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- PDB-9g7k: Staphylococcus aureus MazF in complex with Nanobody 12 -

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基本情報

登録情報
データベース: PDB / ID: 9g7k
タイトルStaphylococcus aureus MazF in complex with Nanobody 12
要素
  • Endoribonuclease MazF
  • Nanobody 12
キーワードTOXIN / Toxin-antitoxin system / Ribonuclease / Nanobody
機能・相同性mRNA interferase PemK-like / PemK-like, MazF-like toxin of type II toxin-antitoxin system / Plasmid maintenance toxin/Cell growth inhibitor / endonuclease activity / 加水分解酵素; エステル加水分解酵素 / DNA binding / RNA binding / Endoribonuclease MazF
機能・相同性情報
生物種Staphylococcus aureus (黄色ブドウ球菌)
Lama glama (ラマ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.08687404886 Å
データ登録者Zorzini, V. / Haesaerts, S. / Loris, R.
資金援助 ベルギー, 1件
組織認可番号国
Vrije Universiteit BrusselSPR13 ベルギー
引用ジャーナル: To Be Published
タイトル: Nanobody-mediated activation and inhibition of Staphylococcus aureus MazF
著者: Prolic-Kalinsek, M. / Zorzini, V. / Haesaerts, S. / De Bruyn, P. / Loris, R.
履歴
登録2024年7月21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
A: Endoribonuclease MazF
B: Endoribonuclease MazF
C: Nanobody 12
D: Nanobody 12
E: Endoribonuclease MazF
F: Endoribonuclease MazF
G: Nanobody 12
H: Nanobody 12
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)122,32639
ポリマ－120,0158
非ポリマー2,31131
水9,692538
1
A: Endoribonuclease MazF
B: Endoribonuclease MazF
C: Nanobody 12
D: Nanobody 12
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)60,91816
ポリマ－60,0074
非ポリマー91012
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area8100 Å2
ΔGint-128 kcal/mol
Surface area20350 Å2
2
E: Endoribonuclease MazF
F: Endoribonuclease MazF
G: Nanobody 12
H: Nanobody 12
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)61,40823
ポリマ－60,0074
非ポリマー1,40119
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area8960 Å2
ΔGint-221 kcal/mol
Surface area20180 Å2
単位格子
Length a, b, c (Å)52.190, 61.270, 97.310
Angle α, β, γ (deg.)89.850, 83.890, 67.190
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
Endoribonuclease MazF / SaMazF / Toxin MazF / mRNA interferase MazF


分子量: 14952.206 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Staphylococcus aureus (黄色ブドウ球菌)
遺伝子: mazF, SA1873 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
参照: UniProt: Q7A4G9, 加水分解酵素; エステル加水分解酵素
#2: 抗体
Nanobody 12


分子量: 15051.495 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Lama glama (ラマ) / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
#3: 化合物
ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 11 / 由来タイプ: 合成 / 式: Cl
#4: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 20 / 由来タイプ: 天然 / 式: SO4
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 538 / 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: 2.59 Å3/Da / 溶媒含有率: 52.44 %
結晶化温度: 293 K / 手法: 蒸気拡散法 / pH: 4.6
詳細: 0.2 M ammonium sulphate, 0.1 M Na-cacodylate pH 4.6, 30% (w/v) PEG-4000

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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: SOLEIL / ビームライン: PROXIMA 1 / 波長: 0.978 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2014年7月18日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.978 Å / 相対比: 1
反射解像度: 2.08687404886→47.8627402241 Å / Num. obs: 61618 / % possible obs: 93.8 % / 冗長度: 1.96 % / Biso Wilson estimate: 33.55607078 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.054 / Net I/σ(I): 9.1
反射 シェル解像度: 2.08687404886→2.21 Å / 冗長度: 1.91 % / Rmerge(I) obs: 0.355 / Num. unique obs: 9022 / CC1/2: 0.859 / % possible all: 85

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解析

ソフトウェア
