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- PDB-8pnr: Structure of human KCTD15 BTB domain mutant G88D crystal form 1 -

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基本情報

登録情報
データベース: PDB / ID: 8pnr
タイトルStructure of human KCTD15 BTB domain mutant G88D crystal form 1
要素BTB/POZ domain-containing protein KCTD15
キーワードGENE REGULATION / Oligomerisation / BTB domain
機能・相同性
機能・相同性情報


Negative regulation of activity of TFAP2 (AP-2) family transcription factors / protein homooligomerization / identical protein binding / nucleus
類似検索 - 分子機能
KCTD15, tetramerisation-type BTB domain / : / BTB/POZ domain-containing protein KCTD1/15, C-terminal domain / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily
類似検索 - ドメイン・相同性
BTB/POZ domain-containing protein KCTD15
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.25 Å
データ登録者Cruz Walma, D.A. / Cros, J. / Bradshaw, W. / Richardson, W. / Chen, Z. / Chalk, R. / Wilkie, A. / Bullock, A.N.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR) 米国
引用ジャーナル: J Med Genet / 年: 2024
タイトル: BTB domain mutations perturbing KCTD15 oligomerisation cause a distinctive frontonasal dysplasia syndrome.
著者: Miller, K.A. / Cruz Walma, D.A. / Pinkas, D.M. / Tooze, R.S. / Bufton, J.C. / Richardson, W. / Manning, C.E. / Hunt, A.E. / Cros, J. / Hartill, V. / Parker, M.J. / McGowan, S.J. / Twigg, S.R. ...著者: Miller, K.A. / Cruz Walma, D.A. / Pinkas, D.M. / Tooze, R.S. / Bufton, J.C. / Richardson, W. / Manning, C.E. / Hunt, A.E. / Cros, J. / Hartill, V. / Parker, M.J. / McGowan, S.J. / Twigg, S.R.F. / Chalk, R. / Staunton, D. / Johnson, D. / Wilkie, A.O.M. / Bullock, A.N.
履歴
登録2023年6月30日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02024年3月20日Provider: repository / タイプ: Initial release
改定 1.12024年5月1日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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
C: BTB/POZ domain-containing protein KCTD15
A: BTB/POZ domain-containing protein KCTD15
J: BTB/POZ domain-containing protein KCTD15
I: BTB/POZ domain-containing protein KCTD15
B: BTB/POZ domain-containing protein KCTD15
E: BTB/POZ domain-containing protein KCTD15
G: BTB/POZ domain-containing protein KCTD15
H: BTB/POZ domain-containing protein KCTD15
K: BTB/POZ domain-containing protein KCTD15
L: BTB/POZ domain-containing protein KCTD15
D: BTB/POZ domain-containing protein KCTD15
F: BTB/POZ domain-containing protein KCTD15


分子量 (理論値)分子数
合計 (水以外)166,97712
ポリマ－166,97712
非ポリマー00
水1,60389
1
C: BTB/POZ domain-containing protein KCTD15
A: BTB/POZ domain-containing protein KCTD15
J: BTB/POZ domain-containing protein KCTD15
I: BTB/POZ domain-containing protein KCTD15
D: BTB/POZ domain-containing protein KCTD15
F: BTB/POZ domain-containing protein KCTD15


分子量 (理論値)分子数
合計 (水以外)83,4886
ポリマ－83,4886
非ポリマー00
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: BTB/POZ domain-containing protein KCTD15
E: BTB/POZ domain-containing protein KCTD15
G: BTB/POZ domain-containing protein KCTD15
H: BTB/POZ domain-containing protein KCTD15
K: BTB/POZ domain-containing protein KCTD15
L: BTB/POZ domain-containing protein KCTD15


