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- PDB-8bhd: N-terminal domain of Plasmodium berghei glutamyl-tRNA synthetase ... -

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基本情報

登録情報
データベース: PDB / ID: 8bhd
タイトルN-terminal domain of Plasmodium berghei glutamyl-tRNA synthetase (Tbxo4 derivative crystal structure)
要素Glutamate--tRNA ligase
キーワードRNA BINDING PROTEIN / aminoacyl-tRNA synthetase / tRNA / protein complex / Cell surface protein / multi-aminoacyl-tRNA synthetase complex (MARS-MSC) / GST-like domain / aminoacyl-tRNA synthetase-interacting multifunctional proteins (AIMP)
機能・相同性
機能・相同性情報


glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / ATP binding / cytoplasm
類似検索 - 分子機能
: / Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / : / tRNA synthetases class I (E and Q), anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / Glutamyl/glutaminyl-tRNA synthetase / Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain / tRNA synthetases class I (E and Q), catalytic domain / Aminoacyl-tRNA synthetase, class I, conserved site ...: / Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / : / tRNA synthetases class I (E and Q), anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / Glutamyl/glutaminyl-tRNA synthetase / Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain / tRNA synthetases class I (E and Q), catalytic domain / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Glutathione S-transferase, C-terminal domain superfamily / Rossmann-like alpha/beta/alpha sandwich fold / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily
類似検索 - ドメイン・相同性
TERBIUM(III) ION / glutamate--tRNA ligase
類似検索 - 構成要素
生物種Plasmodium berghei ANKA (ネズミマラリア原虫)
手法X線回折 / シンクロトロン / 単波長異常分散 / 解像度: 3.17 Å
データ登録者Benas, P. / Jaramillo Ponce, J.R. / Legrand, P. / Frugier, M. / Sauter, C.
資金援助 フランス, 3件
組織認可番号国
Agence Nationale de la Recherche (ANR)ANR-10-IDEX-0002 フランス
Agence Nationale de la Recherche (ANR)ANR 20-SFRI-0012 フランス
Agence Nationale de la Recherche (ANR)ANR-17-EURE-0023 フランス
引用
ジャーナル: Protein Sci. / 年: 2023
タイトル: Solution X-ray scattering highlights discrepancies in Plasmodium multi-aminoacyl-tRNA synthetase complexes.
著者: Jaramillo Ponce, J.R. / Theobald-Dietrich, A. / Benas, P. / Paulus, C. / Sauter, C. / Frugier, M.
#1: ジャーナル: J.Biol.Chem. / 年: 2022
タイトル: Discovery of two distinct aminoacyl-tRNA synthetase complexes anchored to the Plasmodium surface tRNA import protein.
著者: Jaramillo Ponce, J.R. / Kapps, D. / Paulus, C. / Chicher, J. / Frugier, M.
#2: ジャーナル: Acta Crystallogr.,Sect.D / 年: 2012
タイトル: Towards automated crystallographic structure refinement with phenix.refine.
著者: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#3: 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.
#4: ジャーナル: Acta Crystallogr D Biol Crystallogr / 年: 2004
タイトル: Coot: model-building tools for molecular graphics.
著者: Paul Emsley / Kevin Cowtan /
要旨: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality ...CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics. The map-fitting tools are available as a stand-alone package, distributed as 'Coot'.
#5: ジャーナル: Acta Crystallogr.,Sect.D / 年: 2006
タイトル: The Buccaneer software for automated model building. 1. Tracing protein chains.
著者: Cowtan, K.
#6: ジャーナル: Acta Crystallogr.,Sect.D / 年: 2010
タイトル: Recent developments in classical density modification.