名称バージョン分類
PHENIX1.11.1_2575精密化
XDSデータ削減
XDS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: 2.08687404886→47.8627402241 Å / SU ML: 0.276953173526 / 交差検証法: FREE R-VALUE / σ(F): 1.96221656014 / 位相誤差: 29.0561837828
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.233530947746 3079 5.0008933067 %
Rwork0.189174361156 58490 -
obs0.191407936985 61569 93.7737027278 %
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 mean: 46.8787555474 Å2
精密化ステップサイクル: LAST / 解像度: 2.08687404886→47.8627402241 Å
タンパク質核酸リガンド溶媒全体
原子数7450 0 111 538 8099
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.002373016793167707
X-RAY DIFFRACTIONf_angle_d0.52766080655210485
X-RAY DIFFRACTIONf_chiral_restr0.04491299994111160
X-RAY DIFFRACTIONf_plane_restr0.003905182033391338
X-RAY DIFFRACTIONf_dihedral_angle_d10.70479025074564
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0869-2.11950.33088871892880.3035501729261662X-RAY DIFFRACTION58.2750582751
2.1195-2.15420.3282168352161410.2881518623042690X-RAY DIFFRACTION95.4162453657
2.1542-2.19140.3278532795361440.2774661172862721X-RAY DIFFRACTION95.0879522071
2.1914-2.23120.3270938139221390.2696428162212648X-RAY DIFFRACTION95.6089193825
2.2312-2.27410.3254172958941430.2644782072162734X-RAY DIFFRACTION93.9581972567
2.2741-2.32060.2974586450521390.2464948634422647X-RAY DIFFRACTION95.4109589041
2.3206-2.3710.3140396667821460.2407281353512769X-RAY DIFFRACTION95.9197104311
2.371-2.42620.2662738171861410.2429831701582683X-RAY DIFFRACTION96.0544217687
2.4262-2.48680.3063586100971430.2274635998212723X-RAY DIFFRACTION95.8528428094
2.4868-2.55410.2382359721241450.2212743468142743X-RAY DIFFRACTION96.0745176314
2.5541-2.62920.2852126450111420.2238868733032707X-RAY DIFFRACTION95.1569806279
2.6292-2.71410.3007576965871390.2125837523332628X-RAY DIFFRACTION94.2117807286
2.7141-2.81110.2663205450981430.2107078712742717X-RAY DIFFRACTION95.7161981258
2.8111-2.92360.2567615096561420.217863522382704X-RAY DIFFRACTION94.6143617021
2.9236-3.05660.2515247602641440.2102392135852734X-RAY DIFFRACTION95.8055925433
3.0566-3.21780.2685721243161410.1948464221892675X-RAY DIFFRACTION95.489996609
3.2178-3.41930.2173706112921430.173278703382713X-RAY DIFFRACTION95.9355055425
3.4193-3.68320.2010512823161400.1539104942532667X-RAY DIFFRACTION93.9110070258
3.6832-4.05370.1811813715591420.1381994554212701X-RAY DIFFRACTION95.0200534759
4.0537-4.63990.18126977261440.1280996229592731X-RAY DIFFRACTION96.218206158
4.6399-5.84410.1840307402091450.1577401193212752X-RAY DIFFRACTION96.5666666667
5.8441-47.86274022410.2114236223771450.2000238697522741X-RAY DIFFRACTION97.1063257066
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)
14.247831705250.3542725147970.3090125680372.92494430758-1.657387246434.449440056130.02133487314120.8766929238670.234455837946-1.03012942734-0.0972501646712-0.1946380507340.1850659619180.1304919945770.09433764350080.600573784602-0.02525785256440.06124306774760.4046283157320.02771298468280.37897006121918.7165078134-16.5876223042-34.2678926898
29.53343488013-2.09865128382-4.292126198226.411167154981.715074628475.49438597705-0.200316663039-0.04799190525560.5266233223470.1945570420220.32894476254-0.893012681081-0.234697714580.5177912675470.03795899371970.490379106509-0.0997589175003-0.0828395721030.3739892296520.04035702633180.37725212449321.637441937-5.23921889532-17.0238561846
33.31211039279-0.728236145792-0.4463601736684.31963505575-1.291109974332.61810919203-0.03639792968410.243068406916-0.109729286003-0.690605999810.02471288984340.004885370443070.177805618351-0.227620533391-0.01901167642390.443710303056-0.05979571506120.008708500358370.225630812318-0.01100989648380.24058090172414.0796277786-14.1359349048-28.364726664
