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- PDB-7bl7: Crystal structure of UMPK from M. tuberculosis in complex with UD... -

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IDまたはキーワード:

読み込み中...

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基本情報

登録情報
データベース: PDB / ID: 7bl7
タイトルCrystal structure of UMPK from M. tuberculosis in complex with UDP and UTP (P21212 form)
要素Uridylate kinase
キーワードTRANSFERASE (転移酵素) / UMP kinase
機能・相同性
機能・相同性情報


UMP kinase / UMP kinase activity / 'de novo' CTP biosynthetic process / UDP biosynthetic process / リン酸化 / magnesium ion binding / ATP binding / 細胞膜 / 細胞質
類似検索 - 分子機能
Uridylate kinase, bacteria / Uridylate kinase / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily
類似検索 - ドメイン・相同性
URIDINE-5'-DIPHOSPHATE / URIDINE 5'-TRIPHOSPHATE / Uridylate kinase
類似検索 - 構成要素
生物種Mycobacterium tuberculosis H37Rv (結核菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.33 Å
データ登録者Walter, P. / Labesse, G. / Haouz, A. / Mechaly, A.E. / Munier-Lehmann, H.
資金援助 フランス, 2件
組織認可番号国
H2020 Marie Curie Actions of the European Commission675555 フランス
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INBS-05 フランス
引用ジャーナル: FEBS J / 年: 2022
タイトル: Structural basis for the allosteric inhibition of UMP kinase from Gram-positive bacteria, a promising antibacterial target.
著者: Patrick Walter / Ariel Mechaly / Julien Bous / Ahmed Haouz / Patrick England / Joséphine Lai-Kee-Him / Aurélie Ancelin / Sylviane Hoos / Bruno Baron / Stefano Trapani / Patrick Bron / ...著者: Patrick Walter / Ariel Mechaly / Julien Bous / Ahmed Haouz / Patrick England / Joséphine Lai-Kee-Him / Aurélie Ancelin / Sylviane Hoos / Bruno Baron / Stefano Trapani / Patrick Bron / Gilles Labesse / Hélène Munier-Lehmann /
要旨: Tuberculosis claims significantly more than one million lives each year. A feasible way to face the issue of drug resistance is the development of new antibiotics. Bacterial uridine 5'-monophosphate ...Tuberculosis claims significantly more than one million lives each year. A feasible way to face the issue of drug resistance is the development of new antibiotics. Bacterial uridine 5'-monophosphate (UMP) kinase is a promising target for novel antibiotic discovery as it is essential for bacterial survival and has no counterpart in human cells. The UMP kinase from M. tuberculosis is also a model of particular interest for allosteric regulation with two effectors, GTP (positive) and UTP (negative). In this study, using X-ray crystallography and cryo-electron microscopy, we report for the first time a detailed description of the negative effector UTP-binding site of a typical Gram-positive behaving UMP kinase. Comparison between this snapshot of low affinity for Mg-ATP with our previous 3D-structure of the GTP-bound complex of high affinity for Mg-ATP led to a better understanding of the cooperative mechanism and the allosteric regulation of UMP kinase. Thermal shift assay and circular dichroism experiments corroborate our model of an inhibition by UTP linked to higher flexibility of the Mg-ATP-binding domain. These new structural insights provide valuable knowledge for future drug discovery strategies targeting bacterial UMP kinases.
履歴
登録2021年1月18日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02022年3月2日Provider: repository / タイプ: Initial release
改定 1.12022年9月14日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22024年1月31日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
B: Uridylate kinase
A: Uridylate kinase
F: Uridylate kinase
E: Uridylate kinase
D: Uridylate kinase
C: Uridylate kinase
I: Uridylate kinase
J: Uridylate kinase
K: Uridylate kinase
L: Uridylate kinase
G: Uridylate kinase
H: Uridylate kinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)362,61728
ポリマ－355,51112
非ポリマー7,10616
水73941
1
B: Uridylate kinase
A: Uridylate kinase
F: Uridylate kinase
E: Uridylate kinase
D: Uridylate kinase
C: Uridylate kinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)181,30914
ポリマ－177,7556
非ポリマー3,5538
水1086
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area19020 Å2
ΔGint-133 kcal/mol
Surface area48310 Å2
手法PISA
2
I: Uridylate kinase
J: Uridylate kinase
K: Uridylate kinase
L: Uridylate kinase
G: Uridylate kinase
H: Uridylate kinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)181,30914
ポリマ－177,7556
非ポリマー3,5538
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area19420 Å2
ΔGint-127 kcal/mol
Surface area44310 Å2
手法PISA
単位格子
Length a, b, c (Å)151.230, 165.750, 125.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
12
22
13
23

