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- PDB-9g6i: Crystal structure of S. epidermidis ClpP in complex with bortezom... -

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基本情報

登録情報
データベース: PDB / ID: 9g6i
タイトルCrystal structure of S. epidermidis ClpP in complex with bortezomib - cocrystallization
要素ATP-dependent Clp protease proteolytic subunit
キーワードHYDROLASE / Peptidase / ClpP / Proteolysis / Antibiotics
機能・相同性
機能・相同性情報


endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / serine-type endopeptidase activity / identical protein binding / cytoplasm
類似検索 - 分子機能
ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / ClpP/crotonase-like domain superfamily
類似検索 - ドメイン・相同性
ACETATE ION / Chem-BO2 / ATP-dependent Clp protease proteolytic subunit
類似検索 - 構成要素
生物種Staphylococcus epidermidis (表皮ブドウ球菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.74 Å
データ登録者Alves Franca, B. / Rohde, H. / Betzel, C.
資金援助 ドイツ, 3件
組織認可番号国
German Research Foundation (DFG)3907159 ドイツ
German Federal Ministry for Education and Research05K19GU4 ドイツ
German Federal Ministry for Education and Research05K20GUB ドイツ
引用
ジャーナル: Sci Rep / 年: 2024
タイトル: Molecular insights into the dynamic modulation of bacterial ClpP function and oligomerization by peptidomimetic boronate compounds.
著者: Alves Franca, B. / Falke, S. / Rohde, H. / Betzel, C.
#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2024年7月18日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02025年7月30日Provider: repository / タイプ: Initial release

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: ATP-dependent Clp protease proteolytic subunit
B: ATP-dependent Clp protease proteolytic subunit
C: ATP-dependent Clp protease proteolytic subunit
D: ATP-dependent Clp protease proteolytic subunit
E: ATP-dependent Clp protease proteolytic subunit
F: ATP-dependent Clp protease proteolytic subunit
G: ATP-dependent Clp protease proteolytic subunit
H: ATP-dependent Clp protease proteolytic subunit
I: ATP-dependent Clp protease proteolytic subunit
J: ATP-dependent Clp protease proteolytic subunit
K: ATP-dependent Clp protease proteolytic subunit
L: ATP-dependent Clp protease proteolytic subunit
M: ATP-dependent Clp protease proteolytic subunit
N: ATP-dependent Clp protease proteolytic subunit
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)315,69042
ポリマ－309,48414
非ポリマー6,20628
水31,4541746
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: SAXS, native gel electrophoresis
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)95.340, 124.000, 127.840
Angle α, β, γ (deg.)90.000, 91.160, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
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 4 through 5 or (resid 6...
d_2ens_1(chain "B" and (resid 4 through 5 or (resid 6...
d_3ens_1(chain "C" and (resid 4 through 5 or (resid 6...
d_4ens_1(chain "D" and (resid 4 through 5 or (resid 6...
d_5ens_1(chain "E" and (resid 4 through 5 or (resid 6...
d_6ens_1(chain "F" and (resid 4 through 5 or (resid 6...
d_7ens_1(chain "G" and (resid 4 through 5 or (resid 6...
d_8ens_1(chain "H" and (resid 4 through 5 or (resid 6...
d_9ens_1(chain "I" and (resid 4 through 25 or (resid 26...
d_10ens_1(chain "J" and (resid 4 through 5 or (resid 6...
d_11ens_1(chain "K" and (resid 4 through 5 or (resid 6...
d_12ens_1(chain "L" and (resid 4 through 5 or (resid 6...
d_13ens_1(chain "M" and (resid 4 through 5 or (resid 6...
d_14ens_1(chain "N" and (resid 4 through 5 or (resid 6...

