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- PDB-9f18: Crystal structure of a first-in-class antibody for alpha-1,6-fuco... -

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基本情報

登録情報
データベース: PDB / ID: 9f18
タイトルCrystal structure of a first-in-class antibody for alpha-1,6-fucosylated prostate-specific antigen
要素
  • Heavy chain rabbit fab
  • Light chain rabbit fab
キーワードIMMUNE SYSTEM / antibody / fab / prostate-specific antigen / PSA / fucosylation / diagnostic assay
生物種Oryctolagus cuniculus (ウサギ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.52 Å
データ登録者Halldorsson, S.
資金援助 スイス, 1件
組織認可番号国
F. Hoffmann-La Roche LTD スイス
引用
ジャーナル: Sci Rep / 年: 2024
タイトル: Development of a first-in-class antibody and a specific assay for alpha-1,6-fucosylated prostate-specific antigen.
著者: Halldorsson, S. / Hillringhaus, L. / Hojer, C. / Muranyi, A. / Schraeml, M. / Lange, M.S. / Tabares, G.
#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2024年4月18日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02024年7月31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
H: Heavy chain rabbit fab
I: Heavy chain rabbit fab
L: Light chain rabbit fab
M: Light chain rabbit fab


分子量 (理論値)分子数
合計 (水以外)93,4444
ポリマ－93,4444
非ポリマー00
水543
1
H: Heavy chain rabbit fab
L: Light chain rabbit fab


分子量 (理論値)分子数
合計 (水以外)46,7222
ポリマ－46,7222
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-28 kcal/mol
Surface area18870 Å2
手法PISA
2
I: Heavy chain rabbit fab
M: Light chain rabbit fab


分子量 (理論値)分子数
合計 (水以外)46,7222
ポリマ－46,7222
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-30 kcal/mol
Surface area18840 Å2
手法PISA
単位格子
Length a, b, c (Å)72.219, 66.735, 91.713
Angle α, β, γ (deg.)90.000, 112.087, 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: 抗体 Heavy chain rabbit fab


分子量: 23764.570 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Oryctolagus cuniculus (ウサギ) / プラスミド: pUC18 / 細胞株 (発現宿主): HEK293 / 発現宿主: Homo sapiens (ヒト)
#2: 抗体 Light chain rabbit fab


分子量: 22957.355 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Oryctolagus cuniculus (ウサギ) / プラスミド: pUC18 / 細胞株 (発現宿主): HEK293 / 発現宿主: Homo sapiens (ヒト)
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 3 / 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

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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: 2.19 Å3/Da / 溶媒含有率: 43.88 %
結晶化温度: 294 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.5
詳細: 100 mM potassium thiocyanate and 30% w/v PEG MME 2000 (poly[ethylene glycol] methyl ether

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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: SLS / ビームライン: X10SA / 波長: 0.9998 Å
検出器タイプ: DECTRIS EIGER2 X 16M / 検出器: PIXEL / 日付: 2021年9月26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: 0.9998 Å / 相対比: 1
反射解像度: 2.52→66.01 Å / Num. obs: 19541 / % possible obs: 90.5 % / 冗長度: 3.1 % / Biso Wilson estimate: 74.63 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.087 / Net I/σ(I): 15.2
反射 シェル解像度: 2.52→2.8 Å / 冗長度: 2.9 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 978 / CC1/2: 0.503 / Rrim(I) all: 1.089 / % possible all: 50.7