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 29 through 82 or (resid 85...A29 - 81
121(chain 'A' and (resid 29 through 82 or (resid 85...A85 - 156
131(chain 'A' and (resid 29 through 82 or (resid 85...A161 - 187
141(chain 'A' and (resid 29 through 82 or (resid 85...A203 - 260
251(chain 'B' and (resid 29 through 81 or (resid 82...B29 - 81
261(chain 'B' and (resid 29 through 81 or (resid 82...B85 - 156
271(chain 'B' and (resid 29 through 81 or (resid 82...B161 - 187
281(chain 'B' and (resid 29 through 81 or (resid 82...B203 - 260
391(chain 'C' and (resid 29 through 81 or (resid 82...C29 - 81
3101(chain 'C' and (resid 29 through 81 or (resid 82...C85 - 156
3111(chain 'C' and (resid 29 through 81 or (resid 82...C161 - 187
3121(chain 'C' and (resid 29 through 81 or (resid 82...C203 - 260
4131(chain 'D' and (resid 29 through 81 or (resid 82...D29 - 81
4141(chain 'D' and (resid 29 through 81 or (resid 82...D85 - 156
4151(chain 'D' and (resid 29 through 81 or (resid 82...D161 - 187
4161(chain 'D' and (resid 29 through 81 or (resid 82...D203 - 260
5171(chain 'E' and (resid 29 through 81 or (resid 82...E29 - 81
5181(chain 'E' and (resid 29 through 81 or (resid 82...E85 - 156
5191(chain 'E' and (resid 29 through 81 or (resid 82...E161 - 187
5201(chain 'E' and (resid 29 through 81 or (resid 82...E203 - 260
6211(chain 'F' and (resid 29 through 157 or resid 161...F29 - 81
6221(chain 'F' and (resid 29 through 157 or resid 161...F85 - 156
6231(chain 'F' and (resid 29 through 157 or resid 161...F161 - 187
6241(chain 'F' and (resid 29 through 157 or resid 161...F203 - 260
7251(chain 'H' and (resid 29 through 81 or (resid 82...H29 - 81
7261(chain 'H' and (resid 29 through 81 or (resid 82...H85 - 156
7271(chain 'H' and (resid 29 through 81 or (resid 82...H161 - 187
7281(chain 'H' and (resid 29 through 81 or (resid 82...H203 - 260
8291(chain 'I' and (resid 29 through 81 or (resid 82...I29 - 81
8301(chain 'I' and (resid 29 through 81 or (resid 82...I85 - 156
8311(chain 'I' and (resid 29 through 81 or (resid 82...I161 - 187
8321(chain 'I' and (resid 29 through 81 or (resid 82...I203 - 260
9331(chain 'J' and (resid 29 through 81 or (resid 82...J29 - 81
9341(chain 'J' and (resid 29 through 81 or (resid 82...J85 - 156
9351(chain 'J' and (resid 29 through 81 or (resid 82...J161 - 187
9361(chain 'J' and (resid 29 through 81 or (resid 82...J203 - 260
10371(chain 'K' and (resid 29 through 81 or (resid 82...K29 - 81
10381(chain 'K' and (resid 29 through 81 or (resid 82...K85 - 156
10391(chain 'K' and (resid 29 through 81 or (resid 82...K161 - 187
10401(chain 'K' and (resid 29 through 81 or (resid 82...K203 - 260
1412(chain 'G' and (resid 29 through 31 or (resid 32...G29 - 81
1422(chain 'G' and (resid 29 through 31 or (resid 32...G85 - 156
1432(chain 'G' and (resid 29 through 31 or (resid 32...G161 - 185
1442(chain 'G' and (resid 29 through 31 or (resid 32...G233 - 237
2452(chain 'L' and (resid 29 through 92 or (resid 93...L29 - 81
2462(chain 'L' and (resid 29 through 92 or (resid 93...L85 - 156
2472(chain 'L' and (resid 29 through 92 or (resid 93...L161 - 185
2482(chain 'L' and (resid 29 through 92 or (resid 93...L233 - 237
1493chain 'M'M1 - 4
2503chain 'N'N1 - 4

NCSアンサンブル:
ID
1
2
3

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要素

#1: タンパク質
Uridylate kinase / UK / Uridine monophosphate kinase / UMPK


分子量: 29625.893 Da / 分子数: 12 / 由来タイプ: 組換発現
由来: (組換発現) Mycobacterium tuberculosis H37Rv (結核菌)
遺伝子: pyrH, Rv2883c, MTCY274.14c / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P9WHK5, UMP kinase
#2: 化合物
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / UDP / ウリジン二リン酸