著者: Cowtan, K.
#7: ジャーナル: Acta Crystallogr.,Sect.D / 年: 2010
タイトル: Multivariate phase combination improves automated crystallographic model building.
著者: Skubak, P. / Waterreus, W.J. / Pannu, N.S.
#8: ジャーナル: Acta Crystallogr.,Sect.D / 年: 1996
タイトル: Methods used in the structure determination of bovine mitochondrial F1 ATPase.
著者: Abrahams, J.P. / Leslie, A.G.
#9: ジャーナル: Acta Crystallogr.,Sect.D / 年: 2011
タイトル: REFMAC5 for the refinement of macromolecular crystal structures.
著者: Murshudov, G.N. / Skubak, P. / Lebedev, A.A. / Pannu, N.S. / Steiner, R.A. / Nicholls, R.A. / Winn, M.D. / Long, F. / Vagin, A.A.
#10: ジャーナル: Acta Crystallogr.,Sect.D / 年: 2002
タイトル: Substructure solution with SHELXD.
著者: Schneider, T.R. / Sheldrick, G.M.
#11: ジャーナル: Acta Crystallogr.,Sect.A / 年: 2008
タイトル: A short history of SHELX.
著者: Sheldrick, G.M.
#12: ジャーナル: Nat Commun / 年: 2013
タイトル: Automatic protein structure solution from weak X-ray data.
著者: Skubak, P. / Pannu, N.S.
#13: ジャーナル: Acta Crystallogr.,Sect.D / 年: 2010
タイトル: XDS.
著者: Kabsch, W.
#14: ジャーナル: Acta Crystallogr.,Sect.D / 年: 2010
タイトル: Integration, scaling, space-group assignment and post-refinement.
著者: Kabsch, W.
#15: ジャーナル: J.Synchrotron Radiat. / 年: 2019
タイトル: MXCuBE2: the dawn of MXCuBE Collaboration.
著者: Oscarsson, M. / Beteva, A. / Flot, D. / Gordon, E. / Guijarro, M. / Leonard, G. / McSweeney, S. / Monaco, S. / Mueller-Dieckmann, C. / Nanao, M. / Nurizzo, D. / Popov, A.N. / von Stetten, D. ...著者: Oscarsson, M. / Beteva, A. / Flot, D. / Gordon, E. / Guijarro, M. / Leonard, G. / McSweeney, S. / Monaco, S. / Mueller-Dieckmann, C. / Nanao, M. / Nurizzo, D. / Popov, A.N. / von Stetten, D. / Svensson, O. / Rey-Bakaikoa, V. / Chado, I. / Chavas, L.M.G. / Gadea, L. / Gourhant, P. / Isabet, T. / Legrand, P. / Savko, M. / Sirigu, S. / Shepard, W. / Thompson, A. / Mueller, U. / Nan, J. / Eguiraun, M. / Bolmsten, F. / Nardella, A. / Milan-Otero, A. / Thunnissen, M. / Hellmig, M. / Kastner, A. / Schmuckermaier, L. / Gerlach, M. / Feiler, C. / Weiss, M.S. / Bowler, M.W. / Gobbo, A. / Papp, G. / Sinoir, J. / McCarthy, A.A. / Karpics, I. / Nikolova, M. / Bourenkov, G. / Schneider, T. / Andreu, J. / Cuni, G. / Juanhuix, J. / Boer, R. / Fogh, R. / Keller, P. / Flensburg, C. / Paciorek, W. / Vonrhein, C. / Bricogne, G. / de Sanctis, D.
#16: ジャーナル: Eur Phys J Plus / 年: 2017
タイトル: Status of the crystallography beamlines at synchrotron SOLEIL⋆
著者: Coati, A. / Chavas, L.M.G. / Fontaine, P. / Foos, N. / Guimaraes, B. / Gourhant, P. / Legrand, P. / Itie, J.P. / Fertey, P. / Shepard, W. / Isabet, T. / Sirigu, S. / Solari, P.L. / Thiaudiere, D. / Thompson, A.
#17: ジャーナル: Chem Sci / 年: 2017
タイトル: Crystallophore: a versatile lanthanide complex for protein crystallography combining nucleating effects, phasing properties, and luminescence.
著者: Engilberge, S. / Riobe, F. / Di Pietro, S. / Lassalle, L. / Coquelle, N. / Arnaud, C.A. / Pitrat, D. / Mulatier, J.C. / Madern, D. / Breyton, C. / Maury, O. / Girard, E.
履歴
登録2022年10月31日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02023年1月25日Provider: repository / タイプ: Initial release
改定 1.12023年2月8日Group: Database references / カテゴリ: citation
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _citation.journal_volume / _citation.title
改定 1.22024年6月19日Group: Data collection / カテゴリ: chem_comp_atom / chem_comp_bond