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解析

ソフトウェア
名称バージョン分類
PHENIX1.21_5207+SVN精密化
XDS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: 2.52→66.01 Å / SU ML: 0.3938 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 37.5246
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2512 961 4.92 %
Rwork0.1836 18554 -
obs0.1871 19515 70.78 %
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: 80.32 Å2
精密化ステップサイクル: LAST / 解像度: 2.52→66.01 Å
タンパク質核酸リガンド溶媒全体
原子数6450 0 0 3 6453
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00846611
X-RAY DIFFRACTIONf_angle_d0.97219060
X-RAY DIFFRACTIONf_chiral_restr0.05221072
X-RAY DIFFRACTIONf_plane_restr0.00761154
X-RAY DIFFRACTIONf_dihedral_angle_d14.22962262
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.650.5683130.3828241X-RAY DIFFRACTION6.48
2.65-2.820.3502420.3845814X-RAY DIFFRACTION22.05
2.82-3.040.37991460.33062821X-RAY DIFFRACTION75.67
3.04-3.340.32431960.29053672X-RAY DIFFRACTION98.6
3.34-3.830.29881660.22233698X-RAY DIFFRACTION98.45
3.83-4.820.24161850.15693680X-RAY DIFFRACTION97.4
4.82-66.010.20232130.12863628X-RAY DIFFRACTION95.26
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)
13.197258983980.428226610181-0.3087852704732.23289589075-1.309428408485.11922135574-0.212373236338-0.5610844643380.1242369134760.6611951296340.00263458378617-0.529536971911-0.4575164823520.3593313886230.08497780043420.5564086313860.0727482073256-0.1878338120110.422397574868-0.09611955009470.57324362106620.6534741776-16.128512098835.455970399
20.616676857524-0.915771077720.365125745012.47493977578-0.8458555218554.471829770970.00844341286312-0.1542746914030.3535684975320.3383749891320.0391323835206-0.231682794038-0.2525251045910.308154339531-0.05599521605450.505648380040.000577942855908-0.1155897585470.392157579439-0.08034266521120.50306065726919.5417781594-20.583056484330.8521727609
34.64864351231-0.728632617936-0.0885506175023.614501957761.545109125415.246165425370.1986675258580.199524602951-0.7305541794350.427698021392-0.0220872148616-0.6480591719060.6542764590840.353371688106-0.2440018028120.5521703093850.0862863292637-0.1331435693350.363332092493-0.05506312459730.52072501801815.8120130056-49.227788520222.6391206044
44.40405622471-0.804851333062-2.431326632824.178319919441.620354917668.161603223450.2154348855340.156584271354-0.5006625900240.533821795821-0.1524580941110.1670015451410.854812917706-0.0765089955459-0.1477787673830.6889351312670.112882129788-0.1687844474550.4263578664790.006021586316040.59715899348114.1436440352-47.576438253526.368969019
51.879795405980.891824536391-1.330899657256.07446643230.7819192426322.433733932560.565243367068-0.518801738990.5251410692332.47512550847-0.5782356842551.37682100211.20489349516-0.1188841052390.0697298952691.460183586980.1277913405210.4954910475371.209404692030.09398009030370.83367857235646.3260258843-43.422678250636.5110905073
62.759859002680.1642966713010.02025744496950.059848040711-0.1981835178743.809141325380.0363634905151-0.768591672757-0.5574737215991.36004198078-0.2625862147150.4553628026850.9430087775630.1862378983440.1450480131521.0852929422-0.1412761943580.4024872444350.9581276532230.1151151037870.75762132148851.7661561495-48.021998181527.3027914703
76.5710921271-2.139100009180.7048015902780.77144530391-0.314416276170.170579623160.127785241785-0.2163229762660.757108442403-1.318165897680.1089907211460.04968246976910.5262572835661.716640123680.1582569792132.06745255508-0.5765600696530.2906676531771.73444843170.2332347574430.9944064053839.9708663002-59.169617165236.8531066195