タイプ: RNA linking / 分子量: 404.161 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C9H14N2O12P2 / タイプ: SUBJECT OF INVESTIGATION / コメント: UDP*YM
#3: 化合物
ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE / UTP / ウリジン三リン酸


分子量: 484.141 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C9H15N2O15P3 / タイプ: SUBJECT OF INVESTIGATION / コメント: UTP*YM
#4: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 41 / 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: 2.2 Å3/Da / 溶媒含有率: 44.19 %
結晶化温度: 293 K / 手法: 蒸気拡散法 / pH: 8.7 / 詳細: 1 M LiCl, 20 % (w/v) PEG 8K and 0.1 M Tris pH 8.7

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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: 0.979 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2018年7月13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: 0.979 Å / 相対比: 1
反射解像度: 3.08→29.95 Å / Num. obs: 57888 / % possible obs: 98.7 % / 冗長度: 12.3 % / Biso Wilson estimate: 45.11 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.292 / Net I/σ(I): 8.2
反射 シェル解像度: 3.08→3.27 Å / Rmerge(I) obs: 1.263 / Mean I/σ(I) obs: 1.69 / Num. unique obs: 8576 / CC1/2: 0.922

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解析

ソフトウェア
名称バージョン分類
PHENIX1.14_3260精密化
PHASER位相決定
Aimlessデータスケーリング
XDSデータ削減
精密化構造決定の手法: 分子置換
開始モデル: 3NWY