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Glutamate--tRNA ligase
B: Glutamate--tRNA ligase
C: Glutamate--tRNA ligase
D: Glutamate--tRNA ligase
E: Glutamate--tRNA ligase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)152,58436
ポリマ－148,2395
非ポリマー4,34531
水00
1
B: Glutamate--tRNA ligase
C: Glutamate--tRNA ligase
ヘテロ分子


  • 登録者が定義した集合体
  • 根拠: gel filtration, performed on the native (without Tbxo4); see primary citation, light scattering, performed on the native (without Tbxo4); see primary citation, SAXS, performed on the native ...根拠: gel filtration, performed on the native (without Tbxo4); see primary citation, light scattering, performed on the native (without Tbxo4); see primary citation, SAXS, performed on the native (without Tbxo4); see primary citation
  • 60.9 kDa, 2 ポリマー
  • Omokage検索でこの集合体の類似形状データを探す (詳細)
分子量 (理論値)分子数
合計 (水以外)60,88114
ポリマ－59,2962
非ポリマー1,58512
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
D: Glutamate--tRNA ligase
E: Glutamate--tRNA ligase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)60,56710
ポリマ－59,2962
非ポリマー1,2718
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
A: Glutamate--tRNA ligase
ヘテロ分子

A: Glutamate--tRNA ligase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)62,27324
ポリマ－59,2962
非ポリマー2,97822
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
point symmetry operation1
4
A: Glutamate--tRNA ligase
B: Glutamate--tRNA ligase
C: Glutamate--tRNA ligase
D: Glutamate--tRNA ligase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)122,30131
ポリマ－118,5914
非ポリマー3,70927
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
5
A: Glutamate--tRNA ligase
B: Glutamate--tRNA ligase
C: Glutamate--tRNA ligase
D: Glutamate--tRNA ligase
E: Glutamate--tRNA ligase
ヘテロ分子

A: Glutamate--tRNA ligase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)183,72148
ポリマ－177,8876
非ポリマー5,83442
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
point symmetry operation1
単位格子
Length a, b, c (Å)130.110, 88.510, 168.640
Angle α, β, γ (deg.)90.000, 105.700, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDモデル要素
11A-305-

TB

非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and (resid 8 through 35 or resid 46...
d_2ens_1(chain "B" and (resid 8 through 35 or resid 46 through 66 or resid 83 through 224))
d_3ens_1(chain "C" and (resid 8 through 35 or resid 46 through 66 or resid 83 through 224))
d_4ens_1(chain "D" and (resid 8 through 35 or resid 46 through 107 or resid 116 through 224))
d_5ens_1(chain "E" and (resid 8 through 35 or resid 46...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ILETHRA3 - 30
d_12ens_1GLUVALA33 - 53
d_13ens_1SERTHRA55 - 79
d_14ens_1ASNVALA81 - 189
d_21ens_1ILETHRB3 - 30
d_22ens_1GLUVALB38 - 58
d_23ens_1SERVALB60 - 193
d_31ens_1ILETHRC2 - 29
d_32ens_1GLUVALC31 - 51
d_33ens_1SERVALC53 - 186
d_41ens_1ILETHRD1 - 28
d_42ens_1GLUTHRD32 - 77
d_43ens_1ASNVALD79 - 187
d_51ens_1ILETHRE1 - 28
d_52ens_1GLUVALE31 - 51
d_53ens_1SERTHRE53 - 77
d_54ens_1ASNVALE79 - 187