82.925783549333.87336457717-0.08628678112146.01893303584-1.529499802649.82665042168-0.603717733657-1.4796937288-1.241369258081.140074651741.43874749544-0.5480767885030.861488071688-0.6517853840620.127563112631.57668820610.7892505086110.2847731123311.027467195180.3055504059920.86071420672654.7754373155-56.954092095632.5106750943
90.1200831000530.410968838385-0.3349143605851.35085867564-1.064360697210.7665875610790.16435761407-1.245188953570.3241723592912.336720727920.04139728022411.11772793515-0.0530698845213-0.3223739333670.179024695782.024506864230.2977682939261.076165573791.818420309530.3418276651990.97824598900345.0576780046-50.146527527239.8569713857
102.219133291111.497111665191.714191435176.472360094752.41101740611.63026973157-0.426310354789-1.43522261065-1.153616402482.035839199240.3262650132010.2811359304870.116793549482-0.546640271965-0.02514065110011.537839358320.4126874352060.1782409611781.410466369050.2007219576860.63421001479556.2691405693-46.506160401336.4997447591
116.26379656642-0.5699341311431.658437040513.930373153592.709059219662.547464713670.07095787519760.1747892030880.3143767496141.173049400190.9299105503030.7079140772670.171806722829-1.50314822295-0.2890832931710.964466256188-0.2835104073370.4750282566310.9412609615660.2530400828590.82475082207646.53186457-45.284475588828.8476692224
121.36982477154-1.753492794260.7234969337162.23132564415-0.8794033252572.3290065869-0.0199253776879-0.0702819368705-1.671980953052.20330034802-0.2216269825521.65408632970.320421498674-1.329747944990.5959610215151.37800470047-0.1242100901290.7914151506071.414501053680.05981289654481.5044313439733.6364534131-56.320358525523.7036755434
132.99497599509-0.806621705783-0.4657687377432.02270712796-0.2072557085353.13649837465-0.220100878171-0.678212575584-0.03846746010620.7278294129460.1821887582180.4457195323240.33152860426-0.9533721251450.03633937611910.628182693291-0.001916342296380.3304328014880.8131865959110.06694803734780.88466712286249.8327517586-41.217335769429.2837427197
144.67284620158-0.043625518830.6723615842014.80672815557-1.20994060595.281744472330.132962872193-0.7063468464110.3382353153090.623965950707-0.894495531939-0.8057653674951.272851222131.618165398320.2076583560380.8387226538470.0951324536458-0.02774083446021.01910803319-0.06728310139530.38343619678463.3507915158-21.846926380332.6374180474
152.86903895228-4.121753891580.3643792364246.95250892937-3.441312349479.474038893241.578591447481.58612264212.46720607964-0.999626250878-1.06473103768-0.722102112108-2.040206183041.594602358931.030750584881.422309578210.1058251200020.1480790575080.7422810516160.2269394295121.4980818961958.2917133708-3.2459155139412.2018698602
167.256077953960.574912909816-1.193793788796.779591545660.6039781367432.517071514110.568382422919-0.9835888657170.3152716693551.55855988673-0.5424359596420.7235775730960.04742901163510.315691225773-0.2677057253580.6278990670420.01754055631560.03452791722550.748940202211-5.04876471794E-50.44802053429356.1549674917-20.087864734325.5019972308
175.129441523171.29730466948-1.228480186385.683321545690.779137572998.58885590074-0.2189023618910.5911837421470.772841528561.05415670750.09332969499050.6679740748870.8258537136960.234412127597-0.1905001969850.6610853563280.09167694829260.1090725057520.5145033913770.03235881412220.50012986913155.2174189277-22.725992490522.4874239281
189.3721525504-2.034281099630.7527363324558.45490995652-1.250873040652.6455815817-0.117864296494-0.321040611421-0.07146713647511.420737511090.009213300096630.918640126013-0.5164462091890.257927681849-0.1740585468990.4924798101840.2237945542380.01071663675950.590543020335-0.03410664647650.36014323820754.8115995582-18.584558917720.4386979226