NCSドメイン領域:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ILEILETHRTHRAA4 - 64 - 6
d_12TYRTYRALAALAAA18 - 4118 - 41
d_13SERSERGLYGLYAA43 - 9443 - 94
d_14ALAALAPROPROAA96 - 19296 - 192
d_15ACTACTACTACTAO201
d_16BO2BO2BO2BO2AP202
d_21ILEILEALAALABB4 - 414 - 41
d_22SERSERGLYGLYBB43 - 9443 - 94
d_23ALAALAPROPROBB96 - 19296 - 192
d_24ACTACTACTACTBQ201
d_25BO2BO2BO2BO2BR202
d_31ILEILETHRTHRCC4 - 64 - 6
d_32TYRTYRALAALACC18 - 4118 - 41
d_33SERSERGLYGLYCC43 - 9443 - 94
d_34ALAALAPROPROCC96 - 19296 - 192
d_35ACTACTACTACTCS201
d_36BO2BO2BO2BO2CT202
d_41ILEILETHRTHRDD4 - 64 - 6
d_42TYRTYRALAALADD18 - 4118 - 41
d_43SERSERGLYGLYDD43 - 9443 - 94
d_44ALAALAPROPRODD96 - 19296 - 192
d_45ACTACTACTACTDU201
d_46BO2BO2BO2BO2DV202
d_51ILEILETHRTHREE4 - 64 - 6
d_52TYRTYRALAALAEE18 - 4118 - 41
d_53SERSERGLYGLYEE43 - 9443 - 94
d_54ALAALAPROPROEE96 - 19296 - 192
d_55ACTACTACTACTEW201
d_56BO2BO2BO2BO2EX202
d_61ILEILETHRTHRFF4 - 64 - 6
d_62TYRTYRALAALAFF18 - 4118 - 41
d_63SERSERGLYGLYFF43 - 9443 - 94
d_64ALAALAPROPROFF96 - 19296 - 192
d_65ACTACTACTACTFY201
d_66BO2BO2BO2BO2FZ202
d_71ILEILETHRTHRGG4 - 64 - 6
d_72TYRTYRALAALAGG18 - 4118 - 41
d_73SERSERGLYGLYGG43 - 9443 - 94
d_74ALAALAPROPROGG96 - 19296 - 192
d_75ACTACTACTACTGAA201
d_76BO2BO2BO2BO2GBA202
d_81ILEILETHRTHRHH4 - 64 - 6
d_82TYRTYRALAALAHH18 - 4118 - 41
d_83SERSERGLYGLYHH43 - 9443 - 94
d_84ALAALAPROPROHH96 - 19296 - 192
d_85ACTACTACTACTHCA201
d_86BO2BO2BO2BO2HDA202
d_91ILEILEALAALAII4 - 414 - 41
d_92SERSERGLYGLYII43 - 9443 - 94
d_93ALAALAPROPROII96 - 19296 - 192
d_94ACTACTACTACTIEA201
d_95BO2BO2BO2BO2IFA202
d_101ILEILETHRTHRJJ4 - 64 - 6
d_102TYRTYRALAALAJJ18 - 4118 - 41
d_103SERSERGLYGLYJJ43 - 9443 - 94
d_104ALAALAPROPROJJ96 - 19296 - 192
d_105ACTACTACTACTJGA201
d_106BO2BO2BO2BO2JHA202
d_111ILEILETHRTHRKK4 - 64 - 6
d_112TYRTYRALAALAKK18 - 4118 - 41
d_113SERSERGLYGLYKK43 - 9443 - 94
d_114ALAALAPROPROKK96 - 19296 - 192
d_115ACTACTACTACTKIA201
d_116BO2BO2BO2BO2KJA202
d_121ILEILETHRTHRLL4 - 64 - 6
d_122TYRTYRALAALALL18 - 4118 - 41
d_123SERSERGLYGLYLL43 - 9443 - 94
d_124ALAALAPROPROLL96 - 19296 - 192
d_125ACTACTACTACTLKA201
d_126BO2BO2BO2BO2LLA202
d_131ILEILETHRTHRMM4 - 64 - 6
d_132TYRTYRALAALAMM18 - 4118 - 41
d_133SERSERGLYGLYMM43 - 9443 - 94
d_134ALAALAPROPROMM96 - 19296 - 192
d_135ACTACTACTACTMMA201
d_136BO2BO2BO2BO2MNA202
d_141ILEILETHRTHRNN4 - 64 - 6
d_142TYRTYRALAALANN18 - 4118 - 41
d_143SERSERGLYGLYNN43 - 9443 - 94
d_144ALAALAPROPRONN96 - 19296 - 192
d_145ACTACTACTACTNOA201
d_146BO2BO2BO2BO2NPA202

