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- PDB-8t0w: Crystal structure of dimethylsulfone (DMSO2) monooxygenase SfnG f... -

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基本情報

登録情報
データベース: PDB / ID: 8t0w
タイトルCrystal structure of dimethylsulfone (DMSO2) monooxygenase SfnG from Pseudomonas fluorescens with DMSO2 and oxidized FMN bound
要素FMNH(2)-dependent dimethylsulfone monooxygenase
キーワードFLAVOPROTEIN / two-component / ternary complex / FMN-dependent
機能・相同性
機能・相同性情報


dimethylsulfone monooxygenase / alkanesulfonate monooxygenase activity / alkanesulfonate catabolic process
類似検索 - 分子機能
FMNH(2)-dependent dimethylsulfone monooxygenase SfnG / : / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily
類似検索 - ドメイン・相同性
FLAVIN MONONUCLEOTIDE / : / FMNH(2)-dependent dimethylsulfone monooxygenase
類似検索 - 構成要素
生物種Pseudomonas fluorescens (蛍光菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.75 Å
データ登録者Gonzalez, R. / Soule, J. / Dowling, D.P.
資金援助 米国, 1件
組織認可番号
National Science Foundation (NSF, United States)1807480 米国
引用ジャーナル: Proc.Natl.Acad.Sci.USA / : 2024
タイトル: Structural, biophysical, and biochemical insights into C-S bond cleavage by dimethylsulfone monooxygenase.
著者: Gonzalez, R. / Soule, J. / Phan, N. / Wicht, D.K. / Dowling, D.P.
履歴
登録2023年6月1日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年11月27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: FMNH(2)-dependent dimethylsulfone monooxygenase
B: FMNH(2)-dependent dimethylsulfone monooxygenase
C: FMNH(2)-dependent dimethylsulfone monooxygenase
D: FMNH(2)-dependent dimethylsulfone monooxygenase
E: FMNH(2)-dependent dimethylsulfone monooxygenase
F: FMNH(2)-dependent dimethylsulfone monooxygenase
G: FMNH(2)-dependent dimethylsulfone monooxygenase
H: FMNH(2)-dependent dimethylsulfone monooxygenase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)347,82336
ポリマ-342,7678
非ポリマー5,05628
42,1012337
1
A: FMNH(2)-dependent dimethylsulfone monooxygenase
B: FMNH(2)-dependent dimethylsulfone monooxygenase
C: FMNH(2)-dependent dimethylsulfone monooxygenase
D: FMNH(2)-dependent dimethylsulfone monooxygenase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)174,09520
ポリマ-171,3834
非ポリマー2,71216
724
タイプ名称対称操作
identity operation1_555x,y,z1
2
E: FMNH(2)-dependent dimethylsulfone monooxygenase
F: FMNH(2)-dependent dimethylsulfone monooxygenase
G: FMNH(2)-dependent dimethylsulfone monooxygenase
H: FMNH(2)-dependent dimethylsulfone monooxygenase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)173,72716
ポリマ-171,3834
非ポリマー2,34412
724
タイプ名称対称操作
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)104.198, 172.727, 397.356
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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要素

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タンパク質 , 1種, 8分子 ABCDEFGH

#1: タンパク質
FMNH(2)-dependent dimethylsulfone monooxygenase


分子量: 42845.840 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) Pseudomonas fluorescens (蛍光菌) / : Pf0-1 / 遺伝子: sfnG, Pfl01_2879 / プラスミド: pET28a(+) / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): NEB-T7 Express / 参照: UniProt: Q3KC85, dimethylsulfone monooxygenase

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非ポリマー , 5種, 2365分子

#2: 化合物
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / FMN


分子量: 456.344 Da / 分子数: 8 / 由来タイプ: 合成 / : C17H21N4O9P / タイプ: SUBJECT OF INVESTIGATION
#3: 化合物
ChemComp-XZ5 / (methanesulfonyl)methane


