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- PDB-6yay: Crystal structure of a Selenium-derivatized complex of the bacter... -

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基本情報

登録情報
データベース: PDB / ID: 6yay
タイトルCrystal structure of a Selenium-derivatized complex of the bacterial cellulose secretion regulators BcsR and BcsQ, crystallized in the presence of ADP
要素
  • Bacterial cellulose secretion regulator BcsQ
  • Bacterial cellulose secretion regulator BcsR
キーワードSIGNALING PROTEIN / Bacterial biofilms / Bacterial cellulose / Bacterial secretion system / ATP binding protein
機能・相同性
機能・相同性情報


bacterial cellulose biosynthetic process / negative regulation of cell division / cytoplasmic side of plasma membrane / cell division / ATP hydrolysis activity / ATP binding / cytosol
類似検索 - 分子機能
Cellulose synthase operon protein BcsQ / Protein YhjR / Cellulose biosynthesis protein BcsQ / Cellulose biosynthesis protein BcsR-like / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
ADENOSINE-5'-TRIPHOSPHATE / Cell division protein / Cellulose biosynthesis protein BcsR / Protein YhjR / Cellulose biosynthesis protein BcsQ
類似検索 - 構成要素
生物種Escherichia coli (大腸菌)
手法X線回折 / シンクロトロン / 単波長異常分散 / 解像度: 2.09 Å
データ登録者Abidi, W. / Caleechurn, M. / Zouhir, S. / Roche, S. / Krasteva, P.V.
資金援助5件
組織認可番号国
ATIP-Avenir
European Research Council (ERC)BioMatrix, ERC StG #757507
Centre National de la Recherche Scientifique (CNRS)
Institute for Integrative Biology of the Cell (I2BC)
European Institute of Chemistry and Biology (IECB)
引用ジャーナル: Sci Adv / 年: 2021
タイトル: Architecture and regulation of an enterobacterial cellulose secretion system.
著者: Wiem Abidi / Samira Zouhir / Meryem Caleechurn / Stéphane Roche / Petya Violinova Krasteva /
要旨: Many free-living and pathogenic enterobacteria secrete biofilm-promoting cellulose using a multicomponent, envelope-embedded Bcs secretion system under the control of intracellular second messenger c- ...Many free-living and pathogenic enterobacteria secrete biofilm-promoting cellulose using a multicomponent, envelope-embedded Bcs secretion system under the control of intracellular second messenger c-di-GMP. The molecular understanding of system assembly and cellulose secretion has been largely limited to the crystallographic studies of a distantly homologous BcsAB synthase tandem and a low-resolution reconstruction of an assembled macrocomplex that encompasses most of the inner membrane and cytosolic subunits and features an atypical layered architecture. Here, we present cryo-EM structures of the assembled Bcs macrocomplex, as well as multiple crystallographic snapshots of regulatory Bcs subcomplexes. The structural and functional data uncover the mechanism of asymmetric secretion system assembly and periplasmic crown polymerization and reveal unexpected subunit stoichiometry, multisite c-di-GMP recognition, and ATP-dependent regulation.
履歴
登録2020年3月14日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02021年2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
A: Bacterial cellulose secretion regulator BcsQ
B: Bacterial cellulose secretion regulator BcsQ
C: Bacterial cellulose secretion regulator BcsR
D: Bacterial cellulose secretion regulator BcsR
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)74,1628
ポリマ－73,0994
非ポリマー1,0634
水84747
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
  • 根拠: light scattering, SEC-MALS measurements confirmed the existence of a stable and monodisperse BcsR2Q2 heterotetramer in solution.