NCS oper:
IDCodeMatrixベクター
1given(0.3860195916, 0.900858052546, -0.198604239793), (-0.901993571174, 0.323459943276, -0.285974234252), (-0.193381675609, 0.289531404615, 0.93743004714)-7.64192847848, 102.109678547, -18.8084237145
2given(-0.384447720401, 0.902461327759, 0.194328336015), (0.900784758299, 0.320676522474, 0.292836792686), (0.201957345733, 0.287628440586, -0.93620676705)-7.05066015908, -20.9715850127, 116.751804179
3given(-0.688949698332, 0.578541066327, -0.436621744468), (-0.560255662749, -0.807255557296, -0.185612654668), (-0.459849872813, 0.116742022377, 0.880289381218)63.8308629298, 74.618217958, -34.5667585422
4given(0.690610836496, 0.575693295606, 0.437760096295), (0.556353321405, -0.809625007744, 0.187024941109), (0.462090526061, 0.114387832527, -0.879424680967)-65.5672672134, -2.79598319305, 69.6896780929

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要素

#1: タンパク質
Glutamate--tRNA ligase


分子量: 29647.863 Da / 分子数: 5 / 由来タイプ: 組換発現
詳細: Plasmodium berghei Glu-RS with an insertion at position 2 (G2): cloning artifact. Residues I229 to S242 are degenerated from the original genetic sequence as a result of a cloning artifact ...詳細: Plasmodium berghei Glu-RS with an insertion at position 2 (G2): cloning artifact. Residues I229 to S242 are degenerated from the original genetic sequence as a result of a cloning artifact and are followed by a His(6)-tag for purification purposes.
由来: (組換発現) Plasmodium berghei ANKA (ネズミマラリア原虫)
株: Anka / 遺伝子: PBANKA_1362000 / 発現宿主: Escherichia coli BL21 (大腸菌) / 参照: UniProt: A0A509AR09, glutamate-tRNA ligase
#2: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 5 / 由来タイプ: 合成 / 式: SO4
#3: 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 / 式: C3H8O3
#4: 化合物...
ChemComp-TB / TERBIUM(III) ION


分子量: 158.925 Da / 分子数: 22 / 由来タイプ: 合成 / 式: Tb
研究の焦点であるリガンドがあるかN

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 3

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試料調製

結晶マシュー密度: 3.16 Å3/Da / 溶媒含有率: 61.12 %
解説: Crystals with a high solvent content that have required seeding in order to obtain an acceptable resolution.
結晶化温度: 298 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.5
詳細: Stock protein concentration: 6-9 mg/mL Well solution: 0.1 M HEPES-NaOH pH 7.5, 1.4-1.5 M ammonium sulfate, 10-20% (vol) glycerol Mix: 400 nL protein solution/seeds + 400 nL well solution Use ...詳細: Stock protein concentration: 6-9 mg/mL Well solution: 0.1 M HEPES-NaOH pH 7.5, 1.4-1.5 M ammonium sulfate, 10-20% (vol) glycerol Mix: 400 nL protein solution/seeds + 400 nL well solution Use of microseeding technique to improve crystal size. 1 microliter of a 100 mM Tbxo4 solution (ligand code 7MT) was added to the crystallization drop for a soacking of 1-2 minutes before freezing the crystals.

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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: 1.631371 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2020年6月11日 / 詳細: Kirkpatrick-Baez bimorphic mirrors
放射モノクロメーター: channel cut / 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: 1.631371 Å / 相対比: 1
反射解像度: 3.17→47.85 Å / Num. obs: 61436 / % possible obs: 99.83 % / 冗長度: 21.2 % / Biso Wilson estimate: 129 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.1229 / Rpim(I) all: 0.0272 / Rrim(I) all: 0.1259 / Net I/σ(I): 14.87
反射 シェル解像度: 3.17→3.283 Å / 冗長度: 19.8 % / Rmerge(I) obs: 2.335 / Mean I/σ(I) obs: 1.13 / Num. unique obs: 6200 / CC1/2: 0.789 / Rpim(I) all: 0.5287 / Rrim(I) all: 2.395 / % possible all: 99.47