分子量: 94.133 Da / 分子数: 8 / 由来タイプ: 合成 / : C2H6O2S / タイプ: SUBJECT OF INVESTIGATION
#4: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 4 / 由来タイプ: 合成 / : C3H8O3
#5: 化合物
ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 8 / 由来タイプ: 合成 / : Cl
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 2337 / 由来タイプ: 天然 / : H2O

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詳細

研究の焦点であるリガンドがあるかY
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

結晶マシュー密度: 2.6 Å3/Da / 溶媒含有率: 52.65 % / 解説: Seeded Rhombhedral Rods
結晶化温度: 291 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6
詳細: 0.1 M MES pH 6.0, 7.5% (w/v) 2-methyl-2,4-pentanediol (MPD), and 10% (w/v) PEG 6000

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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: APS / ビームライン: 24-ID-C / 波長: 0.9792 Å
検出器タイプ: DECTRIS EIGER2 X 16M / 検出器: PIXEL / 日付: 2021年7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: 0.9792 Å / 相対比: 1
反射解像度: 1.75→99.34 Å / Num. obs: 357463 / % possible obs: 99.83 % / 冗長度: 10.9 % / Biso Wilson estimate: 30.78 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.03 / Rrim(I) all: 0.101 / Rsym value: 0.095 / Net I/σ(I): 14.26
反射 シェル解像度: 1.75→1.813 Å / 冗長度: 11.1 % / Mean I/σ(I) obs: 1.47 / Num. unique obs: 35463 / CC1/2: 0.775 / Rpim(I) all: 0.382 / Rrim(I) all: 1.3 / Rsym value: 1.24 / % possible all: 99.9