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area11370 Å2
ΔGint-80 kcal/mol
Surface area20410 Å2
手法PISA
単位格子
Length a, b, c (Å)57.060, 78.780, 66.600
Angle α, β, γ (deg.)90.000, 99.280, 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 Bacterial cellulose secretion regulator BcsQ / Cellulose biosynthesis protein BcsQ / Cellulose synthase operon protein YhjQ / Cellulose synthase / ...Cellulose biosynthesis protein BcsQ / Cellulose synthase operon protein YhjQ / Cellulose synthase / putative / Bacterial cellulose synthesis subunit Q


分子量: 29479.682 Da / 分子数: 2 / 由来タイプ: 組換発現
詳細: Bacterial cellulose synthesis subunit Q. The coding region corresponding to the BcsRQ tandem was cloned into the pET21b expression vector with a C-terminal hexahistidine Tag on BcsQ. The ...詳細: Bacterial cellulose synthesis subunit Q. The coding region corresponding to the BcsRQ tandem was cloned into the pET21b expression vector with a C-terminal hexahistidine Tag on BcsQ. The purified selenium derivated BcsRQ complex was treated with EDTA and incubated with ADP prior to crystallisation.
由来: (組換発現) Escherichia coli (大腸菌)
遺伝子: bcsQ, yhjQ, A8C65_00290, ACU57_05335, BMT91_17060, BON75_10030, BvCmsHHP019_01723, BvCmsSINP011_05061, C2U48_15650, D3O91_11725, D9H68_14440, D9I18_15755, D9I97_13990, DAH34_22885, DAH37_ ...遺伝子: bcsQ, yhjQ, A8C65_00290, ACU57_05335, BMT91_17060, BON75_10030, BvCmsHHP019_01723, BvCmsSINP011_05061, C2U48_15650, D3O91_11725, D9H68_14440, D9I18_15755, D9I97_13990, DAH34_22885, DAH37_19450, E2127_16420, E2128_18010, E2129_18145, E2134_17810, EAI42_04085, EC1094V2_71, NCTC10429_00778, NCTC11022_03734, NCTC9058_01652
発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: A0A0B1KWQ0, UniProt: P0DP92*PLUS
#2: タンパク質 Bacterial cellulose secretion regulator BcsR / FIG004405: Putative cytoplasmic protein / Protein YhjR / Protein of uncharacterized function ...FIG004405: Putative cytoplasmic protein / Protein YhjR / Protein of uncharacterized function (DUF2629) / Bacterial cellulose synthesis subunit R


分子量: 7069.771 Da / 分子数: 2 / 由来タイプ: 組換発現
詳細: Bacterial cellulose synthesis subunit R. The coding region corresponding to the BcsRQ tandem was cloned into the pET21b expression vector with a C-terminal hexahistidine Tag on BcsQ. The ...詳細: Bacterial cellulose synthesis subunit R. The coding region corresponding to the BcsRQ tandem was cloned into the pET21b expression vector with a C-terminal hexahistidine Tag on BcsQ. The purified selenium derivated BcsRQ complex was treated with EDTA and incubated with ADP prior to crystallisation.
由来: (組換発現) Escherichia coli (大腸菌)
遺伝子: yhjR, A6V01_14365, A8C65_00295, A9R57_18690, AC789_1c39040, ACN002_3620, ACN68_06780, ACN81_08775, ACU57_05330, ACU90_15155, AM270_16530, AM464_10395, AMK83_17075, AML07_15400, APZ14_ ...遺伝子: yhjR, A6V01_14365, A8C65_00295, A9R57_18690, AC789_1c39040, ACN002_3620, ACN68_06780, ACN81_08775, ACU57_05330, ACU90_15155, AM270_16530, AM464_10395, AMK83_17075, AML07_15400, APZ14_14840, AUQ13_21010, AUS26_05355, AW106_19925, BANRA_02188, BANRA_03431, BANRA_04333, BANRA_04566, BB545_03705, BHS81_21135, BHS87_19835, BJJ90_00965, BK292_24575, BMT91_17065, BN17_34711, BOH76_20305, BON63_23095, BON69_12460, BON71_17720, BON72_13310, BON76_21180, BON94_21140, BON95_21275, BTQ06_14355, BUE81_10045