NCS oper:
IDCodeMatrixベクター
1given(0.616843168222, 0.538801411632, 0.573757391796), (-0.520858303348, 0.825952443697, -0.215659890995), (-0.590094173544, -0.165817971204, 0.790122311275)3.0406035459, 15.390767368, 17.2341139318
2given(-0.225745218907, 0.684539524969, 0.693141208482), (-0.617297393637, 0.449919849843, -0.64538055171), (-0.753646484732, -0.573565835343, 0.320997209612)23.0928921748, 23.0106003709, 26.7951058828
3given(-0.89841522694, 0.346533084097, 0.269749701815), (-0.232424727579, 0.145953318104, -0.96160094371), (-0.372597404732, -0.926613431028, -0.0505838257385)45.2452836357, 16.930880646, 21.4460645891
4given(-0.895476466334, -0.232669839563, -0.379455720737), (0.352358247549, 0.150337372326, -0.923711177731), (0.271966107495, -0.960865974129, -0.0526404420024)52.7025107456, 1.79534301186, 5.22618520609
5given(-0.213435580234, -0.613608642886, -0.760216868049), (0.688071939273, 0.457993074547, -0.562849313806), (0.693543264314, -0.643215964543, 0.324454871256)39.8275680905, -10.9205730632, -9.72294186712
6given(0.628678994725, -0.50537880661, -0.591062588413), (0.528379290573, 0.835260248205, -0.152169783671), (0.570594467976, -0.216639284524, 0.792142268482)16.4722699326, -11.6812090203, -12.073895363
7given(0.996428268936, -0.0748319307387, 0.0391265511662), (-0.0746484602598, -0.997191062229, -0.00613129599642), (0.0394754638361, 0.00318865985622, -0.999215452344)-2.90197742568, -43.0105713147, 62.857053528
8given(0.631927016447, 0.469372338896, 0.6167315894), (0.47444320144, -0.863507360316, 0.171051709396), (0.612839207697, 0.184511913327, -0.768364145018)-0.244174036535, -58.6538320881, 45.6456089396
9given(-0.198047661927, 0.629558956615, 0.751287324365), (0.635791086245, -0.500848442482, 0.587299354942), (0.746020655383, 0.593975048137, -0.301076109868)19.4793694498, -67.8643344719, 36.8415071607
10given(-0.88994169826, 0.300598443151, 0.342993221032), (0.302288713501, -0.174357068684, 0.937134540122), (0.341504476381, 0.937678083659, 0.064300109148)41.6844035036, -63.6855146345, 42.8353243506
11given(-0.909443964383, -0.282364602448, -0.305257116102), (-0.278470305913, -0.131615685602, 0.951384044447), (-0.308813802106, 0.950235519536, 0.0410669336656)49.6083843619, -49.1353199544, 59.3854423382
12given(-0.23846851603, -0.675714532019, -0.697526084158), (-0.667473440212, -0.407675105743, 0.623121348349), (-0.705416170408, 0.614174958279, -0.353803825799)37.1627391227, -35.4486732629, 73.8330712014
13given(0.599915587736, -0.581842929483, -0.549144874329), (-0.582662552639, -0.788101401094, 0.198495670851), (-0.54827514748, 0.200885507204, -0.81181240176)13.9159194172, -32.7009551899, 75.3988054949

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要素

#1: タンパク質
ATP-dependent Clp protease proteolytic subunit / Endopeptidase Clp


分子量: 22106.025 Da / 分子数: 14 / 由来タイプ: 組換発現
由来: (組換発現) Staphylococcus epidermidis (表皮ブドウ球菌)
遺伝子: clpP, E1M97_03460, E1M98_06460, E1N00_07180, E1N03_05195, E1N04_00635, E1N05_04945, E1N06_06240, E1N09_07235, E1N11_03825, E1N12_01760, E1N13_04220, FHG76_01330, FHQ17_10195, H3963_07430, I3V53_07130
発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: A0A0N1MQL5, endopeptidase Clp
#2: 化合物
ChemComp-ACT / ACETATE ION


分子量: 59.044 Da / 分子数: 14 / 由来タイプ: 合成 / 式: C2H3O2
#3: 化合物
ChemComp-BO2 / N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE / BORTEZOMIB


分子量: 384.237 Da / 分子数: 14 / 由来タイプ: 合成 / 式: C19H25BN4O4 / コメント: 薬剤*YM
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1746 / 由来タイプ: 天然 / 式: H2O
Has protein modificationY

