[日本語] English
万見
- PDB-9r2l: De novo designed N37 protein fold -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 9r2l
タイトルDe novo designed N37 protein fold
要素N37
キーワードDE NOVO PROTEIN / dark fold / de novo / unnatural
機能・相同性ACETATE ION / ETHANOLAMINE / : / THIOCYANATE ION
機能・相同性情報
生物種synthetic construct (人工物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.2 Å
データ登録者Pacesa, M. / Miao, Y. / Georgeon, S. / Schmidt, J. / Correia, B.E.
資金援助 スイス, 1件
組織認可番号国
Swiss National Science Foundation スイス
引用
ジャーナル: To Be Published
タイトル: Reimagine accessibility of protein space with generative model
著者: Miao, Y. / Pacesa, M. / Georgeon, S. / Schmidt, J. / Lu, T. / Huang, P. / Correia, B.E.
#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2025年4月30日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02025年5月14日Provider: repository / タイプ: Initial release

-
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

-
集合体

登録構造単位
A: N37
B: N37
C: N37
D: N37
E: N37
F: N37
G: N37
H: N37
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)138,95828
ポリマ－137,8828
非ポリマー1,07520
水9,242513
1
A: N37
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)17,4144
ポリマ－17,2351
非ポリマー1783
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: N37
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)17,5106
ポリマ－17,2351
非ポリマー2745
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: N37
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)17,2932
ポリマ－17,2351
非ポリマー581
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: N37
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)17,3523
ポリマ－17,2351
非ポリマー1172
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
5
E: N37
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)17,3924
ポリマ－17,2351
非ポリマー1563
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
6
F: N37
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)17,3323
ポリマ－17,2351
非ポリマー972
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
7
G: N37
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)17,3323
ポリマ－17,2351
非ポリマー972
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
8
H: N37
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)17,3323
ポリマ－17,2351
非ポリマー972
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)62.760, 66.840, 81.120
Angle α, β, γ (deg.)78.814, 74.747, 62.558
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
要素

-
タンパク質 , 1種, 8分子 ABCDEFGH

#1: タンパク質
N37


分子量: 17235.291 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) synthetic construct (人工物) / 発現宿主: Escherichia coli (大腸菌)

-
非ポリマー , 5種, 533分子

#2: 化合物 ChemComp-ETA / ETHANOLAMINE / エタノ-ルアミン


タイプ: L-peptide COOH carboxy terminus / 分子量: 61.083 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C2H7NO
#3: 化合物
ChemComp-ACT / ACETATE ION / 酢酸イオン


分子量: 59.044 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C2H3O2
#4: 化合物
ChemComp-SCN / THIOCYANATE ION / チオシアン酸アニオン


分子量: 58.082 Da / 分子数: 8 / 由来タイプ: 合成 / 式: CNS
#5: 化合物
ChemComp-K / POTASSIUM ION / カリウムカチオン


分子量: 39.098 Da / 分子数: 5 / 由来タイプ: 合成 / 式: K
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 513 / 由来タイプ: 天然 / 式: H2O

-
詳細

研究の焦点であるリガンドがあるかN
Has protein modificationN

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 2.11 Å3/Da / 溶媒含有率: 41.58 %
結晶化温度: 291.15 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 5.5
詳細: 0.2 M Potassium thiocyanate 0.1 M Sodium acetate 5.5 25 % w/v PEG 2000 MME

-
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: ESRF / ビームライン: MASSIF-3 / 波長: 0.87313 Å
検出器タイプ: DECTRIS EIGER X 4M / 検出器: PIXEL / 日付: 2024年11月14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: 0.87313 Å / 相対比: 1
反射解像度: 2.199→77.98 Å / Num. obs: 56016 / % possible obs: 98 % / 冗長度: 4 % / Biso Wilson estimate: 32.53 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.137 / Net I/σ(I): 7.3
反射 シェル解像度: 2.199→2.237 Å / 冗長度: 4.1 % / Rmerge(I) obs: 1.042 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2788 / CC1/2: 0.551 / % possible all: 97.2