3nwy


解像度: 3.33→29.95 Å / SU ML: 0.384 / 交差検証法: THROUGHOUT / σ(F): 1.35 / 位相誤差: 26.8546 / 立体化学のターゲット値: CDL v1.2
Rfactor反射数%反射
Rfree0.2743 2138 4.97 %
Rwork0.1923 40900 -
obs0.1964 43038 92.29 %
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: 48.79 Å2
精密化ステップサイクル: LAST / 解像度: 3.33→29.95 Å
タンパク質核酸リガンド溶媒全体
原子数18959 0 432 41 19432
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.013219609
X-RAY DIFFRACTIONf_angle_d1.27526573
X-RAY DIFFRACTIONf_chiral_restr0.06963165
X-RAY DIFFRACTIONf_plane_restr0.00593453
X-RAY DIFFRACTIONf_dihedral_angle_d25.07177076
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.33-3.410.33541070.22672015X-RAY DIFFRACTION69.08
3.41-3.490.31381050.22782241X-RAY DIFFRACTION76.67
3.49-3.590.34421270.21182440X-RAY DIFFRACTION84.05
3.59-3.690.27591420.20952706X-RAY DIFFRACTION92.62
3.69-3.810.28031510.20142871X-RAY DIFFRACTION98.21
3.81-3.950.28561510.19262869X-RAY DIFFRACTION97.61
3.95-4.10.28021500.17912842X-RAY DIFFRACTION98.03
4.1-4.290.23461500.17312847X-RAY DIFFRACTION97.02
4.29-4.520.22491490.15412829X-RAY DIFFRACTION96.44
4.52-4.80.2241500.16082856X-RAY DIFFRACTION96.16
4.8-5.170.28551490.17562816X-RAY DIFFRACTION95.95
5.17-5.680.30471510.2052874X-RAY DIFFRACTION96.83
5.68-6.50.3241520.21822897X-RAY DIFFRACTION96.89
6.5-8.160.28421520.19522892X-RAY DIFFRACTION96.12
8.16-29.950.24061520.20632905X-RAY DIFFRACTION92.25
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.09056386845-1.453939742672.027031144873.14747610794-0.4611924963994.422455210730.3670992270040.209358020249-0.533605191184-0.233609055329-0.1675890882660.08742609943260.54316813475-0.369434678148-0.1860061794550.180160815251-0.0003785120406380.01661787633540.292644742364-0.09340049027390.18586629704833.6574170308-16.343958844838.4511273202
21.766490104610.614010670558-0.8643668364411.95162590241-0.6034486224184.909351245810.04201092306750.2394037633130.1532135547070.0355817917707-0.170577378571-0.295931955679-0.06097156905190.3638763509360.03761901352110.04740899918650.01014811783910.00530320772113-0.0470331826749-0.1057826193180.1811211093139.1992760632-12.940702012545.8050597474
31.93723948124-0.174120159908-3.034245824272.276671025840.03230910845.483742739040.0513725801320.03699340983870.0251045220880.03348473867290.07442359603-0.553272928218-0.2173830891950.441388113935-0.1661819539950.3144909486340.253703657092-0.00364964088410.529721892929-0.1416171293730.14358565271937.1167571345-2.1259661997843.8218785807
41.047908357620.2069099211860.0006793490420190.793793496748-0.4318975067961.629016281930.032356955658-0.370432412889-0.0885161960519-0.0583806745222-0.142776225510.00343735803331-0.12064806302-0.1437976541720.02925567082280.19016684717-0.0376964876646-0.05628606023650.224120679992-0.0883319006070.13487389685727.5515509382-5.3733344603144.1716175858
53.049702032180.6640715356490.8697396735990.2702972742940.8349633584953.561100304520.5792831310930.472375862012-0.835684073835-0.349674882612-0.2719191779680.2140432752821.03704795601-0.352720557835-0.08727228780910.179741517098-0.217039369603-0.4510976143780.355534643765-0.4671583497580.26664330253521.3780497065-22.382312304433.80199129
63.920641733930.5847928266132.827855248371.836784326430.1836278037426.334368251770.1140826965480.0927059248147-0.785396555072-0.0776849314467-0.3488800581570.6383544281270.787211321064-1.177754024330.2022500993230.53250056003-0.218736666783-0.07771975458790.627321433968-0.2784918289450.57126088166310.9206815085-24.696888264837.4819902608
76.067424029352.788521312270.6975788202671.518621944791.578870057326.483665303910.3358198901140.0590887851766-0.8358959926870.0309807378806-0.174611588702-0.02771269452240.825764139873-0.0173184898026-0.1169965984810.250500242978-0.297620508632-0.06514513107320.245477079227-0.05063673974140.27439805528916.3820985135-19.368356114645.0606799729
83.87975528547-1.45279963921-2.053106979523.702871930020.8508954121233.685338997630.04418659993680.935033629258-0.12881845966-0.851555426292-0.135922837029-0.0527142478587-0.0798592735737-0.151922459335-0.1339042740580.39297493862-0.135066045255-0.02981260942420.483820542863-0.1089113546620.20684284958321.2432549309-16.817055026729.0433527805