190.154423270202-0.2203780054190.0637998771390.330447612474-0.0942925751760.1374294703520.3893585089690.1677758493281.45110107644-0.083085582299-0.08127493310.538317355205-1.74940217202-1.14779751088-0.1665195489361.912106494490.4546071417310.0924480391891.059343868310.08589890515971.6316069486746.2047958987-3.4511055229619.5364797145
207.870901437130.283314800872-1.148254473095.356044465741.364813919889.681365757790.214045736897-1.222827099180.8903463411521.5389604150.513000489007-0.0284206819613-0.4238287493910.0111008380089-0.2094558806130.751911079499-0.1146976245780.1570985781680.945774075881-0.09646548433690.46855680708653.3366442251-19.539576855932.0006281589
217.92367411170.588352243324-1.206711873344.046736690781.275614454042.03203467964-0.0596526095079-1.56033775748-0.2213148339151.138147428950.2147014017180.307113841749-1.313515693140.22130794026-0.3616100880141.140212967320.198245203316-0.03504879064340.884280149831-0.1545264555720.94163653891853.8978820302-15.037885191733.2834444405
228.38449491993-1.196477884870.4846731803520.366406020051-0.9881623238444.294488904360.185915952393-0.1550997528482.95360383146-0.1964933707120.18238024311-0.472564372239-2.18959404815-0.39698080521-0.8582714727462.148461203760.718070310654-0.1359733947170.56634941512-0.1499208126631.5347061345658.2669281339-1.5033832453219.7088853052
237.68211799096-3.25354693264-2.56047184329.142526158870.2454873854594.583336241310.2226249030340.2457816977070.14591632062-0.5550708259420.154621404104-0.229281309114-0.7603845490580.3290890934370.02534160575920.2420770776450.02574047004620.0007089789984860.407570683518-0.04172668503020.35476848230519.3749291709-15.731177118.02557745734
246.046612256951.113700384740.1907084958966.314309114892.148302036687.08792372829-0.115913709286-0.5234663505260.2217749949260.2024742705790.292245169509-0.604969911985-1.039158746060.362262264024-0.01424974629310.7376349900680.000172132359302-0.06005549588370.481757204265-0.1331627310820.6648434712724.6626899494-9.8639866243916.9750287003
254.002915542961.42641344264-0.7720669305213.36828972746-2.15286190616.51560759454-0.0837645956569-0.240032578386-0.3651569723720.136926805224-0.827289278942-0.856771225339-0.04285163976531.305618590940.3037119566110.29582102374-0.0524181466479-0.08851352656910.484882724893-0.04676045180420.73814096894531.2437663543-18.259825098414.6494737006
266.040712498412.102889862241.39957971324.48216986551-0.8913208777346.5833064406-0.1659179582060.283683261197-0.367212023505-0.06591249880190.00107430864855-0.779509197916-0.5330527394420.2322269665420.1246190074090.3444924373410.02126266382910.05362148371280.400562134136-0.02421479163380.49573390538625.4095174163-17.585891691810.7590987701
271.761551519310.185864950997-0.5424435318976.356449150434.765646538864.88544299868-0.538530845058-2.634749942212.151065839971.94006993697-0.03937907581860.0654124253394-4.03610553335-1.537942103220.5672653501512.167021279550.0794994652049-0.1588939591061.00639472199-0.2135264621971.1727228992722.5245120054-0.23145398168128.6170227791
280.00417647666745-0.491476485954-0.5461460327089.684311063357.19954908465.275854665030.08641981437530.1073532829590.04222291144441.22805681796-0.8165787395050.8035929093610.695821386267-1.050109338310.6105216502570.4939930617240.0188380460843-0.09565334228680.55700676799-0.1578775464670.47132731500219.5319950977-20.274088051912.6027539491
291.182001080231.08211249201-1.72084798992.94250418317-0.08386987582116.50531415721-0.193649977079-0.1375697323330.119686325798-0.06025577453940.354998171567-0.0340302983691.43213344633-0.7322818100630.1520231347850.7207107668340.0778571449782-0.09066186630970.442194803697-0.09584641598660.5699554619728.86198379658-49.626994284214.8234622273
