIN L AND RESID 48:73 )L48 - 73
52X-RAY DIFFRACTION52( CHAIN L AND RESID 74:134 )L74 - 134
53X-RAY DIFFRACTION53( CHAIN L AND RESID 135:201 )L135 - 201
54X-RAY DIFFRACTION54( CHAIN L AND RESID 202:269 )L202 - 269
55X-RAY DIFFRACTION55( CHAIN L AND RESID 270:297 )L270 - 297
56X-RAY DIFFRACTION56( CHAIN L AND RESID 298:329 )L298 - 329
57X-RAY DIFFRACTION57( CHAIN C AND RESID 3:52 )C3 - 52
58X-RAY DIFFRACTION58( CHAIN C AND RESID 53:134 )C53 - 134
59X-RAY DIFFRACTION59( CHAIN C AND RESID 135:156 )C135 - 156
60X-RAY DIFFRACTION60( CHAIN C AND RESID 157:251 )C157 - 251
61X-RAY DIFFRACTION61( CHAIN C AND RESID 252:284 )C252 - 284
62X-RAY DIFFRACTION62( CHAIN C AND RESID 285:329 )C285 - 329
63X-RAY DIFFRACTION63( CHAIN F AND RESID 3:27 )F3 - 27
64X-RAY DIFFRACTION64( CHAIN F AND RESID 28:59 )F28 - 59
65X-RAY DIFFRACTION65( CHAIN F AND RESID 60:114 )F60 - 114
66X-RAY DIFFRACTION66( CHAIN F AND RESID 115:134 )F115 - 134
67X-RAY DIFFRACTION67( CHAIN F AND RESID 135:184 )F135 - 184
68X-RAY DIFFRACTION68( CHAIN F AND RESID 185:251 )F185 - 251
69X-RAY DIFFRACTION69( CHAIN F AND RESID 252:313 )F252 - 313
70X-RAY DIFFRACTION70( CHAIN F AND RESID 314:329 )F314 - 329
71X-RAY DIFFRACTION71( CHAIN A AND RESID 3:47 )A3 - 47
72X-RAY DIFFRACTION72( CHAIN A AND RESID 48:74 )A48 - 74
73X-RAY DIFFRACTION73( CHAIN A AND RESID 75:184 )A75 - 184
74X-RAY DIFFRACTION74( CHAIN A AND RESID 185:251 )A185 - 251
75X-RAY DIFFRACTION75( CHAIN A AND RESID 252:313 )A252 - 313
76X-RAY DIFFRACTION76( CHAIN A AND RESID 314:329 )A314 - 329

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月:コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか? / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例:em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る