-
解析

ソフトウェア
名称バージョン分類
PHENIX1.21.2_5419精密化
autoPROC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: 2.2→77.98 Å / SU ML: 0.3094 / 交差検証法: FREE R-VALUE / σ(F): 1.97 / 位相誤差: 27.4944
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2318 2831 5.06 %
Rwork0.1991 53144 -
obs0.2009 55975 97.95 %
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: 44.31 Å2
精密化ステップサイクル: LAST / 解像度: 2.2→77.98 Å
タンパク質核酸リガンド溶媒全体
原子数8959 0 57 513 9529
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00199082
X-RAY DIFFRACTIONf_angle_d0.387312095
X-RAY DIFFRACTIONf_chiral_restr0.03751362
X-RAY DIFFRACTIONf_plane_restr0.00251516
X-RAY DIFFRACTIONf_dihedral_angle_d11.39723687
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.3431520.2912634X-RAY DIFFRACTION97.11
2.24-2.280.37551140.28622628X-RAY DIFFRACTION97.51
2.28-2.320.34261280.28082718X-RAY DIFFRACTION97.6
2.32-2.370.33181370.26372621X-RAY DIFFRACTION97.63
2.37-2.420.33031320.25432668X-RAY DIFFRACTION97.63
2.42-2.480.29871310.25592659X-RAY DIFFRACTION98
2.48-2.540.27061210.23832653X-RAY DIFFRACTION97.61
2.54-2.610.28261390.22392672X-RAY DIFFRACTION97.17
2.61-2.680.30411180.2312671X-RAY DIFFRACTION97.93
2.68-2.770.28021330.22522677X-RAY DIFFRACTION98.11
2.77-2.870.26581420.22732673X-RAY DIFFRACTION98.25
2.87-2.980.28921330.22632650X-RAY DIFFRACTION98.44
2.98-3.120.24511530.21482645X-RAY DIFFRACTION98.11
3.12-3.290.25291370.20152689X-RAY DIFFRACTION98.02
3.29-3.490.22061360.17572669X-RAY DIFFRACTION97.84
3.49-3.760.18341460.17732608X-RAY DIFFRACTION97.97
3.76-4.140.19381710.15972671X-RAY DIFFRACTION98.75
4.14-4.740.16861590.14742642X-RAY DIFFRACTION97.94
4.74-5.970.24641750.17622651X-RAY DIFFRACTION98.95
5.97-77.980.17031740.17942645X-RAY DIFFRACTION98.53
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)
10.0845021549725-0.168139120274-0.2009491811091.058634878850.09537234227790.5195703055920.05141978327560.462309779297-0.0240911483181-0.1531389600910.332669541028-0.2124346282460.03291481182140.6091233632628.64756560028E-50.295148988389-0.1011751715670.01746591015950.338555347543-0.06676247318570.273893898904-7.5467163534-5.808509696493.41499183325
21.69883074551-1.13700862380.02668751886381.213525927830.6997249905240.9039764790810.1443360048830.00355863516860.04335452775290.1752113874530.0674491236224-0.02604958650470.04050911033770.1656385238320.0002942420256890.358540637359-0.0627616732322-0.001409171175370.243183409468-0.02715335011810.332468608327-10.32108017130.3740681899326.04124982148
30.893690894021-0.711612943507-0.7230850726931.07682075275-0.3083334261561.035481198580.210090124303-0.01693058747070.157437161504-0.583284350116-0.00436885955056-0.247385124284-0.4867246626380.1590818108570.0001295325471090.4099374692110.0004920051642090.08558119155340.238984377667-0.009182376468940.3502837075111.025742739873.5212362779-13.3893082767
40.818157543747-0.161489738795-0.4149684044590.902849369049-1.187609059911.757756522120.235104366071-0.2193810923120.226346454571-0.01462049358520.164990877092-0.172679330055-0.2183084119940.2489720525420.002048706709050.18714640967-0.05605851607750.02808961105220.185165010448-0.01517876883090.251327503719-3.15022843465-0.220999160038-3.16822073666
50.4074009937380.068797268604-0.4351261563651.6875389152-0.4477075273030.5338508236320.0393850403126-0.2380150855220.08349453485110.0682564166941-0.1022594888850.8396043629770.1115655234940.442154575102-0.02253185776240.277160388263-0.00119219308721-0.002588334212930.391579799643-0.05087821969520.2428926906610.867959575438-8.73234518531.40495544337