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19.2_4158精密化
XDSFeb 5, 2021データ削減
XDSFeb 5, 2021データスケーリング
PHENIX1.19.2位相決定
精密化構造決定の手法: 分子置換 / 解像度: 1.75→87.05 Å / SU ML: 0.2404 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 18.8975
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
詳細: Refinement of a ternary complex containing an ordered lid region.
Rfactor反射数%反射
Rfree0.1817 17870 5 %
Rwork0.1552 339534 -
obs0.1566 357404 99.77 %
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: 34.01 Å2
精密化ステップサイクル: LAST / 解像度: 1.75→87.05 Å
タンパク質核酸リガンド溶媒全体
原子数22241 0 320 2337 24898
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.010823700
X-RAY DIFFRACTIONf_angle_d1.003132266
X-RAY DIFFRACTIONf_chiral_restr0.09293403
X-RAY DIFFRACTIONf_plane_restr0.00944464
X-RAY DIFFRACTIONf_dihedral_angle_d14.56578454
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.770.46535880.429211150X-RAY DIFFRACTION98.18
1.77-1.790.32295860.319211132X-RAY DIFFRACTION99.93
1.79-1.810.31415910.279911242X-RAY DIFFRACTION99.97
1.81-1.830.26465960.235111344X-RAY DIFFRACTION99.93
1.83-1.860.2435920.208711238X-RAY DIFFRACTION99.95
1.86-1.880.28565910.22511219X-RAY DIFFRACTION99.96
1.88-1.910.30755880.271311209X-RAY DIFFRACTION99.38
1.91-1.940.38255880.34311184X-RAY DIFFRACTION98.51
1.94-1.970.24915900.207511229X-RAY DIFFRACTION99.97
1.97-20.23365940.183411272X-RAY DIFFRACTION99.97
2-2.040.21675900.179911234X-RAY DIFFRACTION99.92
2.04-2.070.25685960.225111296X-RAY DIFFRACTION99.76
2.07-2.110.20595940.171611276X-RAY DIFFRACTION99.94
2.11-2.160.18165940.141711291X-RAY DIFFRACTION99.92
2.16-2.20.18655950.146411292X-RAY DIFFRACTION99.97
2.2-2.250.25055910.198811217X-RAY DIFFRACTION99.36
2.25-2.310.21235920.160711248X-RAY DIFFRACTION99.27
2.31-2.370.18895960.142811319X-RAY DIFFRACTION99.97
2.37-2.440.18835940.149311293X-RAY DIFFRACTION99.98
2.44-2.520.19725990.146211382X-RAY DIFFRACTION100
2.52-2.610.19165950.152611302X-RAY DIFFRACTION99.97
2.61-2.720.19435980.156511359X-RAY DIFFRACTION99.93
2.72-2.840.18475970.154511340X-RAY DIFFRACTION99.95
2.84-2.990.16955990.146611373X-RAY DIFFRACTION99.92
2.99-3.180.16955990.142111389X-RAY DIFFRACTION99.97
3.18-3.420.16535990.144311368X-RAY DIFFRACTION99.97
3.42-3.770.14856030.133911452X-RAY DIFFRACTION99.99
3.77-4.310.1376040.122211480X-RAY DIFFRACTION99.95
4.31-5.430.13096080.119411556X-RAY DIFFRACTION99.94
5.43-87.050.16616230.153111848X-RAY DIFFRACTION99.7
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)
11.79101661510.531425971331-0.8523558456570.4800243605660.4440123397171.99971979995-0.1266097624260.123978553537-0.1274002571780.0415338084777-0.0002791873565090.1137889161470.02196235941020.04379699359650.1224325737040.2781287702460.005798813905130.03611393779620.3081918558230.06459203226180.23813606250729.07278.424-77.724
22.000360482520.6483242955560.3257594806631.33416401601-0.3954027089412.24612287549-0.07166821431940.1404208452790.114184245081-0.222743401381-0.06858841024140.225074087413-0.0606777195862-0.1406239193460.1093635089250.3639629156540.03332086655730.01486197867570.3641475105560.0703644515650.25652591937321.4180.745-84.908
31.048792335080.193592038033-0.2574803721391.063664643980.0262780168811.82434442465-0.02539517907210.0007026088226560.06671548139-0.04441765197330.01118853486940.0301685000439-0.04135352808270.05971661519340.018798814020.2617984418180.01711868181720.002628160720860.2678613571520.02834949240750.24477352431420.06475.128-74.576