, BvCms12BK_03867, BvCms2454_00062, BvCms28BK_00015, BvCmsHHP001_04915, BvCmsHHP019_01722, BvCmsHHP056_04702, BvCmsKKP036_02918, BvCmsKKP061_02263, BvCmsKSNP073_03410, BvCmsKSNP081_04400, BvCmsKSP011_02716, BvCmsKSP024_02867, BvCmsKSP026_02341, BvCmsKSP045_00352, BvCmsKSP067_01939, BvCmsNSNP036_04602, BvCmsNSP006_05307, BvCmsNSP047_03956, BvCmsNSP072_04054, BvCmsOUP014_03413, BvCmsSINP011_05062, BvCmsSIP019_02407, BvCmsSIP044_03516, BVL39_08345, BW690_01625, BZL31_14290, C2U48_15645, C5N07_21610, C5P01_24180, C6669_10230, C7235_01450, C7B02_19840, C9098_17010, C9114_22000, C9141_22075, C9160_22970, C9162_26275, C9182_22470, C9201_19395, C9306_17625, C9E25_16190, C9Z03_00095, C9Z28_19620, C9Z37_15395, C9Z39_13945, C9Z69_16745, C9Z89_13935, CA593_08480, CI641_010930, COD30_23820, COD46_13475, CR538_01230, CRD98_22705, CRM83_21580, CWS33_18425, D0X26_22825, D2184_20785, D2185_17650, D3821_09240, D3Y67_04435, D6T60_22230, D9D20_19605, D9E35_13135, D9H68_14435, D9I18_15750, D9I97_13985, D9J11_18915, D9J44_18935, D9K48_10615, D9K54_10550, DAH18_11545, DAH30_06135, DAH32_17855, DAH34_22880, DAH37_19445, DBQ99_02170, DEN89_25155, DEN97_17470, DEO04_20390, DEO19_17140, DIV22_07035, DJ503_16110, DL545_01700, DL800_25095, DP277_20930, DQF57_09495, DQO13_19235, DS732_25515, DTL43_22125, DXT69_13975, DXT71_18500, DXT73_16115, E0I42_16815, E0J34_09730, E0K84_22700, E2119_10885, E2127_16425, E2128_18015, E2129_18150, E2134_17815, E2135_13675, E2855_04489, E2863_04566, E3B71_14240, E5P22_13630, E5P28_15170, E5P37_17785, E5S35_16770, E5S47_16125, EAI42_04080, EC1094V2_70, EC3234A_62c00180, EC3426_04694, EC95NR1_02922, ED600_16775, EEP23_03690, EHH55_25990, EJC75_16880, EKI52_16535, EL75_0168, EL79_0179, EL80_0171, ELT20_13340, ELV08_08625, EPT01_13645, EQ825_24275, ERS085365_03384, ERS085374_03939, ERS085379_03461, ERS085416_01810, ERS139211_03246, EXX13_15900, EXX71_20125, EXX78_22145, EYD11_00910, EYY78_10840, F0312_08835, F1E03_18480, F1E19_10145, F7F23_20655, F7F29_18335, FORC82_0211, FQ915_11140, FQR64_01380, FRV13_18835, FTV90_03830, FTV92_19380, FV293_20875, FWK02_16270, FY127_16255, HW43_22525, NCTC10090_03288, NCTC10418_00365, NCTC10429_00777, NCTC10865_00350, NCTC11022_03735, NCTC11126_00353, NCTC11181_02507, NCTC11341_02195, NCTC13148_03788, NCTC8009_01140, NCTC8179_05669, NCTC8500_00017, NCTC8960_02842, NCTC8985_04684, NCTC9045_00297, NCTC9055_02150, NCTC9058_01653, NCTC9062_02927, NCTC9111_00632, NCTC9703_04725, NCTC9706_02488, PGD_04560, PU06_03455, RG28_22775, RK56_020175, RX35_03299, SAMEA3472043_03895, SAMEA3472055_04880, SAMEA3472070_03765, SAMEA3472114_02155, SAMEA3484427_00198, SAMEA3484429_02974, SAMEA3752553_00829, SAMEA3752557_03916, SAMEA3752559_00583, SAMEA3753064_01978, SAMEA3753290_02280, SAMEA3753300_03978, SK85_03853, UN86_19365, WQ89_12680, WR15_14750
発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: J7QAC9, UniProt: P0ADJ3*PLUS
#3: 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: 2 / 由来タイプ: 合成 / 式: Mg
#4: 化合物 ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / ATP


分子量: 507.181 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C10H16N5O13P3 / タイプ: SUBJECT OF INVESTIGATION / コメント: ATP, エネルギー貯蔵分子*YM
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 47 / 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: 2.11 Å3/Da / 溶媒含有率: 41.75 %