48.68315454429-0.4891527552440.8711816156180.176292302718-0.6050133134192.08783143018-0.610919347379-0.3610311796560.0384653079520.3577263629630.198688064651-0.0482653236759-0.2709185271110.394821899620.4043588407450.615419224538-0.0117254576398-0.03616560195760.3827138425330.05530975661690.38241822490819.5131767749-20.8309539514-10.028699212
57.54727789798-0.146335492729-3.562758594080.148635029767-0.3376888613934.29331036237-0.316221918151-0.734678627947-0.673692274994-0.1683919491640.0830017072891-0.2075367065010.4056673651670.6224876614240.3121326923780.496770774982-0.01586805592120.07889006106340.241832940528-0.01699201306260.39970710312522.0033738615-26.7726505437-19.2113388254
62.84553688371-0.38000640712-1.553718426177.1359870123-4.315687565813.75001032337-0.885693485208-0.336411537747-0.1985431989960.693506181503-0.372343652089-1.73622633370.02684092913491.519592998891.092694480580.5948271333140.0263714918333-0.0682211904360.697328904160.03004271393720.62218829575328.816559133-23.9188714224-19.8217079661
71.24442203625-0.4057461646040.5051284945971.3332593438-0.2185749062422.65616784119-0.0583881791231-0.07973651960930.135649322182-0.0705960420945-0.103983334691-0.129536935647-0.143468658076-0.06625747511280.1222108515180.423174563638-0.0485484808288-0.01946457905270.223551314683-0.0198472942360.28483500816.6447657562-11.4508164746-22.3868828771
87.019249151271.31801795824-2.271399559256.34856544734-3.475609211167.62495509986-0.272222512017-0.11160053781-0.392715860886-1.02408500589-0.280059004006-0.5503697944880.6441156687280.7832143575140.4046043243260.546299790503-0.0241432839374-0.008853424781090.381852937167-0.06267818318890.28778602539321.6887440755-20.6152770556-30.2367165559
97.36909260203-3.87354232988-3.608830554666.646801810083.916399132938.393230751660.1646382630240.315149766622-0.749445385649-0.460141723601-0.236046141141-0.1561798701150.452570645213-0.3452950576020.08606091051270.564166915419-0.132779797437-0.02674714561160.3127152794010.001176890757090.3468425104339.11798840211-24.8120164462-19.5062971097
106.42664127585-5.334472037321.70567596486.226802203011.139502921224.07404157565-0.0759652073352-0.474503537574-0.5875505398510.5718803391530.02414364472631.125684308920.893571479853-1.230949866050.168477794060.590884510569-0.191555279128-0.03913142349650.4532736958170.01107815316580.342925183757-0.000695826788493-18.5834126817-14.660943459
113.299205310780.6263183858821.751497590023.032781898412.041348866163.643331740170.520283763663-1.142762990680.6048417394560.711097654965-0.627203118026-0.031340352952-0.152738825469-0.225652759450.1079492175150.556025480511-0.02808871922550.01032277023430.479444057007-0.1248153018880.411407188874.21675350081-1.29645981572-7.83941294395
123.660276108712.25996194610.4409028608178.731945283845.197118530588.18462670627-0.0552900469031-0.1373148035880.235269997336-0.04737624467380.283947728167-0.387689496516-1.432191068420.570028312798-0.1481934171020.636389865441-0.14312813758-0.060667174060.3323404175310.01347383461980.33964476564714.47516489961.2756046207-25.2757995879
135.911926120231.32141312542-0.2717774785444.678306564522.861027614871.951195010630.0464627381583-0.434272547092-0.2277673490640.645735803392-0.1357637184840.103249594336-0.0662895747107-0.2716763680090.1066887555990.405670936921-0.0580253223009-0.03705780129420.294692498474-0.02731981562480.2006830322416.92144581564-6.53695128876-11.6864320246