41.223363622020.5318701895010.6584170495961.66327986459-0.5698579421970.863203877928-0.003794311263140.123028787052-0.10452101217-0.1443597903280.0211901708672-0.04310244543130.1407995681730.0247675079414-0.02080459374230.2656049355470.0419279491520.02230984063990.2752203595940.01185121055550.2474859949922.13963.856-72.865
53.00349350624-0.3963844207750.4242631058190.952527793663-0.658823320181.528815447270.0271700842747-0.02889870410230.119769305895-0.0357182124655-0.07086980088320.0908978728047-0.13211962271-0.03827843721190.02862285294280.2359164894390.0172076333829-0.0004281187966510.2453273011320.01147107650560.27619895021818.73877.892-55.956
61.100755504390.5648754268250.685726321083.899078833941.377181356811.04117051983-0.0082955952710.00882433492050.01292837965950.07454354771250.0584752785822-0.3177723021530.05078160581120.176040676085-0.03667301551340.2435133146850.0241989323140.01198102120850.3011885899830.04427749131640.24808112007427.65264.393-58.609
71.073199024530.280752067771-0.2357989337871.41750543462-0.3404398234651.08534197332-0.02334331653790.0374506364109-0.0901892690615-0.0712115800199-0.0433296621997-0.1395145052390.1466813095880.1355481349980.06230436766640.2372788699960.03145184920130.00663371584890.2776512123090.03341016814520.24009573010729.52462.482-62.643
80.4725473959990.1114581251310.2866422432177.59678208006-4.766901661473.257481099720.05524308357260.0297979362595-0.00878036346173-0.216143394821-0.560911930599-0.664225153692-0.03511740584590.6180563328960.5214326226060.2407891292174.81866838264E-50.0190358546530.4874648659210.07526498680620.42101330413445.9573.876-63.245
90.960374694167-0.6832858056950.6118059971713.46695686256-1.789828722992.188702214660.01956866594440.132359900924-0.0424945180974-0.3143957794420.00382888254546-0.121937440120.09000662840050.1787582378790.01644452880960.278641754053-0.006733171344510.04921410387390.343775649460.05622198829160.30130036556138.48677.229-74.636
100.8944821506080.0126396243721-0.3132955532752.66292620637-1.476053349993.36403389939-0.04470127718530.04492734115130.2438214828230.06606578722030.0137351921104-0.0558860053981-0.4915410205930.07160141161890.04100066715540.3621521538-0.0438167535350.002960021057280.2845516671450.03273103977880.32989397913530.36591.077-66.68
111.74532127854-0.0679308441931-0.1522889030051.23130421032-0.5418958466051.82411346026-0.01251191066820.1556969317680.2135620692880.00529202740582-0.0780718862916-0.203524224942-0.290168929590.3852780717960.06999354283540.305210279669-0.06725142457860.03399752561710.3656083127790.09059382920490.31656634589639.2186.345-76.115
121.870999135290.2084694958770.3064143321671.19660826247-0.4888319087961.55195106761-0.01015509041170.384651270065-0.0226671021425-0.27997836245-0.102778538706-0.164679753446-0.07270608447220.4106009824290.07936977135230.3306825165160.005344808179260.07275821259260.4698286350760.0746186504410.29233351177938.79378.938-85.748
132.315170443630.238235198530.537948314151.6699229362-0.4584624408432.66626714925-0.1948038624490.23328823791-0.1211314827030.002679222139720.157738764293-0.1210070285880.249697696619-0.07770328530240.01342469588570.335556058413-0.0486534318985-0.04135749438920.370816724987-0.04711518922210.312886488462-0.90250.94-77.04
142.721299337060.03991603735290.1485272160761.53214070739-0.01243860970092.4649396498-0.05416793328170.673960247618-0.0589125673871-0.356550801631-0.0542078237201-0.1033202795690.1963077568310.2180625725810.02295095917780.39988031043-0.02230617054370.002727493595560.396372226892-0.09527046612770.2706721403256.16148.527-84.037