60.182191684103-0.14618854595-0.2635218223681.67285676414-1.036159318261.784684699560.0859393687307-0.2457386509950.2958860416010.214969814545-0.111968660279-0.384894028983-0.3116756941071.083494867640.002648812215960.29453713338-0.1208863054140.002182936534320.479732943021-0.05560872120350.3637280266726.421113024650.2537579434560.148879925034
72.86096285116-0.805439217463-1.333076517721.59271133537-0.4114319468881.060767320890.01273620133550.132799632206-0.1489494470340.00716343453512-0.0578051934682-0.1272391307890.5386826407520.00566255044024-0.0002171887711260.225911835715-0.02215976877860.04306847230370.220913421150.01252571540350.260430596479-19.2663159062-32.88909277537.29802003134
81.24757685680.06582284451-0.5968163633760.1293397963580.45008942561.119695369940.219707496877-0.01555304661990.02895159946040.181514851806-0.02657953517970.215950523467-0.0456728033172-0.4054890173070.0001745821208350.362624230981-0.01484014588470.004622651637960.399175783109-0.03616451408480.292712293573-23.7828083519-28.42858069710.683598924778
90.274342088299-0.0812049176849-0.3292337019760.569751932529-0.3303053013711.87617770288-0.0904843776475-0.07794777602370.17724084602-0.0301313805310.24842400297-0.201733745429-0.3134446666980.1089793781134.65983949772E-50.316974637183-0.031743282418-0.0006809155543840.32352738868-0.07471044604260.354546230462-10.3644097247-25.3292993456-13.0693426672
100.913108649425-0.246915148342-0.2916834175910.296125743831-0.5854593663041.506954868860.2695564071340.1590291764150.19375696967-0.02528131686670.0419210025879-0.0829618128878-0.212450032644-0.1761513590089.4174635997E-50.2265496867120.01186236785820.02571072452890.232531599909-0.01119085187770.277155662985-14.8207731448-28.8438759829-2.58064214382
111.260952973990.1119977541621.017469073073.087897280271.167824595841.684113243450.543299604636-0.470594997395-0.1225848583670.546437064468-0.627148716651-0.2147416135260.686274509847-0.140420157137-0.04136745662330.390476920820.0696276281591-0.04486700522820.3164777788230.02164588296160.36889708715-10.8165204521-37.00663539242.46672103728
121.28486213104-0.172929186593-1.150365081110.8856411278951.150204296022.05872187337-0.016119330013-0.03412550355060.02294337657220.09219317328320.126976053169-0.219517990628-0.04116633359440.2358476944470.0001895478408270.2590034821060.0145881922781-0.0218561911340.367134594883-0.02702786560980.317500249235-5.76935597035-28.88917110711.10142633386
131.32395759040.491908513659-0.01322190273312.565664503681.62421957053.1749494584-0.0110424119385-0.1459762174210.4490873861580.6032815888680.09215351108220.6853619952530.68858535309-0.571728528088-0.1101183182710.3440043064420.0983037087411-0.08536288452460.3366720483710.07394761980030.365220890759-14.525428640611.7999947205-36.4299642921
142.60030103976-3.827363994971.473490031467.23160455139-1.281435719751.53145719466-0.00374483404778-0.612649648483-0.6234791237571.231146969720.7450964912021.84341624287-0.288276115723-0.915467353113-0.02182718749750.144782790129-0.06046319198030.1084173086780.312598880778-0.001978384695810.583704734834-15.84469969662.9958399205-28.5708083353
152.054762311020.04831278702210.596619977422.17778997939-1.673852332711.709945500160.196961906424-0.01481905966050.0430807117960.477013459408-0.1649899685730.1366014900880.195346571125-0.146874214756-0.003268626609860.293143245810.019698160954-0.0006656282974550.245686371944-0.01623761914220.314611458924-4.50211397933.9625330005-28.2461595725