結晶化温度: 277.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: PEG 2000, MES pH6.5, glycerol

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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 2 / 波長: 0.97857 Å
検出器タイプ: DECTRIS EIGER2 X 9M / 検出器: PIXEL / 日付: 2017年3月11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: 0.97857 Å / 相対比: 1
反射解像度: 2.09→50 Å / Num. obs: 66678 / % possible obs: 98.4 % / 冗長度: 3.9 % / Biso Wilson estimate: 43.53 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.56
反射 シェル解像度: 2.09→2.22 Å / 冗長度: 3.52 % / Mean I/σ(I) obs: 1.15 / Num. unique obs: 10300 / CC1/2: 0.612 / % possible all: 94

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解析

ソフトウェア
名称バージョン分類
PHENIX1.17rc2_3619精密化
Cootモデル構築
PHASER位相決定
SHELXDE位相決定
XDSデータスケーリング
XDSdata processing
XDSデータ削減
精密化構造決定の手法: 単波長異常分散 / 解像度: 2.09→46.64 Å / SU ML: 0.271 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 33.8254
Rfactor反射数%反射
Rfree0.2231 1711 5.02 %
Rwork0.192 --
obs0.1936 34116 98.73 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso mean: 67.37 Å2
精密化ステップサイクル: LAST / 解像度: 2.09→46.64 Å
タンパク質核酸リガンド溶媒全体
原子数4349 0 64 47 4460
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00224520
X-RAY DIFFRACTIONf_angle_d0.49796163
X-RAY DIFFRACTIONf_chiral_restr0.038695
X-RAY DIFFRACTIONf_plane_restr0.0026821
X-RAY DIFFRACTIONf_dihedral_angle_d12.47242702
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.150.46391280.44852490X-RAY DIFFRACTION91.38
2.15-2.220.41161420.37782689X-RAY DIFFRACTION99.37
2.22-2.30.36271450.31432715X-RAY DIFFRACTION99.2
2.3-2.390.28511420.26552700X-RAY DIFFRACTION99.16
2.39-2.50.31671440.23282705X-RAY DIFFRACTION99.13
2.5-2.630.26361430.20932676X-RAY DIFFRACTION99.47
2.63-2.80.26231420.19882723X-RAY DIFFRACTION99.34
2.8-3.010.22561450.18592729X-RAY DIFFRACTION99.52
3.01-3.320.2241400.18222711X-RAY DIFFRACTION99.27
3.32-3.80.19571450.17192726X-RAY DIFFRACTION99.45
3.8-4.780.17481470.1552746X-RAY DIFFRACTION99.66
4.78-46.640.18391480.16532795X-RAY DIFFRACTION99.86
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)
10.1310488724580.1585945766350.04404680007660.203091595282-0.09869682134360.1803178722480.0152488632518-0.152207756594-0.102008882707-0.9193778481140.1779396005020.5459957877290.00427710367172-0.03753080279084.42141213437E-50.659191464613-0.0125233234085-0.1187196558130.538010914794-0.01124191448930.5775493758917.34587574958-17.66048878097.7979324466
20.599332691824-0.0899800363543-0.2092569272940.01104404551280.0294335448490.1185476601050.4349314617570.0973346898647-0.495622261438-0.304591895613-0.06193692172050.0744770008953-0.0506429816090.150429271091-5.75917331539E-51.09415990871-0.0101008417136-0.2651010927010.595707077678-0.06273307314520.6816594964779.17540487875-19.2522063718-0.291529663703
30.650327151440.0907395513269-0.2230389387180.1382575743080.2164998236340.4453736178070.07541412794230.621197266629-0.0942303116408-1.36316269681-0.00211219531736-0.00460300947135-0.004855479567080.477947320134-0.01068286759291.25327083091-0.0460755012651-0.06234012539940.673951577178-0.0008255035745220.46735628087416.9833188976-12.8883896712-6.89548838284