140.00282186536878-0.03645602506580.004199217644.08828750172-0.515963182490.064610007752-0.3702479484880.2760171365650.74851338418-2.1935924572-0.4881879744471.15456556224-1.0695168107-0.5620095313050.7410022025250.9114414323710.0624095560313-0.2807037285360.423238415954-0.02612102921560.505951031327-1.44580500711-1.24676850616-29.7596759247
153.698361502871.45937574709-1.114041489892.254541608181.987353105086.64180672775-0.1503673211020.3577279764071.2659464772-0.5555545178410.1610217297121.05974054602-0.979567824763-1.24891010162-0.1521557058070.6973768533510.20183690727-0.0508099586270.482914426902-0.03132970530520.712644554775-5.965593798483.09027594752-21.625023755
162.01648362716-0.9850206983170.8526884169994.85923017092-0.1116745335576.10965458466-0.0444752080430.9030377282340.507238438641-0.412593207923-0.2230115753360.112458787705-1.16352154460.0976077519350.2023799693250.4533821687080.00619210761599-0.03363057895710.2962694209320.003911593961110.288455556942.25148211978-3.6423498707-25.4319607004
176.561825811750.889222975314-0.9615152921758.83991599267-0.6109819639592.686209236740.203532776992-0.03501820602310.185146088826-0.0429273896813-0.0963511455464-0.314531080305-0.505133631915-0.148915738084-0.1413203701660.447231554072-0.0172135252516-0.08859371742690.277068349607-0.007041037332070.26136989382913.3438623823-3.18363766824-14.088980885
183.820753396463.749419328314.466173365475.457663771164.097512138815.287665073850.525502787067-0.5172339988140.9604405774860.595354686253-0.6668851678690.396906141871-0.238247708336-0.7225266647650.2014745514530.7228670089290.0293611213406-0.08382494790670.386441843677-0.08838726559650.33974881816-0.4306876095191.52921900581-10.7222231995
193.10932711886-4.10150443399-3.197918712979.48940712595.06860790293.60177053194-0.199742129979-0.6843849628610.1325488770760.6508869942920.06661376636430.4785918674380.914319850228-0.6536504168170.1911257762120.443271462467-0.104024814123-0.05971500871940.480562182953-0.014611240440.306238019833-4.45142258912-11.4984384003-20.7332953077
209.47243522308-5.67816526291-4.43743365655.466952884130.1870224237255.034757340040.08029379872390.396186162404-0.836089180126-1.642845552640.5562541289762.438998846161.77801062165-1.1803973528-0.2653922594810.736670239333-0.164771542891-0.2203265150270.4831324439030.145239566050.7099291513660.931728320257-22.2794856977-26.3475560348
214.813957829711.19131931936-2.019997743825.78960044172-1.624220155528.371399386430.16705254703-0.0802258199133-0.4645867443690.718658623987-0.352595968572-0.910005246801-0.9849933189860.1593466590120.2370859207790.532849069506-0.0433429553936-0.08844955149960.329276270847-0.01834086986240.39061109333131.10149496983.928430695623.42294082746
220.685278767072-0.691059746835-0.5287900989325.26828940894-4.014506844114.914661463170.138199170598-0.887377285469-0.3331668570060.835705188738-0.0135706036047-0.855098943962-0.3147866072170.04906298880280.4685514517180.70142523535-0.181110271032-0.3839652493040.8826728929690.3045567376770.70198756952531.4119799783-11.640301584419.1125944621
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精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -3 through 11 )
2X-RAY DIFFRACTION2chain 'A' and (resid 12 through 22 )
3X-RAY DIFFRACTION3chain 'A' and (resid 23 through 47 )
4X-RAY DIFFRACTION4chain 'A' and (resid 48 through 57 )
5X-RAY DIFFRACTION5chain 'A' and (resid 58 through 66 )
6X-RAY DIFFRACTION6chain 'A' and (resid 67 through 71 )
7X-RAY DIFFRACTION7chain 'A' and (resid 72 through 86 )
8X-RAY DIFFRACTION8chain 'A' and (resid 87 through 95 )
9X-RAY DIFFRACTION9chain 'A' and (resid 96 through 109 )