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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: 2.44 Å3/Da / 溶媒含有率: 49.62 %
結晶化温度: 293.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 4.5
詳細: 0.5 M NaOAc (pH 4.5), 30 - 40% (v/v) MPD, and 30 - 40 mM CaCl2

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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: PETRA III, DESY / ビームライン: P11 / 波長: 1.0332 Å
検出器タイプ: DECTRIS EIGER2 X 16M / 検出器: PIXEL / 日付: 2023年9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: 1.0332 Å / 相対比: 1
反射解像度: 1.74→44.96 Å / Num. obs: 300453 / % possible obs: 98.98 % / 冗長度: 6.9 % / Biso Wilson estimate: 27.12 Å2 / CC1/2: 1 / Net I/σ(I): 11.89
反射 シェル解像度: 1.74→1.8 Å / Num. unique obs: 29956 / CC1/2: 0.66

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解析

ソフトウェア
名称バージョン分類NB
PHENIX1.21_5207精密化
pointlessデータスケーリング
XDSデータ削減
PHENIX位相決定
精密化構造決定の手法: 分子置換 / 解像度: 1.74→44.96 Å / SU ML: 0.1911 / 交差検証法: FREE R-VALUE / σ(F): 1.38 / 位相誤差: 21.0835
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2072 3156 1.05 %
Rwork0.1776 297365 -
obs0.1779 29952 98.9 %
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: 31.82 Å2
精密化ステップサイクル: LAST / 解像度: 1.74→44.96 Å
タンパク質核酸リガンド溶媒全体
原子数19244 0 448 1746 21438
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.009720025
X-RAY DIFFRACTIONf_angle_d1.061627044
X-RAY DIFFRACTIONf_chiral_restr0.06473118
X-RAY DIFFRACTIONf_plane_restr0.00883528
X-RAY DIFFRACTIONf_dihedral_angle_d18.04997560
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.462666544557
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.509490697009
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.420942361629
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS0.507366344871
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS0.528429605259
ens_1d_7AAX-RAY DIFFRACTIONTorsion NCS0.521891530326
ens_1d_8AAX-RAY DIFFRACTIONTorsion NCS0.449825949459
ens_1d_9AAX-RAY DIFFRACTIONTorsion NCS0.549945872135
ens_1d_10AAX-RAY DIFFRACTIONTorsion NCS0.551520984084
ens_1d_11AAX-RAY DIFFRACTIONTorsion NCS0.516746422242
ens_1d_12AAX-RAY DIFFRACTIONTorsion NCS0.532385413407
ens_1d_13AAX-RAY DIFFRACTIONTorsion NCS0.505805767759
ens_1d_14AAX-RAY DIFFRACTIONTorsion NCS0.488482157721
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.770.28991340.290212641X-RAY DIFFRACTION96.97
1.77-1.790.30931370.268712903X-RAY DIFFRACTION99.13
1.79-1.820.27931370.249312895X-RAY DIFFRACTION99.12
1.82-1.850.27011370.230412924X-RAY DIFFRACTION99.07
1.85-1.890.27961360.214512862X-RAY DIFFRACTION99.09
1.89-1.920.24891380.208512951X-RAY DIFFRACTION99.17
1.92-1.960.22831370.206212973X-RAY DIFFRACTION99.18
1.96-2.010.22821380.207612933X-RAY DIFFRACTION99.17
2.01-2.050.21511370.186512941X-RAY DIFFRACTION99.15
2.05-2.10.21611370.180912882X-RAY DIFFRACTION98.8
2.1-2.160.23011340.169712686X-RAY DIFFRACTION97.11
2.16-2.220.18271370.170212915X-RAY DIFFRACTION99.07
2.22-2.30.22441380.171112956X-RAY DIFFRACTION99.32
2.3-2.380.22141370.172712961X-RAY DIFFRACTION99.25
2.38-2.470.20261380.180712967X-RAY DIFFRACTION99.16
2.47-2.590.221370.178212933X-RAY DIFFRACTION99.16
2.59-2.720.22011380.181312999X-RAY DIFFRACTION99.3
2.72-2.890.20471380.183712980X-RAY DIFFRACTION99.13
2.89-3.120.22821350.18712745X-RAY DIFFRACTION97.45
3.12-3.430.1971390.179513097X-RAY DIFFRACTION99.81
3.43-3.930.17941390.161413088X-RAY DIFFRACTION99.77
3.93-4.940.2041390.146513061X-RAY DIFFRACTION99.23
4.94-44.960.1691390.174813072X-RAY DIFFRACTION98.18
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)