41.12488268142-0.324344056084-0.3588546370040.163230140797-0.1220095010570.653809521786-0.03541777248320.1867814578330.170362788705-0.2064204832830.119512908749-0.174376920303-0.1251059144090.175648412066-0.0001073963168691.26376143028-0.0774323336276-0.109804215980.5839954923250.01905380923710.62758096160615.676394136-4.29949593193-1.97379295901
50.90324604906-0.526489104676-0.7016547843270.2906947293780.3856505264490.5558952647280.1350912955470.207057757421-0.174827546338-1.760531329620.2090725362030.229174911658-0.160194575070.0889569205730.07728757471931.12113803113-0.0467634918531-0.3078147063190.564225296047-0.03454352079770.6547690370661.88106151278-13.3042227443-6.2038664474
60.16768671261-0.00794344250323-0.0421732616140.1241984146320.06948306718910.04297528125940.706206748750.5404353726370.236193890363-0.144756928318-0.2598529954260.216034151927-0.435643033230.4388651125697.57500735159E-51.15458212451-0.000735443556107-0.1755726847580.651391059247-0.02482668809520.7820406805234.11313414656-3.172234585933.5795714322
70.2188926192750.3661636379550.5360007664690.8431679478750.8226234538630.8268221931860.171429888955-0.1555482728930.0357259639467-0.304764923722-0.099372136870.6233602944580.450101352212-0.55438593645.89337072582E-50.44967773248-0.061297263101-0.02104743966550.581297080083-0.01540684815810.6415357614492.50927832418-14.199088370121.5035270542
80.2324031002260.308863657008-0.1067750438350.39632488734-0.181680477870.1472168555750.4819810560790.4340296768780.441943665799-0.572861314846-0.215899145071-0.161311707120.126851276963-0.1096158703220.0001245366120350.556573908559-0.0854435526337-0.0536611496350.638002452170.02304815596340.7395958390721.12026893012-20.93134906918.6043226489
90.166024048204-0.392595419784-0.1848197054080.751476222690.3846550927941.066538301660.4224631224810.0198527288864-0.609443332343-0.472643616423-0.04810559771230.145479021980.8630193768980.03486622776720.0001412460764940.743194537322-0.0754709190142-0.1496559685050.5554977433570.01240046038370.6588722864978.41496791422-26.76930033428.95092073895
101.435230576460.317362092897-0.2884303858831.225171874060.6124733665660.711439453182-0.137128872823-0.09707954657130.180809495788-0.0372331161017-0.0391827381336-0.0392833347678-0.611081275535-0.0998914510019-0.006209234884210.5069032705930.0409316453559-0.003224207840090.478436159712-0.03115843989340.49453746422814.55804424836.0009719843428.1345200271
110.289425095873-0.3998054671560.2716521186561.33779771860.4024213736650.419971827349-0.02590391158420.07331257035460.0855630005382-0.409221497027-0.1486886739730.459490053916-0.395444578230.06634220707760.0004035935327620.619498060240.0522814861516-0.1456181295460.542457247541-0.01485218619010.5970777318757.806007636148.7736454777318.7360668636
121.190355580310.4147449645190.4477285698741.133246037951.348214378712.17404317374-0.03362636704340.1036225898510.000544221657299-0.4221555049680.151606526496-0.16598453391-0.2275928546850.2306931546785.12126078554E-50.427286859311-0.01455796109940.1032239025310.4820125951130.0005383176184570.4325394266125.7679244985-3.1434957592119.3207217852
130.565226988448-0.5747689706130.2383199830221.451985061170.3916729591420.7286485345090.115989023907-0.0272345167535-0.2532191954170.6278317079110.0523587330112-0.3942976364450.21695642183-0.05244282874013.95427789396E-50.4535002954940.0169393496925-0.007345034086810.481785308585-0.03452120725430.5279502574923.0200617259-5.8160116117934.4454081123