92.71325931214-0.0756561392552.414224022321.698780932150.5424571193846.250767944110.144978831883-0.464398366578-0.8333689902410.2465995208630.225037102315-0.3002025326770.9101064861350.0799924150969-0.3970993788370.2837098937370.0301315608069-0.09357330406950.4801323404040.149423523040.67650294497355.0368824497-23.785461635461.8253633296
104.96242166101-0.8748757426891.744397957014.03541940944-0.9444929370063.077502563390.0336448445058-0.1571502478310.31960839332-0.235144910668-0.243807966737-0.59405746694-0.1126563751130.05268237917680.1753456036480.1977308451570.065330784327-0.0003337700759550.2049466600620.005541435619510.39978064646548.6499474793-13.398980825455.1389371665
115.54897299506-0.775863304065-0.9024721817133.36807905371.812996237063.188872300880.0936169740965-0.4321127256680.06548446862860.0281686306792-0.107901189532-0.6685645129-0.0462748009120.252849051382-0.01623962093540.2288562712770.0142188416436-0.1065233959040.4584449221190.1400821014180.52193524872165.9073028377-15.775388796959.807425998
122.63700790687-1.64669898622-2.570049024114.318832941151.103592788274.86109245508-0.197355376902-0.2957506698030.2780268151630.2294702388520.60365298492-0.936489863827-0.3658838946221.50567006128-0.259087856230.230654204744-0.03882952509230.001188084902470.538968614622-0.02501097480230.42666567594157.72796288928.471231221841.8717845796
132.45157235539-0.198904361593-0.9223157783596.466072155495.487706772142.00298825474-0.04791006831380.3528534600120.75892920783-0.7883393342540.01677537639-0.460360608446-1.485817440070.483650644885-0.07151640417540.408909436084-0.1859126359090.1335197444020.198453320470.081120713750.6072256542352.117161829835.141969876436.4326789703
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613.465875979693.42274608303-3.944751843677.70311167067-7.860245374099.251998541770.04536271875550.08599943530760.42852550464-0.214900880166-0.01956836848540.314185604032-0.5629635029820.398774826915-0.1878617276480.3786038591110.0986710773162-0.03742739746320.618433333003-0.1543189032530.26843074056933.46794257220.3134388453.06425739911
621.01429102750.124531186081.433275905653.19118070318-0.5117927586165.018802585540.0470812815916-0.3008694626690.0568146676893-0.1020562708460.319386381717-0.584769386190.05623119701620.68645953074-0.2983626720070.171741369426-0.052872055739-0.02351268093530.529131170076-0.1043714000360.26391945301138.08823443619.803814572235.48624610609
630.9497476127560.4556834025020.603446181540.616251080245-0.2657123402172.875956917690.00676029826684-0.04308980031230.087572216913-0.254948092034-0.2371291274520.03413731146550.2902930059940.09922581857560.106218253240.2707728262150.0298916026245-0.05833423907770.430335036897-0.06475606860130.19643996025529.35443943164.964157254796.81324430427
643.675913023370.547209076805-0.03227146672770.318481460493-0.01354590397728.210974861810.13601325273-0.4126143407670.671416754366-0.0404069188766-0.1101182975940.256688884913-1.11524965111-0.3848637019690.00922446784350.2390989788580.0382883077137-0.1110561932120.678461768275-0.1686587084990.20136815899221.601898356917.05170237512.0865354446
655.92376049224-0.53107162475-1.937170623623.551797403742.071703109861.664194741980.06898783627750.04352240075250.634789869917-0.919089073308-0.1681955814560.496608754659-1.17730315287-1.71283952980.08488913227010.9883464532040.500160936327-0.1935715838711.36311041884-0.1688383756570.555967546168.9354582181824.361005767910.3319252273
666.98012490489-2.48896781911-2.72125326871.47655452767-0.9999112434457.64266453617-0.248461827336-0.7308662725320.9593979055070.3586913639090.1667740489910.000862321860633-0.8828153294070.04231178052280.06239866706020.4871009510520.247141216864-0.103860637890.543102451585-0.2335599087530.34455881022615.898299958519.89030283045.18194118354
673.39274026968-0.194561727851-0.1794075355042.751827613771.365959768035.536386085190.209878159565-0.857022180130.4423407343470.673745543957-0.136947935557-0.07207762869160.0558412781281-0.5721123632340.06205697349480.635914369243-0.01139562770560.01936647261630.238946600767-0.1023368746070.29132528691320.738280369917.86942950521.4306889186
686.41387861734-3.42843521324-3.277553922043.372068192832.360330321732.774674029720.907155416947-0.1118119988471.32186306493-0.1183516920560.116916949419-0.734570224793-0.8394309992080.876073635475-1.009893739690.802633369934-0.4893532242640.2314569796331.61001247779-0.1248088587930.8448826153155.731575753923.5899796891-6.56181433062