151.051231568830.93292890114-0.1338572762521.5443586094-0.5435099558051.56723774238-0.100286855190.127506342835-0.0582033031321-0.1149299103410.0550149087304-0.114323141315-0.0117127461372-0.1398334519940.03625812321750.26224965392-0.01031728927070.02267133544840.287712759271-0.0195520746410.2618921043337.65653.445-73.49
161.457941735530.563462846385-0.9022185951281.566723555450.2997647791870.869639894227-0.0475531499490.2457410308530.129712811022-0.2012337414860.0819705318670.09124149381410.026449120648-0.103253298009-0.02825555488830.2379949038980.0125459338983-0.01793508355160.2859859675510.02697878070170.2431922292715.27866.122-72.976
172.56724534446-0.5147349206230.2688065533560.9051650915820.6651320238110.7969053004190.117350896708-0.02833596105840.0238546415249-0.0537518414893-0.051627269644-0.1462435855180.0967959879393-0.0555885618697-0.08785516825430.296107827917-0.0200006660345-0.0003638464764170.274025796480.02182269755610.3329945798358.49452.793-55.399
181.576307548140.540607201369-0.8196217880723.67344541875-1.211740768031.124636307640.15302928178-0.0108213877348-0.03397538773270.254192367116-0.01023740359720.36139900009-0.143623637632-0.118804409183-0.09558437421780.2353075810740.0152975408707-0.006393899437920.3111927859490.007518383995640.270440568807-0.51766.333-58.825
191.208650998221.13955366741-0.2764656488262.04864305462-0.1959697678210.388884818580.04912165405250.03857793687380.0857855315637-0.0008212287721370.01827287929630.1529338542640.00823806979228-0.122657848504-0.07528404593160.2583110196420.0223916988291-0.01106375076550.3459824701680.0278238017940.31383151215-2.50468.009-62.891
201.21801978853-0.0957427404884-0.1208257982697.749050481125.161407417974.247437668820.142910619897-0.0683050012112-0.00117033180635-0.0307604851964-0.4366525915570.5235319805440.13539341782-0.6696323288030.3147917555570.289539491799-0.0395389788661-0.0294126610370.5036046778390.01186917214930.429650350406-18.75457.64-63.013
211.37029357699-0.293129622655-0.2077341366264.223498296452.241661531933.649739790440.09906261023170.313518887254-0.150047827556-0.363023967901-0.1563491996280.3748988902040.0902008629599-0.4644859730610.08851949458840.307254597724-0.0536496014167-0.04251227740270.4411843756150.004544650458780.356493009091-10.93352.118-75.423
221.196333273830.5154459234021.021068520932.068061544981.553631748473.668659150740.01613994553840.10474807746-0.4052543196250.03472660872590.0961527035399-0.07724516179790.6534556178110.0125409060663-0.05739808071540.495940124913-0.0773168751767-0.01069145989770.367316109882-0.008830729038210.442516924231-3.12339.444-65.374
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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 C AND RESID 4:21 )C4 - 21
2X-RAY DIFFRACTION2( CHAIN C AND RESID 22:45 )C22 - 45
3X-RAY DIFFRACTION3( CHAIN C AND RESID 46:77 )C46 - 77
4X-RAY DIFFRACTION4( CHAIN C AND RESID 78:118 )C78 - 118
5X-RAY DIFFRACTION5( CHAIN C AND RESID 119:135 )C119 - 135
6X-RAY DIFFRACTION6( CHAIN C AND RESID 136:155 )C136 - 155
7X-RAY DIFFRACTION7( CHAIN C AND RESID 156:209 )C156 - 209
8X-RAY DIFFRACTION8( CHAIN C AND RESID 210:226 )C210 - 226
9X-RAY DIFFRACTION9( CHAIN C AND RESID 227:244 )C227 - 244
10X-RAY DIFFRACTION10( CHAIN C AND RESID 245:289 )C245 - 289
11X-RAY DIFFRACTION11( CHAIN C AND RESID 290:321 )C290 - 321
12X-RAY DIFFRACTION12( CHAIN C AND RESID 322:358 )C322 - 358
13X-RAY DIFFRACTION13( CHAIN D AND RESID 4:21 )D4 - 21
14X-RAY DIFFRACTION14( CHAIN D AND RESID 22:45 )D22 - 45