303.415599089233.14108872906-2.026374057825.56390656598-2.081766659495.28145768659-0.0343637273770.3430879244840.136087871916-0.1733639593490.2692015904360.2459043522330.0273721248887-0.5005925756380.005058818401670.4263215388520.0875976786531-0.07209897933090.498403854501-0.1402436204410.6164699534457.48778767937-43.74539391610.3345405691
314.343356783553.12056408947-0.6418778798736.10104306797-1.368983942373.873786059570.6250557191140.4814910532480.5869992087920.137613826521-0.2661606127131.2137666563-0.0154881395945-1.27961407558-0.1757037744670.6274576170350.2140168894170.07710422497170.8309303940220.003709543312980.873108385181-0.601210864337-42.136270522612.7250463294
322.425641418391.75897431582-1.427836766475.18834499377-1.089691252073.406968850260.01291324007640.0930969201886-0.07049094791450.0795049506175-0.1199905572650.3186901960610.116637093098-0.6760954095810.02074552311530.4990215881180.0509151494998-0.03685391470980.58402151831-0.1080762404810.5645920622036.22691218096-45.165894380911.813491626
334.519374898073.0931682306-3.253351766525.18975054736-1.726703309475.97072661299-0.2103427201030.361518439607-0.37273803459-0.07870531294010.3355345126860.6181534361640.938734880077-0.8484055926280.2559196925950.641681994988-0.164828058093-0.03351437979170.770237359314-0.04777424812110.5893111703373.71627369903-54.87128214268.99710328693
343.58103968276-1.088800435330.8336090671393.344629784710.08249045121097.164171376730.00891706803844-0.123179998274-0.4688169177710.302325282314-0.271528378450.4015451862070.575881595478-0.3637723634340.1316743851390.460488873944-0.08684415607380.1707596390650.4767838225360.132009437340.63412435108848.2713005527-48.825947883211.7755242267
356.029938005360.715126025738-0.1324474142716.111667708360.1484898247473.56951003496-0.253308959434-0.368395557994-0.3254698274280.503577708454-0.04012083902241.290008989830.844315539604-0.4264540293530.07818071428460.554613498617-0.05432299797920.1930337812640.5357485969190.06886362938940.59826648416142.5944172986-48.722790363710.1923096368
361.70117155812-2.028187372242.559803717593.67438927894-3.694498844868.007256737580.132894142814-0.921689277675-0.8579775171972.105830233641.131319702571.114612770874.016377630920.2547389459410.7761841775662.10085567211-0.05145653181720.6774821610420.4239801746981.223275094630.0076702321893950.0552277689-61.42859116626.1845595669
374.81041339321-2.963074409213.137427670643.698065380280.07415411188734.17705583102-0.965693294172-0.25019785672-0.11218143670.279164485536-0.661913609426-1.65390786121-0.4526690567541.470061404491.232087117040.3170829509460.1833848333440.03105425931080.5846751179270.1899098943840.64068070430552.5356119131-40.16667208547.35920085622
383.759118773081.13958090437-1.243351947088.697033740490.2403330301586.53119068756-0.0465087910756-0.6145038025-0.0181152025014-1.35180214864-0.0894953059160.518356021567-0.943659830777-0.613872744182-0.1151711638460.4383180301140.05637777405680.004325640984740.3731400397370.1924496843590.49149789143858.7416756062-17.0490475668.22557043526
392.46880344554.59304932195-1.208036000538.53877584712-2.247780968918.977791671420.403029380843-2.020117431350.2182080605552.03608323725-0.366067440337-0.457148522529-1.786946391540.3928628526440.01080272485471.46845241413-0.3809366978080.04113170655041.1031168831-0.1194963852270.57273979175269.6892923391-10.660577775228.2280188596