694.22857500798-0.663916783449-5.675330219252.879658832660.85052034528.069116353840.539958864130.1174885472450.777782155356-0.092690617627-0.279435997228-0.805015718807-1.150160348570.479164861171-0.2025398248490.627491388801-0.5003689181010.1578948656690.9647982563070.163491340791.1063251702452.356954728128.9083557593-15.85566566
700.364353496686-0.597010023137-0.07313408773431.53723844488-0.1976779113930.232125764543-0.0855972250432-0.264977789118-0.1352699080910.1155642101260.157403292331-1.00812326615-0.1248790148311.205946247650.02511235671820.587301636784-0.283618719703-0.020102037891.2164635235-0.04404462534520.85274122475952.844418147217.4923466041-0.580241797798
713.827393243210.995211016032-0.17262173833.53493524514-1.358322950923.203648401040.1489527315390.250834255015-0.225882250466-0.139998957876-0.112254742641-0.4935802552290.06074023969190.2703654687410.05505445866680.228987949754-0.312328951780.02302177431490.945553916879-0.1576645817740.41575649065547.015541659115.7886020157-2.54093354821
722.324908833050.723589995365-0.1622986073330.801996595338-1.199144374542.286845981560.05803974841390.216653680178-0.210756402904-0.859278100307-0.425507544887-0.8841795735370.3222885965250.8279040883630.3298575561760.679173324818-0.2160463204840.4078963384351.08467583783-0.1726800226430.80029622251847.618686259710.5926300684-15.5493186717
734.42505759301-2.25415431618-1.014669186352.723481088351.003594866790.376386273293-0.229117612598-0.8047720580220.2484756877160.07056696907130.412261334644-0.758224468348-0.2180558248660.3792355571910.06025208067110.648238023696-0.2934409407270.2679003815671.75625264213-0.1615431342490.94211888887760.087557455513.0725833229-9.93268371416
741.352194171120.242391779248-0.2521635717091.371953817280.8518943320411.388769791420.1081535147530.176741086912-0.628334905824-0.298618235577-0.102045424701-0.2450484352230.3390436048370.363043760074-0.1192902743030.5964693178420.816787556497-0.1467924279091.61152767047-0.253158834680.70453655012658.3198753415-26.6324068598.74964149786
750.9074879772170.263409501925-0.09421258213080.9479365549320.5904559519772.385848059720.1719191775570.144082493517-0.708584027161-0.011061316707-0.20412264976-0.08950321783570.4061934311410.224337042425-0.05879209067470.7631497211580.487978757622-0.2371306779631.26088828104-0.1773473965930.84673287158453.2571330064-29.003127905412.3727770415
764.71066343689-6.355382438514.120537230158.57253287779-5.557245209493.59899105382-0.337909233091.307221403411.89346691227-0.6052687240260.2464279207290.458265661791-1.11906022576-0.9029261731930.08356913702880.789412881468-0.229980360703-0.07830363897821.31642907072-0.4852305108491.2874646230864.6524443439-20.6658168582-11.7400586564
771.24563639547-0.6884185196760.02436213782531.914785395091.222193151772.07270007157-0.0795820390575-0.109343410523-0.0990073991248-0.06630745205970.177471672631-0.2578100193490.3493151855760.2345401726650.03327398561770.4104971988220.409439470590.01031189114260.985270073537-0.6887724077820.30778256496248.0739044803-20.35458345672.97559884068
784.343643430222.338672949361.52052345832.62022871229-1.462961241624.845185180790.07024197177970.2318333561630.168249196930.009190841666550.06855689616390.0849398746561-0.09397426099090.513899009449-0.07383006400960.3428916970640.197990054217-0.1707014706490.720483325867-0.225197770370.34610449909645.6960091634-15.77107252615.7824127218
791.547997906691.111062729311.623479711745.62597335373-0.03336509992331.99587816556-0.5554631256390.601668653771-0.544932713278-0.8452475761130.658711425559-0.9623983417780.2567327836421.03883532360.02578005862250.5063985900710.103609996701-0.04217061815361.52310533494-0.1664002491961.124171526559.3467564754-13.41277521428.97046030249
800.02189894819140.0992593927531-0.3196997183750.41478133751-1.374941825294.533050372680.000837887571688-0.282542132393-0.180753499980.3117296834-0.126190849145-0.2281761441610.3306953394680.5108667311530.1499159966371.037199863270.394070820344-0.2376226178932.235692111-0.7322767427561.2392671288266.4664729525-23.978032228916.8319013284