10X-RAY DIFFRACTION10chain 'A' and (resid 110 through 115 )
11X-RAY DIFFRACTION11chain 'B' and (resid -3 through 11 )
12X-RAY DIFFRACTION12chain 'B' and (resid 12 through 22 )
13X-RAY DIFFRACTION13chain 'B' and (resid 23 through 45 )
14X-RAY DIFFRACTION14chain 'B' and (resid 46 through 57 )
15X-RAY DIFFRACTION15chain 'B' and (resid 58 through 71 )
16X-RAY DIFFRACTION16chain 'B' and (resid 72 through 78 )
17X-RAY DIFFRACTION17chain 'B' and (resid 79 through 86 )
18X-RAY DIFFRACTION18chain 'B' and (resid 87 through 95 )
19X-RAY DIFFRACTION19chain 'B' and (resid 96 through 109 )
20X-RAY DIFFRACTION20chain 'B' and (resid 110 through 116 )
21X-RAY DIFFRACTION21chain 'C' and (resid 1 through 7 )
22X-RAY DIFFRACTION22chain 'C' and (resid 8 through 17 )
23X-RAY DIFFRACTION23chain 'C' and (resid 18 through 28 )
24X-RAY DIFFRACTION24chain 'C' and (resid 29 through 51 )
25X-RAY DIFFRACTION25chain 'C' and (resid 52 through 60 )
26X-RAY DIFFRACTION26chain 'C' and (resid 61 through 73 )
27X-RAY DIFFRACTION27chain 'C' and (resid 74 through 91 )
28X-RAY DIFFRACTION28chain 'C' and (resid 92 through 113 )
29X-RAY DIFFRACTION29chain 'C' and (resid 114 through 123 )
30X-RAY DIFFRACTION30chain 'C' and (resid 124 through 130 )
31X-RAY DIFFRACTION31chain 'D' and (resid 1 through 7 )
32X-RAY DIFFRACTION32chain 'D' and (resid 8 through 17 )
33X-RAY DIFFRACTION33chain 'D' and (resid 18 through 28 )
34X-RAY DIFFRACTION34chain 'D' and (resid 29 through 39 )
35X-RAY DIFFRACTION35chain 'D' and (resid 40 through 51 )
36X-RAY DIFFRACTION36chain 'D' and (resid 52 through 60 )
37X-RAY DIFFRACTION37chain 'D' and (resid 61 through 83 )
38X-RAY DIFFRACTION38chain 'D' and (resid 84 through 100 )
39X-RAY DIFFRACTION39chain 'D' and (resid 101 through 113 )
40X-RAY DIFFRACTION40chain 'D' and (resid 114 through 123 )
41X-RAY DIFFRACTION41chain 'D' and (resid 124 through 131 )
42X-RAY DIFFRACTION42chain 'E' and (resid -3 through 5 )
43X-RAY DIFFRACTION43chain 'E' and (resid 6 through 11 )
44X-RAY DIFFRACTION44chain 'E' and (resid 12 through 22 )
45X-RAY DIFFRACTION45chain 'E' and (resid 23 through 45 )
46X-RAY DIFFRACTION46chain 'E' and (resid 46 through 71 )
47X-RAY DIFFRACTION47chain 'E' and (resid 72 through 113 )
48X-RAY DIFFRACTION48chain 'F' and (resid -1 through 5 )
49X-RAY DIFFRACTION49chain 'F' and (resid 6 through 11 )
50X-RAY DIFFRACTION50chain 'F' and (resid 12 through 22 )
51X-RAY DIFFRACTION51chain 'F' and (resid 23 through 47 )
52X-RAY DIFFRACTION52chain 'F' and (resid 48 through 57 )
53X-RAY DIFFRACTION53chain 'F' and (resid 58 through 71 )
54X-RAY DIFFRACTION54chain 'F' and (resid 72 through 95 )
55X-RAY DIFFRACTION55chain 'F' and (resid 96 through 113 )
56X-RAY DIFFRACTION56chain 'G' and (resid 1 through 17 )
57X-RAY DIFFRACTION57chain 'G' and (resid 18 through 28 )
58X-RAY DIFFRACTION58chain 'G' and (resid 29 through 83 )
59X-RAY DIFFRACTION59chain 'G' and (resid 84 through 100 )
60X-RAY DIFFRACTION60chain 'G' and (resid 101 through 113 )
61X-RAY DIFFRACTION61chain 'G' and (resid 114 through 123 )
62X-RAY DIFFRACTION62chain 'G' and (resid 124 through 131 )
63X-RAY DIFFRACTION63chain 'H' and (resid 1 through 28 )
64X-RAY DIFFRACTION64chain 'H' and (resid 29 through 60 )
65X-RAY DIFFRACTION65chain 'H' and (resid 61 through 83 )
66X-RAY DIFFRACTION66chain 'H' and (resid 84 through 100 )
67X-RAY DIFFRACTION67chain 'H' and (resid 101 through 113 )
68X-RAY DIFFRACTION68chain 'H' and (resid 114 through 123 )
69X-RAY DIFFRACTION69chain 'H' and (resid 124 through 130 )

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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