10.1818933379170.0616350540032-0.1577665101210.08133954813150.02323783807220.1349022652910.1211200848080.03473525669110.232482932030.302501139424-0.131379196012-0.0143024695447-0.155643573030.215803317562-0.0001623511205370.354819775949-0.0142632642053-0.0004374488288740.3449191545380.02993288719940.29547139714813.9281537257-1.46580577113-2.40375163384
20.5058148191920.466170827039-0.2473634112451.175472149250.2798097469060.9089210264410.003419176960790.01792643204240.0438111339076-0.0703868187699-0.08833951004560.0499577675698-0.03808398201870.0623490407985.22994866758E-50.1803257335170.0278587671885-0.04390619484090.266497519430.02339114123460.261355798058-1.63383156738-7.883088574764.1399725828
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470.304689163389-0.08980045974440.008929923653470.872479713780.1328955565380.3558438778380.0398984540963-0.07042425528-0.1108490445430.1067125163110.0905218926049-0.07904931742940.06208441611290.05756078153717.81565568471E-50.235203791289-0.00334506372116-0.03981332131080.222932471890.02103437704570.24216717569753.6715007562-42.989145210452.9822841094
480.1755407861150.172387057623-0.1407017799370.498912592906-0.0007870944089180.3066710238470.00577303777294-0.0257243386033-0.0513432422405-0.1872047417130.0799272238306-0.04270984763060.007611834486550.03693134772811.80329200906E-50.242855235271-0.00694235668668-0.03933980194910.2536389948430.0005632378727560.21136517041256.0891061413-37.059144923243.4208638198
490.5725261741070.1000523812750.2044353162760.1948054567110.09138233645430.624937822417-0.0646352803764-0.08956531155140.1680873521640.5102609749970.0130298496624-0.454093250055-0.1784974891940.0962968492538-0.001031505453980.250457795362-0.0547432913805-0.04992217947560.2673707335280.01500572013110.22977026416859.1977358918-23.565364217249.2046250158
500.3234985686490.275358815496-0.1833063028620.207992401854-0.2196071558710.348400051133-0.0531387746237-0.05437842923060.08271404192930.06838557126410.00611879980684-0.230804761734-0.1655319195720.4084182301980.000349385282130.228401499895-0.0385877878659-0.03026236416240.3474774277660.001088922561510.31420602645365.1016500287-36.08088215739.2636717625
510.2440986584270.10136161624-0.0980230478530.383721330611-0.2653874558180.2867025991020.1705342749250.12630640146-0.631973977020.291442038782-0.0152850605029-0.1541371754630.2601231004890.3108052203670.005368559765120.2440264284950.0395830625371-0.05214248061930.295786633166-0.04081982969510.38991432239761.9130700951-51.901626107243.8715986548
520.0362016118526-0.117804326405-0.08736491625810.1675475220270.1657530517540.1180839559650.06013230101510.137257502681-0.1126999317660.177412414171-0.2082175159230.02787785751360.649948185213-0.285709475413-0.001655200225240.3347228935140.02633206834790.02773553493930.3251872855440.02247412882370.3041557367136.7032145052-45.421844691263.9366116341
530.0629757396164-0.102089196712-0.1136530923630.06168834672550.01096100547850.0945124330507-0.1740257431040.124260759861-0.160223772409-0.1961846757950.1646165956250.1237450538740.0732217065683-0.002500788781140.0003015853043180.332547269666-0.0196453825543-0.05441111675780.2889016922840.04659867227090.22755586109537.7583048735-32.337410331864.0087604021
540.4715530968630.3790356417990.1154118021680.2752480596260.1336402880610.1024260619920.0553308662774-0.107377387422-0.0891847445217-0.01656981982880.1857912152190.3904406841450.198538481134-0.3217093373610.002993902747780.3007838004870.04483556918930.02019274143860.2812625275430.06764259762530.25099253869930.642539802-32.500172643469.848230725