812.10838142228-0.7698295883260.9577396313330.9362489823-0.3636202417741.874059623490.100509983915-0.206428016315-0.431826637999-0.02157644658990.110224398504-0.3296182186660.3585250255420.465492783578-0.1280540938230.9402002194940.3684206757360.1652346766870.520837848232-0.3543376412930.4561616452148.517342962-25.6944816161-22.6855944443
823.7080036122-1.47818229212.817390780491.47536222997-1.185967979226.137689703460.09795016406640.2492447127680.0386894257381-0.440434885508-0.173624116174-0.6008899071050.3222570580190.874556169570.01701794608280.5898338778440.3706683094370.2488036624920.779042195957-0.6790479467040.80718318118955.8760509697-20.6398811132-27.8904410318
831.510883748-0.106515044054-0.5728042822454.34251107737-3.671281722346.870863738430.136501146285-0.0925085051472-0.0539424078074-0.08269364524240.560797449478-0.3055500425190.7085062093630.0978984664696-0.6142401444370.4329914938420.205721785168-0.05189102343030.780747505987-0.2236972706740.50438741094344.9044040306-28.5811263344-12.1839656413
844.72829615035-0.11510621508-1.799654680663.42836365369-1.45642003974.80442626546-0.1586536374330.195392418810.168215213855-0.06602990189630.128048999028-0.6684056970350.05478201532840.544496803192-0.09298253753130.3566365720140.188962148453-0.04115661648110.628710303782-0.2826095883060.47808387021649.2151472793-21.2842011813-11.8678744049
854.883372780640.0913476577078-1.307784388232.80289906511-1.834965968552.95951850516-0.1600889285280.1005374521760.475326687775-0.0353573553995-0.0253129753799-0.590970408519-0.2575804399620.5425609184140.009241137764940.2074414387340.201961848804-0.01235685142780.587892206719-0.3070701376610.58561109270244.7012643012-11.2504441438-13.9176394912
861.094633503350.131952707571-0.5242798212170.7838954559680.8679630204842.224417500970.1356316292740.32164618114-0.229328816601-0.330295200285-0.205117523868-0.3385424999840.225705588041-0.2059283376360.080458852260.5100789178280.1046848192160.02830923097380.456113312343-0.179450236840.3969539067738.5715379276-18.098468331-20.8051749141
870.913186280657-0.5009021244381.42239870020.918644166568-0.3273722317082.50135220970.01430466946390.230401293138-0.0341011537954-0.04665969733980.104103700125-0.145802859929-0.01687426030510.276111587587-0.06395267207140.9397591574130.466764529260.1696095893090.626144913199-0.7868079481970.50744856883141.3988785035-37.4192498036-33.7089582526
885.61121885768-1.289990034911.833455914814.33444669587-0.4064109603935.19102611844-0.02335135594440.388777579984-0.725026369761-0.1450900236320.03387117898980.031847470630.696398413371-0.1667320553870.01925410758861.240885480160.0205985228669-0.1067914421350.498422451147-0.3889416058310.90153311922432.6478003928-38.6275408372-27.9333712439
891.245802437120.313531159288-0.575882100172.405442575710.8441156291762.737624381370.07116403044210.381384046948-0.373673050961-0.5793099757690.00756407069579-0.02211060697910.1371078758040.345909901654-0.00877193930350.725499502980.1736418637210.006670673880720.775676221769-0.358333674660.57779318847339.9749581765-28.3225511634-31.8562330619
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 28 through 92 )
2X-RAY DIFFRACTION2chain 'B' and (resid 93 through 117 )
3X-RAY DIFFRACTION3chain 'B' and (resid 118 through 138 )
4X-RAY DIFFRACTION4chain 'B' and (resid 139 through 176 )
5X-RAY DIFFRACTION5chain 'B' and (resid 177 through 202 )
6X-RAY DIFFRACTION6chain 'B' and (resid 203 through 215 )
7X-RAY DIFFRACTION7chain 'B' and (resid 216 through 231 )
8X-RAY DIFFRACTION8chain 'B' and (resid 232 through 261 )
9X-RAY DIFFRACTION9chain 'A' and (resid 28 through 67 )
10X-RAY DIFFRACTION10chain 'A' and (resid 68 through 138 )
11X-RAY DIFFRACTION11chain 'A' and (resid 139 through 261 )
12X-RAY DIFFRACTION12chain 'F' and (resid 29 through 50 )
13X-RAY DIFFRACTION13chain 'F' and (resid 51 through 67 )
14X-RAY DIFFRACTION14chain 'F' and (resid 68 through 92 )
15X-RAY DIFFRACTION15chain 'F' and (resid 93 through 118 )
16X-RAY DIFFRACTION16chain 'F' and (resid 119 through 138 )
17X-RAY DIFFRACTION17chain 'F' and (resid 139 through 155 )
18X-RAY DIFFRACTION18chain 'F' and (resid 156 through 165 )
19X-RAY DIFFRACTION19chain 'F' and (resid 166 through 176 )
20X-RAY DIFFRACTION20chain 'F' and (resid 177 through 221 )