163.227522247040.919413290722-1.580294090742.19142134309-1.847185707841.65327495540.1005387635740.2446577644220.187199206635-0.516095668049-0.192419789303-0.3002150598440.151082560817-0.254658434869-8.30765981816E-50.3366024691580.01601130868760.007415476441320.343528149644-0.02140401752330.335611892605-2.43616828238.04734353127-38.2459914825
170.3176017262710.431091159101-0.4719128324881.28003719383-0.7084357623980.593629856189-0.2442563740640.1370835200730.105990975167-0.42873294656-0.1519810003620.319456346252-0.846558773424-0.144272729289-0.001194224168920.262626833650.0994327315542-0.03568949447210.4764909988410.01943678505790.318682685886-27.2212834371-18.8915091756-36.6265839524
182.85343218307-0.7708449241520.0201950826181.54620138332-0.8785123682240.5773326095210.08718156238470.143414942753-0.229990297767-0.233587025597-0.075520301788-0.03164088146830.028072883374-0.893674023348-1.82047347943E-50.281875260950.00943077089901-0.008618846542810.411410655748-0.01529588548430.285395636433-31.1565643336-21.462572446-38.8805132817
190.6100497998790.271960033020.4786173971510.1290662632290.09689796798480.6797138526460.150765542173-0.22960358285-0.295371459451-0.2485467857960.1601632005040.03826647992570.345125922366-0.6584847675090.002623026375130.2748036378940.007620678543770.03150177255020.2834477569290.004430361998330.240864892084-30.9473138072-25.3937286599-29.8531314064
200.543867252625-1.051100543470.7497537117711.98057026846-1.350300444011.473135008040.1119592227020.134985318444-0.06061117692480.2129132389820.00717858807018-0.2299478740430.07068815757030.250397410856-0.0004201190492930.262289582424-0.009506925914490.007996140142020.287519103214-0.07612097750290.290176565983-12.7440841816-28.574784945-23.4503632123
211.009121086640.3020966975540.003972652600981.111410350210.988720673010.833016446690.186664519327-0.0377509869188-0.06423246572830.104575458291-0.112910720510.02758301532310.277756787941-0.2159905794830.0004607756593860.155856096009-0.0340367115037-0.02230331934820.2164081999930.01127645826690.22796014461-21.4482590565-24.8051575234-33.8797705648
220.248538135463-0.02870510389450.6141302278930.118648663201-0.03837896472871.53894849093-0.0247411391723-0.298227813120.0845161891837-0.4400996589730.123087462256-0.346230718484-0.276476851317-0.211367625002-0.0204218259310.457814634715-0.02061685906720.02304355167980.3113337691850.06323506553290.493711243994-18.1055131826-9.9739439353-31.2301467115
231.216208798340.3515972115330.8741794097680.4609145622970.5260802954940.72275009378-0.09691625935170.190360477667-0.467690973962-0.2201594582760.0788090977521-0.7114686511790.133622315578-0.07450163435950.0001408930740680.2710414986510.03459576173590.05580757132350.3588436044950.0008969763638430.347685736204-12.3410611555-25.1466182478-36.3280188748
240.964437561799-0.03692936321951.09604365777.025834307941.499525566091.63300970567-0.104920124680.2006788830010.48059434526-1.57613252679-0.00286350409851-1.32211151926-0.3523963582110.5320579484890.1813183782820.3523981958160.09854883659440.09592852922930.3393175787270.0371137091930.448549024424-18.869275045-23.7209631496-41.4083287271
250.5521047180670.016806496437-0.2842917892160.04924795145570.1939850201551.29447891555-0.187258630320.03415259955760.201657967151-0.116681973406-0.0418218468981-0.2912666218750.208452640561-0.794311737689-0.1749924061290.3930823668030.01275110969750.04904021933140.2560808965810.01438110442840.312034443506-22.67333944011.0180785552119.0027516721