550.75000960471-0.2656639245030.04608044662090.737465788053-0.2338933149570.106785790322-0.051952388133-0.0705112843868-0.08884355333720.135790630230.0284723402052-0.00236616872792-0.003903074239580.022628320618-1.75043991536E-50.2822786816420.0502562295381-0.009888914659490.2323790779250.02632841165290.20591611157740.5118229017-27.207690769869.4830192622
560.1952261150880.1660867364020.1086602777930.524947298675-0.00778309916238-0.0797651834201-0.0267658570053-0.0696647533170.06186598217550.001161948426330.0667356036577-0.1455163710850.00139131983891-0.07112003681580.0001393232025940.2886122132120.0252526474941-0.02257264072670.2371571463080.01492813966740.21023889645344.5355812032-19.45430432662.2634783243
570.3793167528210.3311176862320.02964800612060.6343052723180.07451628753260.0541635752282-0.110247973287-0.1786365388340.07959736846930.3593028234590.0814983355529-0.0599243643395-0.00694649175694-0.195182462223-0.000331849038160.3514458077310.0344462294635-0.02212327906150.254969473097-0.0004986359842120.20764783593736.0380857938-7.6126471895765.3357436482
580.267923644084-0.211777127448-0.1431171289480.175462890227-0.05692035056480.173332723157-0.0719464613873-0.02420185599370.3154368432470.28923907015-0.116184900334-0.484824867402-0.3630080917550.261595682884-0.01061928373590.373289242328-0.0191378947932-0.1170145086380.2823948162980.02093603636510.29506051673352.0589915982-13.100678860163.9164557411
590.0266002328898-0.02957887367610.01980892349830.03901639532790.02729718898250.173227352705-0.03708629875480.2640245201730.1058199994170.02918258101730.0993104793761-0.4429993657430.2114703218450.366377318995-0.001050796525360.3407164309240.0468938551915-0.06933304102380.32030646324-0.008863487914850.2707510077355.6519853265-28.499152750669.2292204966
600.176984886294-0.1142668819170.09498786296040.1293873835230.0058611903290.0720845362757-0.07191765899610.139011468886-0.2751960224320.05715819684130.06506757582720.3197239548310.178730783068-0.05545453681150.0004469509097510.3774257876270.02049086333290.01840180491750.3395035829840.05565870187860.38141740620324.7427440455-40.572390204269.3842549897
610.832942077094-0.2143458574560.1081895753261.289712343180.1010672439160.325241434653-0.100755073551-0.16691770964-0.06059798163220.1124056958060.02476779995650.02705420099140.0838925903451-0.0602968719013-0.002657695361260.3325858687010.07076495917940.0825107078760.3333003041320.08670034326580.23233914353415.2364588864-24.747918817371.3905883759
620.74762201916-0.3753142072880.1008554431990.6952167407230.09572270741730.362553906951-0.18774593692-0.136120126240.01386307375120.08595187866280.04343238000040.283710733046-0.0963700121182-0.112303148044-0.03244544749630.2479207744040.04377206159410.06618813176880.3144515354020.02883342275150.296496380285.2125658422-8.8511103999859.6846440949
630.7155077978240.6391003408490.0008733512176180.6016179214220.1603341262320.317868377194-0.0624314011927-0.1472692333910.1688106639520.2517015065680.035894563031-0.0137165435198-0.08001970822510.0748270385961-0.0006547683755520.3738441311170.11542276360.04205874970610.3646625964010.02954190735740.24363042191219.67340564-7.7673076488273.5016107826
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 4 through 27 )AA4 - 271 - 15
22chain 'A' and (resid 28 through 122 )AA28 - 12216 - 110
33chain 'A' and (resid 123 through 158 )AA123 - 158111 - 146
44chain 'A' and (resid 159 through 192 )AA159 - 192147 - 180
55chain 'B' and (resid 4 through 27 )BD4 - 271 - 13
66chain 'B' and (resid 28 through 122 )BD28 - 12214 - 108