401.682853161850.236538312858-1.435557916464.994149283530.2414689761825.45614850426-0.0747938571149-0.3619458869970.07768511873910.1867989899530.0033285909128-0.305653476333-0.0876224295011.310796688490.05328740761010.4061680180210.104377636719-0.02037589269950.6641962000970.1413240823310.49341282486764.8380382661-21.478929674112.6183980015
414.345523670071.541425246140.6978149359428.162926585742.075738279165.35754142983-0.403611187498-0.528484746432-0.600943836722-0.1776890047670.336092188344-1.19815134097-0.3745034602322.76076805258-0.2366022092770.420228634817-0.172153048837-0.09163871062471.206745611760.1314949125960.63899904617271.3570347847-14.71965300898.98659994984
422.21798074295-1.839324122791.024979347332.37671320635-1.839771940144.031660033250.317791299406-1.124197365030.529971499776-0.00308259218333-0.858307719054-0.834779892276-1.257426659780.702909485787-0.06203816144250.783958589615-0.3445073979120.155980695880.8542586951050.004091669833230.75494737178767.5739102583-11.44526779497.68847445553
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 'H' and (resid 2 through 83 )HA2 - 832 - 83
22chain 'H' and (resid 84 through 130 )HA84 - 13084 - 130
33chain 'H' and (resid 131 through 176 )HA131 - 176131 - 176
44chain 'H' and (resid 177 through 224 )HA177 - 224177 - 224
55chain 'I' and (resid 2 through 33 )IB2 - 331 - 32
66chain 'I' and (resid 34 through 51 )IB34 - 5133 - 50
77chain 'I' and (resid 52 through 58 )IB52 - 5851 - 57
88chain 'I' and (resid 59 through 68 )IB59 - 6858 - 67
99chain 'I' and (resid 69 through 77 )IB69 - 7768 - 76
1010chain 'I' and (resid 78 through 91 )IB78 - 9177 - 90
1111chain 'I' and (resid 92 through 99 )IB92 - 9991 - 98
1212chain 'I' and (resid 100 through 110 )IB100 - 11099 - 109
1313chain 'I' and (resid 111 through 123 )IB111 - 123110 - 122
1414chain 'I' and (resid 124 through 135 )IB124 - 135123 - 134
1515chain 'I' and (resid 136 through 145 )IB136 - 145135 - 144
1616chain 'I' and (resid 146 through 165 )IB146 - 165145 - 164
1717chain 'I' and (resid 166 through 186 )IB166 - 186165 - 185
1818chain 'I' and (resid 187 through 196 )IB187 - 196186 - 195
1919chain 'I' and (resid 197 through 201 )IB197 - 201196 - 200
2020chain 'I' and (resid 202 through 211 )IB202 - 211201 - 210
2121chain 'I' and (resid 212 through 219 )IB212 - 219211 - 218
2222chain 'I' and (resid 220 through 224 )IB220 - 224219 - 223
2323chain 'L' and (resid 1 through 25 )LC1 - 251 - 25
2424chain 'L' and (resid 26 through 38 )LC26 - 3826 - 38
2525chain 'L' and (resid 39 through 67 )LC39 - 6739 - 67
2626chain 'L' and (resid 68 through 91 )LC68 - 9168 - 91
2727chain 'L' and (resid 92 through 101 )LC92 - 10192 - 101
2828chain 'L' and (resid 102 through 113 )LC102 - 113102 - 113
2929chain 'L' and (resid 114 through 134 )LC114 - 134114 - 134
3030chain 'L' and (resid 135 through 155 )LC135 - 155135 - 155
3131chain 'L' and (resid 156 through 168 )LC156 - 168156 - 168
3232chain 'L' and (resid 169 through 205 )LC169 - 205169 - 205
3333chain 'L' and (resid 206 through 217 )LC206 - 217206 - 217
3434chain 'M' and (resid 2 through 48 )MD2 - 481 - 47
3535chain 'M' and (resid 49 through 93 )MD49 - 9348 - 92
3636chain 'M' and (resid 94 through 104 )MD94 - 10493 - 103
3737chain 'M' and (resid 105 through 113 )MD105 - 113104 - 112
3838chain 'M' and (resid 114 through 127 )MD114 - 127113 - 126
3939chain 'M' and (resid 128 through 134 )MD128 - 134127 - 133
4040chain 'M' and (resid 135 through 192 )MD135 - 192134 - 191
4141chain 'M' and (resid 193 through 203 )MD193 - 203192 - 202
4242chain 'M' and (resid 204 through 217 )MD204 - 217203 - 216

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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