21X-RAY DIFFRACTION21chain 'F' and (resid 222 through 250 )
22X-RAY DIFFRACTION22chain 'F' and (resid 251 through 260 )
23X-RAY DIFFRACTION23chain 'E' and (resid 29 through 50 )
24X-RAY DIFFRACTION24chain 'E' and (resid 51 through 67 )
25X-RAY DIFFRACTION25chain 'E' and (resid 68 through 82 )
26X-RAY DIFFRACTION26chain 'E' and (resid 83 through 92 )
27X-RAY DIFFRACTION27chain 'E' and (resid 93 through 117 )
28X-RAY DIFFRACTION28chain 'E' and (resid 118 through 138 )
29X-RAY DIFFRACTION29chain 'E' and (resid 139 through 208 )
30X-RAY DIFFRACTION30chain 'E' and (resid 209 through 221 )
31X-RAY DIFFRACTION31chain 'E' and (resid 222 through 249 )
32X-RAY DIFFRACTION32chain 'E' and (resid 250 through 261 )
33X-RAY DIFFRACTION33chain 'D' and (resid 28 through 75 )
34X-RAY DIFFRACTION34chain 'D' and (resid 76 through 92 )
35X-RAY DIFFRACTION35chain 'D' and (resid 93 through 185 )
36X-RAY DIFFRACTION36chain 'D' and (resid 186 through 208 )
37X-RAY DIFFRACTION37chain 'D' and (resid 209 through 221 )
38X-RAY DIFFRACTION38chain 'D' and (resid 222 through 261 )
39X-RAY DIFFRACTION39chain 'C' and (resid 28 through 50 )
40X-RAY DIFFRACTION40chain 'C' and (resid 51 through 66 )
41X-RAY DIFFRACTION41chain 'C' and (resid 67 through 92 )
42X-RAY DIFFRACTION42chain 'C' and (resid 93 through 185 )
43X-RAY DIFFRACTION43chain 'C' and (resid 186 through 195 )
44X-RAY DIFFRACTION44chain 'C' and (resid 196 through 215 )
45X-RAY DIFFRACTION45chain 'C' and (resid 216 through 250 )
46X-RAY DIFFRACTION46chain 'C' and (resid 251 through 261 )
47X-RAY DIFFRACTION47chain 'I' and (resid 28 through 75 )
48X-RAY DIFFRACTION48chain 'I' and (resid 76 through 92 )
49X-RAY DIFFRACTION49chain 'I' and (resid 93 through 185 )
50X-RAY DIFFRACTION50chain 'I' and (resid 186 through 215 )
51X-RAY DIFFRACTION51chain 'I' and (resid 216 through 231 )
52X-RAY DIFFRACTION52chain 'I' and (resid 232 through 261 )
53X-RAY DIFFRACTION53chain 'J' and (resid 29 through 50 )
54X-RAY DIFFRACTION54chain 'J' and (resid 51 through 66 )
55X-RAY DIFFRACTION55chain 'J' and (resid 67 through 92 )
56X-RAY DIFFRACTION56chain 'J' and (resid 93 through 185 )
57X-RAY DIFFRACTION57chain 'J' and (resid 186 through 215 )
58X-RAY DIFFRACTION58chain 'J' and (resid 216 through 230 )
59X-RAY DIFFRACTION59chain 'J' and (resid 231 through 261 )
60X-RAY DIFFRACTION60chain 'K' and (resid 27 through 66 )
61X-RAY DIFFRACTION61chain 'K' and (resid 67 through 92 )
62X-RAY DIFFRACTION62chain 'K' and (resid 93 through 138 )
63X-RAY DIFFRACTION63chain 'K' and (resid 139 through 164 )
64X-RAY DIFFRACTION64chain 'K' and (resid 165 through 205 )
65X-RAY DIFFRACTION65chain 'K' and (resid 206 through 215 )
66X-RAY DIFFRACTION66chain 'K' and (resid 216 through 231 )
67X-RAY DIFFRACTION67chain 'K' and (resid 232 through 261 )
68X-RAY DIFFRACTION68chain 'L' and (resid 29 through 50 )
69X-RAY DIFFRACTION69chain 'L' and (resid 51 through 66 )
70X-RAY DIFFRACTION70chain 'L' and (resid 67 through 92 )
71X-RAY DIFFRACTION71chain 'L' and (resid 93 through 116 )
72X-RAY DIFFRACTION72chain 'L' and (resid 117 through 147 )
73X-RAY DIFFRACTION73chain 'L' and (resid 148 through 238 )
74X-RAY DIFFRACTION74chain 'G' and (resid 29 through 50 )
75X-RAY DIFFRACTION75chain 'G' and (resid 51 through 80 )
76X-RAY DIFFRACTION76chain 'G' and (resid 81 through 92 )
77X-RAY DIFFRACTION77chain 'G' and (resid 93 through 138 )
78X-RAY DIFFRACTION78chain 'G' and (resid 139 through 155 )
79X-RAY DIFFRACTION79chain 'G' and (resid 156 through 184 )
80X-RAY DIFFRACTION80chain 'G' and (resid 185 through 258 )
81X-RAY DIFFRACTION81chain 'H' and (resid 29 through 50 )
82X-RAY DIFFRACTION82chain 'H' and (resid 51 through 66 )
83X-RAY DIFFRACTION83chain 'H' and (resid 67 through 92 )
84X-RAY DIFFRACTION84chain 'H' and (resid 93 through 118 )
85X-RAY DIFFRACTION85chain 'H' and (resid 119 through 138 )
86X-RAY DIFFRACTION86chain 'H' and (resid 139 through 185 )
87X-RAY DIFFRACTION87chain 'H' and (resid 186 through 208 )
88X-RAY DIFFRACTION88chain 'H' and (resid 209 through 221 )
89X-RAY DIFFRACTION89chain 'H' and (resid 222 through 261 )

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万見について

-
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

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