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解析

ソフトウェア
名称バージョン分類
PHENIXdev_4701精密化
CRANK2位相決定
XSCALEデータスケーリング
XDSデータ削減
MxCuBEデータ収集
精密化構造決定の手法: 単波長異常分散 / 解像度: 3.17→47.85 Å / SU ML: 0.4742 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 28.5422
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2373 3073 5.01 %
Rwork0.192 58286 -
obs0.1942 61359 99.86 %
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: 169.93 Å2
精密化ステップサイクル: LAST / 解像度: 3.17→47.85 Å
タンパク質核酸リガンド溶媒全体
原子数8125 0 71 0 8196
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0038355
X-RAY DIFFRACTIONf_angle_d0.583211285
X-RAY DIFFRACTIONf_chiral_restr0.04731253
X-RAY DIFFRACTIONf_plane_restr0.00411382
X-RAY DIFFRACTIONf_dihedral_angle_d11.88893029
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.786938003489
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.876337916278
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.97296313749
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS1.09860076341
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.17-3.220.38761380.37592594X-RAY DIFFRACTION99.38
3.22-3.270.36611430.35122696X-RAY DIFFRACTION99.58
3.27-3.330.31181400.29692588X-RAY DIFFRACTION99.74
3.33-3.390.26691420.26272717X-RAY DIFFRACTION100
3.39-3.450.27431380.25492624X-RAY DIFFRACTION99.96
3.45-3.520.26621390.25472662X-RAY DIFFRACTION99.93
3.53-3.60.3221430.26562657X-RAY DIFFRACTION99.89
3.6-3.690.34021350.22162623X-RAY DIFFRACTION99.89
3.69-3.780.26781410.20732671X-RAY DIFFRACTION99.96
3.78-3.880.22541400.18632629X-RAY DIFFRACTION99.93
3.88-3.990.20021400.17192650X-RAY DIFFRACTION99.82
3.99-4.120.2251430.17742675X-RAY DIFFRACTION100
4.12-4.270.20421370.1722594X-RAY DIFFRACTION100
4.27-4.440.25281440.17652700X-RAY DIFFRACTION99.96
4.44-4.640.20581430.15982690X-RAY DIFFRACTION99.96
4.64-4.890.21041350.15862636X-RAY DIFFRACTION99.93
4.89-5.190.22121350.17742636X-RAY DIFFRACTION99.93
5.19-5.590.25151440.19092652X-RAY DIFFRACTION99.93
5.59-6.150.20521360.20972642X-RAY DIFFRACTION100
6.16-7.040.27331390.23652668X-RAY DIFFRACTION100
7.04-8.860.24931380.18932652X-RAY DIFFRACTION100
8.87-47.850.21011400.16092630X-RAY DIFFRACTION99.32
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)
16.458962195440.8300155714450.3660248254142.037716098352.130813843794.852675980450.540309240145-0.663105010188-0.3240110220730.231550055484-0.450807432848-0.5073085158910.1441031402980.613583878226-0.1166589310461.07970526611-0.0575463462367-0.07606610160381.099458414830.1354425537721.2805946111845.788648856323.783930812196.6737721371
23.66988592565-0.689604384849-0.2831618050640.831050897992.260282958284.914034649270.5341936298050.119577437307-1.13655016318-0.757268113920.03654354514550.8363119010090.154694656084-0.355242353331-0.5400752538730.772590377483-0.01814861911990.02775266853720.9511866039930.03466673701721.2419603784833.899864104322.457367431782.2498156325
36.15879213428-1.683061666430.005399357489714.56302818188-1.220871111252.42839647205-0.00614827087376-0.839428727390.6108096235970.303685249901-0.1119167202980.150757048881-0.46813045226-0.02959840760930.01208289182871.10476351328-0.1163389067130.09926316836311.10484107606-0.02725974429291.2612184312626.881758635933.009173029295.4050183226
43.55375213949-1.4787709411.319123246535.954017455111.678307455466.594026868280.149258013729-0.805187926341-0.2673153914490.310286952306-0.1866899898320.7899366384670.384163202068-0.859152402754-0.03438882174491.05081460495-0.05758628597530.06517223132141.297022478610.02795606396161.406059756617.3392028423242.262475573972.3564175646