15X-RAY DIFFRACTION15( CHAIN D AND RESID 46:77 )D46 - 77
16X-RAY DIFFRACTION16( CHAIN D AND RESID 78:118 )D78 - 118
17X-RAY DIFFRACTION17( CHAIN D AND RESID 119:135 )D119 - 135
18X-RAY DIFFRACTION18( CHAIN D AND RESID 136:155 )D136 - 155
19X-RAY DIFFRACTION19( CHAIN D AND RESID 156:209 )D156 - 209
20X-RAY DIFFRACTION20( CHAIN D AND RESID 210:227 )D210 - 227
21X-RAY DIFFRACTION21( CHAIN D AND RESID 228:244 )D228 - 244
22X-RAY DIFFRACTION22( CHAIN D AND RESID 245:289 )D245 - 289
23X-RAY DIFFRACTION23( CHAIN D AND RESID 290:358 )D290 - 358
24X-RAY DIFFRACTION24( CHAIN A AND RESID 4:21 )A4 - 21
25X-RAY DIFFRACTION25( CHAIN A AND RESID 22:45 )A22 - 45
26X-RAY DIFFRACTION26( CHAIN A AND RESID 46:77 )A46 - 77
27X-RAY DIFFRACTION27( CHAIN A AND RESID 78:118 )A78 - 118
28X-RAY DIFFRACTION28( CHAIN A AND RESID 119:135 )A119 - 135
29X-RAY DIFFRACTION29( CHAIN A AND RESID 136:155 )A136 - 155
30X-RAY DIFFRACTION30( CHAIN A AND RESID 156:209 )A156 - 209
31X-RAY DIFFRACTION31( CHAIN A AND RESID 210:226 )A210 - 226
32X-RAY DIFFRACTION32( CHAIN A AND RESID 227:244 )A227 - 244
33X-RAY DIFFRACTION33( CHAIN A AND RESID 245:289 )A245 - 289
34X-RAY DIFFRACTION34( CHAIN A AND RESID 290:321 )A290 - 321
35X-RAY DIFFRACTION35( CHAIN A AND RESID 322:358 )A322 - 358
36X-RAY DIFFRACTION36( CHAIN B AND RESID 4:45 )B4 - 45
37X-RAY DIFFRACTION37( CHAIN B AND RESID 46:77 )B46 - 77
38X-RAY DIFFRACTION38( CHAIN B AND RESID 78:118 )B78 - 118
39X-RAY DIFFRACTION39( CHAIN B AND RESID 119:135 )B119 - 135
40X-RAY DIFFRACTION40( CHAIN B AND RESID 136:175 )B136 - 175
41X-RAY DIFFRACTION41( CHAIN B AND RESID 176:209 )B176 - 209
42X-RAY DIFFRACTION42( CHAIN B AND RESID 210:226 )B210 - 226
43X-RAY DIFFRACTION43( CHAIN B AND RESID 227:244 )B227 - 244
44X-RAY DIFFRACTION44( CHAIN B AND RESID 245:289 )B245 - 289
45X-RAY DIFFRACTION45( CHAIN B AND RESID 290:321 )B290 - 321
46X-RAY DIFFRACTION46( CHAIN B AND RESID 322:358 )B322 - 358
47X-RAY DIFFRACTION47( CHAIN F AND RESID 4:77 )F4 - 77
48X-RAY DIFFRACTION48( CHAIN F AND RESID 78:118 )F78 - 118
49X-RAY DIFFRACTION49( CHAIN F AND RESID 119:209 )F119 - 209
50X-RAY DIFFRACTION50( CHAIN F AND RESID 210:244 )F210 - 244
51X-RAY DIFFRACTION51( CHAIN F AND RESID 245:321 )F245 - 321
52X-RAY DIFFRACTION52( CHAIN F AND RESID 322:357 )F322 - 357
53X-RAY DIFFRACTION53( CHAIN E AND RESID 4:45 )E4 - 45
54X-RAY DIFFRACTION54( CHAIN E AND RESID 46:226 )E46 - 226
55X-RAY DIFFRACTION55( CHAIN E AND RESID 227:358 )E227 - 358
56X-RAY DIFFRACTION56( CHAIN H AND RESID 4:21 )H4 - 21
57X-RAY DIFFRACTION57( CHAIN H AND RESID 22:45 )H22 - 45
58X-RAY DIFFRACTION58( CHAIN H AND RESID 46:77 )H46 - 77
59X-RAY DIFFRACTION59( CHAIN H AND RESID 78:118 )H78 - 118
60X-RAY DIFFRACTION60( CHAIN H AND RESID 119:135 )H119 - 135
61X-RAY DIFFRACTION61( CHAIN H AND RESID 136:155 )H136 - 155
62X-RAY DIFFRACTION62( CHAIN H AND RESID 156:209 )H156 - 209
63X-RAY DIFFRACTION63( CHAIN H AND RESID 210:226 )H210 - 226
64X-RAY DIFFRACTION64( CHAIN H AND RESID 227:244 )H227 - 244
65X-RAY DIFFRACTION65( CHAIN H AND RESID 245:289 )H245 - 289
66X-RAY DIFFRACTION66( CHAIN H AND RESID 290:321 )H290 - 321
67X-RAY DIFFRACTION67( CHAIN H AND RESID 322:357 )H322 - 357
68X-RAY DIFFRACTION68( CHAIN G AND RESID 4:118 )G4 - 118
69X-RAY DIFFRACTION69( CHAIN G AND RESID 119:209 )G119 - 209
70X-RAY DIFFRACTION70( CHAIN G AND RESID 210:321 )G210 - 321
71X-RAY DIFFRACTION71( CHAIN G AND RESID 322:358 )G322 - 358

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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