77chain 'B' and (resid 123 through 158 )BD123 - 158109 - 144
88chain 'B' and (resid 159 through 192 )BD159 - 192145 - 178
99chain 'C' and (resid 4 through 27 )CG4 - 271 - 15
1010chain 'C' and (resid 28 through 122 )CG28 - 12216 - 110
1111chain 'C' and (resid 123 through 158 )CG123 - 158111 - 146
1212chain 'C' and (resid 159 through 193 )CG159 - 193147 - 181
1313chain 'D' and (resid 4 through 27 )DJ4 - 271 - 14
1414chain 'D' and (resid 28 through 122 )DJ28 - 12215 - 109
1515chain 'D' and (resid 123 through 158 )DJ123 - 158110 - 145
1616chain 'D' and (resid 159 through 192 )DJ159 - 192146 - 179
1717chain 'E' and (resid 4 through 27 )EM4 - 271 - 14
1818chain 'E' and (resid 28 through 122 )EM28 - 12215 - 109
1919chain 'E' and (resid 123 through 158 )EM123 - 158110 - 145
2020chain 'E' and (resid 159 through 193 )EM159 - 193146 - 180
2121chain 'F' and (resid 4 through 27 )FP4 - 271 - 14
2222chain 'F' and (resid 28 through 122 )FP28 - 12215 - 109
2323chain 'F' and (resid 123 through 158 )FP123 - 158110 - 145
2424chain 'F' and (resid 159 through 192 )FP159 - 192146 - 179
2525chain 'G' and (resid 4 through 27 )GS4 - 271 - 16
2626chain 'G' and (resid 28 through 122 )GS28 - 12217 - 111
2727chain 'G' and (resid 123 through 158 )GS123 - 158112 - 147
2828chain 'G' and (resid 159 through 193 )GS159 - 193148 - 182
2929chain 'H' and (resid 4 through 27 )HV4 - 271 - 16
3030chain 'H' and (resid 28 through 122 )HV28 - 12217 - 111
3131chain 'H' and (resid 123 through 158 )HV123 - 158112 - 147
3232chain 'H' and (resid 159 through 192 )HV159 - 192148 - 181
3333chain 'I' and (resid 4 through 27 )IY4 - 271 - 13
3434chain 'I' and (resid 28 through 122 )IY28 - 12214 - 108
3535chain 'I' and (resid 123 through 158 )IY123 - 158109 - 144
3636chain 'I' and (resid 159 through 192 )IY159 - 192145 - 178
3737chain 'J' and (resid 4 through 27 )JAB4 - 271 - 16
3838chain 'J' and (resid 28 through 122 )JAB28 - 12217 - 111
3939chain 'J' and (resid 123 through 158 )JAB123 - 158112 - 147
4040chain 'J' and (resid 159 through 193 )JAB159 - 193148 - 182
4141chain 'K' and (resid 4 through 27 )KK4 - 271 - 16
4242chain 'K' and (resid 28 through 122 )KK28 - 12217 - 111
4343chain 'K' and (resid 123 through 158 )KK123 - 158112 - 147
4444chain 'K' and (resid 159 through 192 )KK159 - 192148 - 181
4545chain 'L' and (resid 4 through 27 )LL4 - 271 - 14
4646chain 'L' and (resid 28 through 54 )LL28 - 5415 - 41
4747chain 'L' and (resid 55 through 106 )LL55 - 10642 - 93
4848chain 'L' and (resid 107 through 132 )LL107 - 13294 - 119
4949chain 'L' and (resid 133 through 158 )LL133 - 158120 - 145
5050chain 'L' and (resid 159 through 183 )LL159 - 183146 - 170
5151chain 'L' and (resid 184 through 192 )LL184 - 192171 - 179
5252chain 'M' and (resid 4 through 27 )MM4 - 271 - 14
5353chain 'M' and (resid 28 through 37 )MM28 - 3715 - 24
5454chain 'M' and (resid 38 through 54 )MM38 - 5425 - 41
5555chain 'M' and (resid 55 through 106 )MM55 - 10642 - 93
5656chain 'M' and (resid 107 through 132 )MM107 - 13294 - 119
5757chain 'M' and (resid 133 through 158 )MM133 - 158120 - 145
5858chain 'M' and (resid 159 through 183 )MM159 - 183146 - 170
5959chain 'M' Nd (resid 184 through 192 )MM184 - 192171 - 179
6060chain 'N' and (resid 4 through 27 )NN4 - 271 - 16
6161chain 'N' and (resid 28 through 122 )NN28 - 12217 - 111
6262chain 'N' and (resid 123 through 158 )NN123 - 158112 - 147
6363chain 'N' and (resid 159 through 192 )NN159 - 192148 - 181

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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