55.179571354431.702986982310.3532531189895.105153119460.4357709139355.09352488362-0.9279190770082.215062741340.121825107174-1.065346317390.6048463107810.4564926282730.3926550835760.6996691758880.4357790024211.092048520620.052489148542-0.1902812543791.01426473036-0.01894033694071.2831126655110.33469914737.31089306671.5493522107
63.46100074615-0.8974605233490.3237288258414.146920178350.5417664034091.238516313320.2993522006650.1269622360110.0528268519733-0.30697316484-0.1543224416960.4548765822580.123082234862-0.15163778667-0.1609692979911.29106086180.137658109571-0.09628564484691.17176872869-0.02002088371411.3630387205111.762997171843.800583142762.722580539
72.757802063192.60670895898-0.04944052479194.951359443362.722371745775.2901536222-0.2731468138120.0382789004170.762506260823-0.3553972975280.366616097005-0.671527941833-0.1158899464931.12196038193-0.06516897317021.107745189820.1911384033750.006574590211941.09104093272-0.005380266207141.7407968154917.15679031562.443068430864.1396469484
82.20401663157-2.68131710724-0.4823477714068.155913200070.3043363915783.53402842596-0.383276321571-0.4193645646150.482640239890.8446423498630.317895604539-0.480006485559-0.3689968349060.08776685331130.07779951259220.9787395378630.115522257920.1251116577341.20126826738-0.1177466390171.3218570489111.340612329559.779549305676.5539504722
96.03572295875-2.20908935527-0.829288689487.483186037310.4737149015185.669761491960.4875521475111.638434025450.118980322986-1.539085243860.250695296720.415646194256-0.4276773964590.109739221624-0.5907165691051.668378058040.4915902398490.0626115561081.677654685110.3054324428311.3384294950416.086436864253.500600164838.6202284225
103.486077285164.26667955333.306416530694.611949008213.380359103355.01797443644-0.033576948841-2.207160374930.271037026022-0.881650548331-0.6888747686020.0601552822553-1.17575315437-1.066201607060.5049562780391.43312016020.1069474839640.06020355930881.743606553850.140981305631.7653648814217.056261365560.869052896840.8994975503
115.242082495930.881797805396-0.8272122345083.26352626134-1.168752485212.821958495520.7183275181580.821755218164-0.312936215566-0.0141038080113-0.2112279437620.09327161396460.100709656497-0.0291543941009-0.5286872384391.397497163080.3672918311150.03278904326311.455300014460.1410624592391.3683230592813.34189907152.274780031848.512062331
129.626302544534.27549283425-5.572188734923.31089681221-1.356552333013.49949460171.28685473403-1.38021470209-1.46916106559-0.515929101639-1.34574505326-0.3918629372480.3364395020090.6725992255180.09424580342021.165957608490.382668829429-0.04709320521951.19002461968-0.1642502417141.1558877341119.703181607940.711385948255.76608256
135.56937915778-0.75189555036-0.9894709734883.98039057618-0.394011069434.258130528991.4040263403-0.3421731076890.551301786780.514560767398-1.765495491650.976995889186-0.631290475120.2964613604550.2574959172421.186027641270.2259094817850.3013342381921.99280709656-0.02045934596621.5039375873436.29712024642.493365398752.1056983817
142.844394875771.33521613244-0.2605568997446.76581482732-0.7517689257356.328000235920.1374630556361.46431424764-0.818350513860.166884467231-0.0351875142558-0.6674694629551.810112891420.495049557076-0.04272078952051.813235043330.3941017496190.002158357040572.09203612280.167350127941.2015148047922.949943511732.099868247847.0913104353
154.75562656621-2.876517657370.3676613891773.621135035470.4837719800013.791330810140.5808328466780.6182095789331.30162400059-1.43821895725-0.0962370350347-1.601239519270.5009405867840.427348868634-0.6303408395651.449047318420.4167408148620.2361448085211.793850509980.0563137180881.2777869812333.070382754940.390735001540.6335818476