261.707155521560.209603420875-1.41739265741.25536609012-0.4281924281471.17702282546-0.01801539696420.0910094317161-0.0670818306136-0.02310238695510.0626540783818-0.0730189852582-0.003441217249920.1751974166610.0001802361782290.3684265040260.03226390451840.04068101159390.207792391195-0.02451740755870.264193351235-16.45852694791.0331143802518.964831653
271.08214779744-0.654069693719-0.3287717742640.689280382587-0.6734332408362.08985524242-0.226902623037-0.214729356690.242197571846-0.09962047331730.178046680604-0.171117051993-0.3593496674430.15153884599-0.0002016373873470.406478722194-0.08213993613980.07045269364910.333837316264-0.03351068736340.351333103518-20.087462051512.55475379936.8693657749
281.3980102003-0.1472689524141.154203620181.740503644840.812567595691.349442866280.1242132067070.07471415689110.1435116230790.05143652252450.0752638778270.0584112324905-0.1296848735260.0384564090745-7.44595433721E-50.3016797745510.01932286040290.02186806347860.16643313072-0.02916239228870.277915620904-20.06265067877.0882656408226.6246867413
290.9534498016910.8174689921030.4061704892030.6488223849040.3960699209910.653472309937-0.127961965008-0.440028605855-0.0106435049995-0.577037009636-0.1317710192770.1304303830480.4607207719370.396838901926-0.006457620313280.3381587514380.02840514342250.0594520686470.418431731817-0.02773046175530.359542557241-28.876899684.4520201809221.8934125022
301.35544196803-0.4309453296090.3017037816311.1418395231-0.2599367588621.53516351606-0.00437109731369-0.1632747728770.8879445942750.2058593870980.0004427546183420.294444376506-0.432855751495-0.1920122334740.002831267476190.4449392833530.1271252513030.04222078390260.2837536440750.02469526998530.445300104411-25.659614206314.620381366823.3651840727
310.4139150479170.506916045720.1950058165620.5085201382930.2406982003360.206601167369-0.4026095701950.0241464033295-0.237930462047-0.4764275747110.2230504011410.1436919821280.598043480547-0.530684724918-1.34442023625E-50.38748070391-0.02038654131930.03613466602010.274749066085-0.0003360425100070.306958847048-35.4610250535-27.118805464817.9769160606
321.65910840297-0.458373617938-1.271364204430.3275714290150.5787622736031.10838948819-0.1079253329980.160765211759-0.1581495959820.01252376166670.0591741628043-0.04254463652080.3627121388750.1122544072980.001374891352380.296441323029-0.006621573205270.01173485691590.237204010785-0.006135362038150.240437586932-29.3601675148-27.190690312818.37227297
330.8224092805860.00490758722812-0.156544179241.100595864731.153717472121.113268732210.1458480663130.4408680361190.474340803548-0.07835621720320.103177445953-0.00416729416887-0.1495716673950.0804180932519-3.35813164566E-50.2331560866040.02279145956720.01795003249990.2777908720.0556819924530.235268714098-34.2730199173-15.696973451336.3129878179
340.1238187973880.23341510751-0.3980135945770.619571143433-0.4015929922391.171535620940.0240298086659-0.1216778200860.12912146392-0.0972275268560.0978402210495-0.03694279036750.1266468924220.009389599040550.0001042088373920.233458059866-0.007579969397170.02496872851720.281770665773-0.01114638634830.290524161173-33.3020394971-21.17845986726.0213270499
351.244417822670.474333771611-0.8633192766080.62155648438-0.4014244625493.20333397671-0.1081307692020.2233810536620.14487232586-0.1614381592260.06904285169420.299547882854-0.123227434749-0.3710304694853.08889004742E-50.221921123061-0.0289552398186-0.009207726960660.3470797528330.01715786006160.306394710288-40.8440888122-18.302180038622.8012596712