140.01113424450150.007114000336960.01103104269180.002940530546190.01008465104220.00924202399564-0.0346279689030.235358817437-0.1687078709250.1089169315511.186709712190.0737145617738-0.01489708228360.3205979673060.0001253337911191.14937976203-0.04436446282-0.01791610383040.972743778480.1479179474381.2696214975626.842114045912.99343804618.018470424
150.1162735902440.06441313593790.1460481706690.06342718808170.04034753230490.1268464204460.2296209397350.03911817243310.4742100140440.218486886086-0.0471905421374-0.48773759285-0.6587868247460.876836797736-0.0002271008934090.971029417189-0.07779384246630.20582626990.917010242408-0.07801769370270.98946298323533.274766165-3.573375495869.09337253731
160.0142047457115-0.006066168333440.0008400438385020.0159788650592-0.02018107064120.015736670878-0.178772417388-0.230859355924-0.2106996455120.032590083929-0.1018202247880.0125536403704-0.1029219625780.6752652828120.0001975635709330.847303420216-0.0228074206196-0.02125396992311.18494170439-0.1888789003291.6227879813943.6734057649-20.307262424311.7952638891
171.34176380317-0.511792858817-0.1208810845111.50040075714-0.6166614958810.366150842556-0.205222213050.554292802137-0.90475496881-0.3874165895180.575838212629-0.2068320486850.2732556914570.5487611741860.6383469472690.6067071846870.1893154357550.2540503677590.788921265034-0.2086581360490.8214181256432.8333037472-23.93354940538.53628560482
180.472652128415-0.0323659313694-0.03744455894570.07376688797270.0585405112450.0492834825369-0.06526880824270.114473160379-0.0383614954624-0.428288437173-0.7655649670570.6210682142820.460225074540.0458139880055-0.0002939993419860.9949068094840.06732567232170.1112160040411.18531058738-0.03655822914331.20085916923-7.3958025868-10.172092280425.1816488884
190.0300681480616-0.0368833327195-0.07302553134060.4010312342590.6968082906451.19311482840.027784268814-0.7581211735480.3989260766910.329476958894-0.1130068777530.4769914456890.699856987437-0.5498050943210.05985015675110.495416041151-0.06934086425090.1999744073820.777785986015-0.01391082958060.695933429449-0.258906214507-8.8284802618636.0058710542
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 43 )
3X-RAY DIFFRACTION3chain 'A' and (resid 44 through 76 )
4X-RAY DIFFRACTION4chain 'A' and (resid 77 through 102 )
5X-RAY DIFFRACTION5chain 'A' and (resid 103 through 125 )
6X-RAY DIFFRACTION6chain 'A' and (resid 126 through 139 )
7X-RAY DIFFRACTION7chain 'A' and (resid 140 through 190 )
8X-RAY DIFFRACTION8chain 'A' and (resid 191 through 202 )
9X-RAY DIFFRACTION9chain 'A' and (resid 203 through 242 )
10X-RAY DIFFRACTION10chain 'B' and (resid 2 through 76 )
11X-RAY DIFFRACTION11chain 'B' and (resid 77 through 102 )
12X-RAY DIFFRACTION12chain 'B' and (resid 103 through 202 )
13X-RAY DIFFRACTION13chain 'B' and (resid 203 through 240 )
14X-RAY DIFFRACTION14chain 'C' and (resid 17 through 26 )
15X-RAY DIFFRACTION15chain 'C' and (resid 27 through 36 )
16X-RAY DIFFRACTION16chain 'C' and (resid 37 through 42 )
17X-RAY DIFFRACTION17chain 'C' and (resid 43 through 60 )
18X-RAY DIFFRACTION18chain 'D' and (resid 28 through 44 )
19X-RAY DIFFRACTION19chain 'D' and (resid 45 through 61 )

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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