164.469767148544.740121819443.308028376959.64578947921.853926727482.712321667030.183321405344-0.518881197407-0.80395261561-1.140457334020.12171382818-2.13325869098-1.12801745364-1.02869636927-0.19711739232.026785330010.5197466033970.4612442062551.793889956560.06011760911721.2329012881226.409064989150.860718285833.0629582197
174.32934788580.7441506535121.081999473280.947307226047-0.06934162977891.49062024749-0.107769521426-0.493495510348-0.1014607392660.7604792907860.3942140088540.1551581989611.11069512707-0.548512421296-0.2793893807022.5063107616-0.0356050556465-0.1711224513012.12356158418-0.03722986898741.924213297714.2069919925312.29714726632.6968246572
186.92220813160.5714446709730.2892015188112.540776267930.159282632684.408652555240.7550321703362.13137023670.306571471514-0.449047062562-0.7889248556830.1111820501231.41187860034-0.021089005244-0.08918847524521.983314776940.29260546718-0.3040002260271.98013254297-0.2608889348671.5032260406717.507769561222.245503568124.9901815314
192.43280721108-0.713050353710.2554449922524.771278672630.8936318811964.799392279420.0936703963505-0.0136072472882-0.850559900728-0.4859014669220.162188508522-0.9300941652780.582022855115-0.486560160446-0.1710109834192.338882373680.375391723589-0.3536509358081.82263304858-0.03224534355951.6492044752830.603383021211.533619722434.8009939745
204.302053865620.463732930630.1282467994441.73113428436-0.4744891153590.5878250875071.321491760480.899096654861-0.2635551162270.23931801662-0.951969830063-0.7188194258760.6231569681851.10582135746-0.4141787079312.347885521620.456087752605-0.1510922097681.85216095124-0.06967647865391.2370892788923.952442548917.898214258541.5025783921
212.214825322591.105858142020.3701363361990.8195226051070.2609611107360.0209998588688-0.374572643976-0.505617969982-0.776267779758-1.16017551715-0.634999703475-0.391859345353.568886279610.3469920905750.7804737877673.15787456923-0.1953894519150.2373408870472.261927483130.1210945387011.080048124639.4429497259512.951307745445.8493981742
228.95514630281-0.02524044537014.205964139881.264873099321.966403541836.339408460552.718222130992.25140686289-2.54219210872-2.016967506990.355931558097-2.255738429141.382089562972.29537568875-1.479266266322.062084610550.2607223667450.3051783545423.64536775853-0.4935621087161.3142845540428.289595843217.57377259857.88242327094
233.036452024773.74451382859-0.7187225105614.61014117668-0.01867043311986.501748626610.1361751986381.39266795429-0.5988493290810.05325480606090.0879661633786-0.1061787356482.923966336291.73332524017-0.575010890662.56772054007-0.0845188317129-0.2985051581592.09352668376-0.3740133521741.5395923447514.659988496623.08736773952.08027125169
242.8512692213.15305251986-1.534582293884.347824964250.1641432105084.53008908322-1.21810240951.227220050750.950382290673-0.6988232820560.6156781833970.701620284329-0.1562187437210.5873723460310.1928799258262.21410732161-0.305853688582-0.005804780870792.770096602410.2397208551961.7657999695418.9447251229.3383341923.55746566071
256.27831583781-2.39227746027-1.86927016231.273500441041.834945766994.356847116792.598974042790.0951233104865-1.29037943017-0.838026747363-2.11348990640.674637327015-1.07348741252-0.644104898926-0.4561814663492.653578525960.430258571958-0.09149288027422.63065480025-0.4992585266981.8864230432132.063345388115.882221483511.8768371714
262.81532762416-0.755496445687-1.335612465151.396098138680.6491629265521.951782211771.034821521540.54764369432-0.128619976513-0.917906691933-0.387994986630.725504832471.07613873074-0.259519937768-0.6511096288562.334190652950.216001918481-0.4166550756761.87631740485-0.1012002292111.4753261413411.64107377416.310081970715.4615419901