361.02610261766-0.163773855917-0.03244803029950.6435129285320.1076479403051.2066691525-0.7008249354330.5217815681620.393252763344-0.354423548760.670257022255-0.2161233463920.1012593977930.188735080274-8.17059248258E-50.27460207870.01168833357430.008317857254350.217985403974-0.02619749577430.28094275075-38.4528914215-16.802711976717.3227071824
370.577867385352-0.409162453539-0.4862690591861.760688522550.3920205913470.3559376426880.441497016002-0.535736725206-0.2402199946970.417258961175-0.0330063811647-0.3461805747070.567915426039-0.03959006867490.0007962310454050.537480884749-0.0973082766907-0.1124934366490.5181180640040.008316742149250.545130415935-26.6366960502-1.79438421196-17.0524833418
381.35098718267-0.2557480968530.1624338460340.629737778651-0.05477008127520.0127321430702-0.1892506689330.345265527028-0.351731042603-0.158361632660.128080668073-0.608858110272-0.2572504238360.4703680835180.03005788921290.5355152180280.0680094513698-0.1109579040530.402824892685-0.005801390973360.590881515727-29.956513466-8.08536622207-23.4737307348
391.08716858198-0.5468970110861.045316886051.134347607220.203546678991.507904273990.163850696172-0.263385949921-0.122419092805-0.255756616139-0.1718585454910.861139008014-0.0715259892769-0.2076444820710.004025971638130.466663844737-0.0282954759040.04498592247930.24457407337-0.01463183565090.374109496653-42.39664543662.86772968732-30.6649332631
401.68522956487-0.3912434190770.07506588349911.383488818791.479680134481.663359102550.0571511614196-0.170315714683-0.196695011-0.446350747503-0.0760349551742-0.3770903174010.6233875469320.18877400265-0.0001127010463640.282917899619-0.0955600835203-0.04569413272010.34645070608-0.005550508473090.321001600965-35.2327451016-1.06909584764-22.2707441698
411.40976586257-0.887634363857-0.9908472445083.063598978330.7398956971210.8712746089110.120919744495-1.060863825610.697812800269-0.3745981703820.025952910342-0.5354825955010.158616483780.0316766569187-0.04794212142710.412781594806-0.0155059057975-0.0460061879890.689005595581-0.1226587878020.372990839199-30.04958151785.84854730942-15.7290168762
421.00980172993-0.0963163954725-0.1065723616091.22927213343-0.9290703331940.6606669122960.153669049511-1.14654279910.1711651361690.682606361863-0.4448318718460.2083840660210.13816118974-0.609993203205-0.04088235272250.502738136896-0.09267993207170.1045189729080.644849193934-0.06069463389080.434338872194-40.25187183724.98209622965-15.8641888525
432.31481922147-0.4184052657961.141089910942.00353734240.2100795879430.624544846539-0.0748200553243-0.2750407196070.03941165818310.2364418582580.16579802884-0.2261623872630.511565273760.4401719501960.04236566959630.2990477582130.0744438156491-0.05170337513280.4036363858210.04511814957520.274824297874-40.4028555341-31.6384878497-14.9924772948
441.904464211690.1978129891310.7760219085010.8341076123770.5901961159651.767400416590.07902182833-0.0188771405725-0.106407691694-0.1789640344410.13158717320.04141382031170.160043703712-0.1408471692510.0001067575195450.259648143615-0.002807794254530.05121591570170.2691195195790.02297003400550.284073888152-50.7975625495-30.3814763189-28.1104831363
451.79601233056-0.129603189333-0.1129744425470.887284496078-0.3216967084850.74934827718-0.0329454553953-0.0739939651831-0.0777921556035-0.06582737262460.1276833169470.0009983098762650.1935645806240.1191468921260.001279261119840.1785265692520.0308593184634-0.03217453551150.265235914501-0.005680927387240.239225396265-48.5640817861-29.627797807-20.3026944215