279.59362845335-0.4608176684970.75037608977.684994667920.3700585438855.48777882581-2.69893153676-2.82304233432-0.92520108089-1.580280828761.73263973996-0.0129057615376-3.497739940780.2201119074651.096370311292.677898006010.220992675041-0.1672083559581.657281309750.08886419273151.4323615093614.015837246-3.86455808319.75334774527
280.6631254029661.42810138113-0.2195995878012.81369425937-0.5101770597610.1046546994410.0805271532614-1.81340748448-1.170371946180.766813949419-0.5943715609740.5334177440142.270617907560.6238935741560.3304460764573.25445622572-0.050053149415-0.224976216982.11438415867-0.008442793428341.612128910351.590361489838.344184497927.09844617968
290.135404308729-0.158629042430.3133966936430.785447186552-0.417565946311.18832019579-0.7500542038550.06662652887350.4226882816291.043358713391.35489303971-2.07094977147-1.176188260240.123189035546-0.3821345836392.743628217260.333682568157-0.4300289956942.07016518594-0.4600258913131.7082845815316.36433236944.356857674422.2336166661
300.811862033901-0.732987473170.53912216430.579589883864-0.4733288579920.35486293336-0.180928572941-1.40775575906-0.3890739914181.40489209975-0.131339058594-0.2083290593740.394570076709-1.750414428570.4898114489065.389641794020.157689228711-1.688035352081.8328666621-0.9558221060551.5914887794615.6025189857-7.14926479568-3.30018022948
313.91464366529-0.253464685933-0.1661618341932.200581263980.434276964510.192979830803-1.13581749730.4959197606060.155003122472-0.5532820763620.527503761208-1.373598223661.743114868991.837733715410.4684618031913.538264102980.315273365502-0.2518439546562.69490710967-0.2351923803580.62201428727314.69146985259.58240727465-3.35078420387
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 6 through 99 )AA6 - 991 - 71
22chain 'A' and (resid 100 through 134 )AA100 - 13472 - 99
33chain 'A' and (resid 135 through 227 )AA135 - 227100 - 192
44chain 'B' and (resid 6 through 37 )BB6 - 371 - 32
55chain 'B' and (resid 38 through 60 )BB38 - 6033 - 52
66chain 'B' and (resid 61 through 116 )BB61 - 11653 - 85
77chain 'B' and (resid 117 through 155 )BB117 - 15586 - 124
88chain 'B' and (resid 156 through 227 )BB156 - 227125 - 196
99chain 'C' and (resid 7 through 34 )CC7 - 341 - 28
1010chain 'C' and (resid 35 through 60 )CC35 - 6029 - 45
1111chain 'C' and (resid 61 through 116 )CC61 - 11646 - 78
1212chain 'C' and (resid 117 through 134 )CC117 - 13479 - 96
1313chain 'C' and (resid 135 through 153 )CC135 - 15397 - 115
1414chain 'C' and (resid 154 through 166 )CC154 - 166116 - 128
1515chain 'C' and (resid 167 through 207 )CC167 - 207129 - 169
1616chain 'C' and (resid 208 through 227 )CC208 - 227170 - 189
1717chain 'D' and (resid 8 through 99 )DD8 - 991 - 69
1818chain 'D' and (resid 100 through 134 )DD100 - 13470 - 97
1919chain 'D' and (resid 135 through 155 )DD135 - 15598 - 118
2020chain 'D' and (resid 156 through 207 )DD156 - 207119 - 170
2121chain 'D' and (resid 208 through 225 )DD208 - 225171 - 188
2222chain 'E' and (resid 8 through 17 )EE8 - 171 - 10
2323chain 'E' and (resid 18 through 34 )EE18 - 3411 - 27
2424chain 'E' and (resid 35 through 52 )EE35 - 5228 - 37
2525chain 'E' and (resid 53 through 64 )EE53 - 6438 - 49
2626chain 'E' and (resid 65 through 133 )EE65 - 13350 - 96
2727chain 'E' and (resid 134 through 155 )EE134 - 15597 - 118
2828chain 'E' and (resid 156 through 166 )EE156 - 166119 - 129
2929chain 'E' and (resid 167 through 184 )EE167 - 184130 - 147
3030chain 'E' and (resid 185 through 194 )EE185 - 194148 - 157
3131chain 'E' and (resid 195 through 224 )EE195 - 224158 - 187

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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