460.9068102970230.5003378807710.6869881863221.22266304187-0.8156850476362.45046716755-0.122365484743-0.3378013970990.3908079198630.394613881156-0.007828112714940.371373207587-0.419757086626-0.430231263704-0.005914729987040.3753389105750.113528872576-0.03296372637260.305399227801-0.02705419299860.300222673035-50.6588333041-23.0917986667-17.7638296732
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 'A' and (resid 1 through 22 )AA1 - 221 - 22
22chain 'A' and (resid 23 through 43 )AA23 - 4323 - 43
33chain 'A' and (resid 44 through 65 )AA44 - 6544 - 65
44chain 'A' and (resid 66 through 90 )AA66 - 9066 - 90
55chain 'A' and (resid 91 through 108 )AA91 - 10891 - 108
66chain 'A' and (resid 109 through 136 )AA109 - 135109 - 135
77chain 'B' and (resid 1 through 27 )BE1 - 271 - 27
88chain 'B' and (resid 28 through 43 )BE28 - 4328 - 43
99chain 'B' and (resid 44 through 65 )BE44 - 6544 - 65
1010chain 'B' and (resid 66 through 90 )BE66 - 9066 - 90
1111chain 'B' and (resid 91 through 108 )BE91 - 10891 - 108
1212chain 'B' and (resid 109 through 138 )BE109 - 138109 - 138
1313chain 'C' and (resid 2 through 29 )CJ2 - 291 - 22
1414chain 'C' and (resid 30 through 46 )CJ30 - 4623 - 39
1515chain 'C' and (resid 47 through 90 )CJ47 - 9040 - 83
1616chain 'C' and (resid 91 through 138 )CJ91 - 13884 - 131
1717chain 'D' and (resid 1 through 11 )DM1 - 111 - 11
1818chain 'D' and (resid 12 through 27 )DM12 - 2712 - 27
1919chain 'D' and (resid 28 through 43 )DM28 - 4328 - 43
2020chain 'D' and (resid 44 through 65 )DM44 - 6544 - 65
2121chain 'D' and (resid 66 through 99 )DM66 - 9966 - 99
2222chain 'D' and (resid 100 through 108 )DM100 - 108100 - 108
2323chain 'D' and (resid 109 through 126 )DM109 - 126109 - 126
2424chain 'D' and (resid 127 through 138 )DM127 - 138127 - 138
2525chain 'E' and (resid 1 through 11 )EO1 - 111 - 11
2626chain 'E' and (resid 12 through 43 )EO12 - 4312 - 43
2727chain 'E' and (resid 44 through 65 )EO44 - 6544 - 65
2828chain 'E' and (resid 66 through 90 )EO66 - 9066 - 90
2929chain 'E' and (resid 91 through 108 )EO91 - 10891 - 108
3030chain 'E' and (resid 109 through 135 )EO109 - 135109 - 135
3131chain 'F' and (resid 1 through 11 )FR1 - 111 - 11
3232chain 'F' and (resid 12 through 43 )FR12 - 4312 - 43
3333chain 'F' and (resid 44 through 65 )FR44 - 6544 - 65
3434chain 'F' and (resid 66 through 90 )FR66 - 9066 - 90
3535chain 'F' and (resid 91 through 126 )FR91 - 12691 - 126
3636chain 'F' and (resid 127 through 138 )FR127 - 138127 - 138
3737chain 'G' and (resid 2 through 28 )GT2 - 281 - 22
3838chain 'G' and (resid 29 through 43 )GT29 - 4323 - 37
3939chain 'G' and (resid 44 through 65 )GT44 - 6538 - 59
4040chain 'G' and (resid 66 through 90 )GT66 - 9060 - 84
4141chain 'G' and (resid 91 through 108 )GT91 - 10885 - 102
4242chain 'G' and (resid 109 through 137 )GT109 - 137103 - 131
4343chain 'H' and (resid 1 through 27 )HV1 - 271 - 27
4444chain 'H' and (resid 28 through 65 )HV28 - 6528 - 65
4545chain 'H' and (resid 66 through 99 )HV66 - 9966 - 99
4646chain 'H' and (resid 100 through 140 )HV100 - 140100 - 140

+
万見について

-
お知らせ

-
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

-
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

+
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

+
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

+
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。

-
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