分子量 (理論値)分子数
合計 (水以外)83,4886
ポリマ－83,4886
非ポリマー00
水1086
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)151.081, 151.081, 155.987
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
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 6 through 15 or resid 17...
d_2ens_1(chain "B" and ((resid 6 through 7 and (name N...
d_3ens_1(chain "C" and (resid 6 through 15 or resid 17...
d_4ens_1(chain "D" and (resid 6 through 15 or resid 17...
d_5ens_1(chain "E" and ((resid 6 through 7 and (name N...
d_6ens_1(chain "F" and (resid 6 through 15 or resid 17...
d_7ens_1(chain "G" and ((resid 6 through 7 and (name N...
d_8ens_1(chain "H" and ((resid 6 through 7 and (name N...
d_9ens_1(chain "I" and ((resid 6 through 7 and (name N...
d_10ens_1(chain "J" and ((resid 6 through 7 and (name N...
d_11ens_1(chain "K" and ((resid 6 through 7 and (name N...
d_12ens_1(chain "L" and (resid 6 through 15 or resid 17...

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_11ASNASNGLYGLYEF6 - 156 - 15
d_12METMETASNASNEF17 - 3817 - 38
d_13TYRTYRARGARGEF52 - 5652 - 56
d_14GLYGLYPHEPHEEF58 - 6158 - 61
d_15TYRTYRPROPROEF63 - 7663 - 76
d_16PHEPHEALAALAEF79 - 8979 - 89
d_17TYRTYRTRPTRPEF91 - 10491 - 104
d_21ASNASNGLYGLYFL6 - 156 - 15
d_22METMETASNASNFL17 - 3817 - 38
d_23TYRTYRARGARGFL52 - 5652 - 56
d_24GLYGLYPHEPHEFL58 - 6158 - 61
d_25TYRTYRPROPROFL63 - 7663 - 76
d_26PHEPHEALAALAFL79 - 8979 - 89
d_27TYRTYRTRPTRPFL91 - 10491 - 104
d_31ASNASNGLYGLYBE6 - 156 - 15
d_32METMETASNASNBE17 - 3817 - 38
d_33TYRTYRARGARGBE52 - 5652 - 56
d_34GLYGLYPHEPHEBE58 - 6158 - 61
d_35TYRTYRPROPROBE63 - 7663 - 76
d_36PHEPHEALAALABE79 - 8979 - 89
d_37TYRTYRTRPTRPBE91 - 10491 - 104
d_41ASNASNGLYGLYID6 - 156 - 15
d_42METMETASNASNID17 - 3817 - 38
d_43TYRTYRARGARGID52 - 5652 - 56
d_44GLYGLYPHEPHEID58 - 6158 - 61
d_45TYRTYRPROPROID63 - 7663 - 76
d_46PHEPHEALAALAID79 - 8979 - 89
d_47TYRTYRTRPTRPID91 - 10491 - 104
d_51ASNASNGLYGLYLJ6 - 156 - 15
d_52METMETASNASNLJ17 - 3817 - 38
d_53TYRTYRARGARGLJ52 - 5652 - 56
d_54GLYGLYPHEPHELJ58 - 6158 - 61
d_55TYRTYRPROPROLJ63 - 7663 - 76
d_56PHEPHEALAALALJ79 - 8979 - 89
d_57TYRTYRTRPTRPLJ91 - 10491 - 104
d_61ASNASNGLYGLYJC6 - 156 - 15
d_62METMETASNASNJC17 - 3817 - 38
d_63TYRTYRARGARGJC52 - 5652 - 56
d_64GLYGLYPHEPHEJC58 - 6158 - 61
d_65TYRTYRPROPROJC63 - 7663 - 76
d_66PHEPHEALAALAJC79 - 8979 - 89
d_67TYRTYRTRPTRPJC91 - 10491 - 104
d_71ASNASNGLYGLYGG6 - 156 - 15
d_72METMETASNASNGG17 - 3817 - 38
d_73TYRTYRARGARGGG52 - 5652 - 56
d_74GLYGLYPHEPHEGG58 - 6158 - 61
d_75TYRTYRPROPROGG63 - 7663 - 76
d_76PHEPHEALAALAGG79 - 8979 - 89
d_77TYRTYRTRPTRPGG91 - 10491 - 104
d_81ASNASNGLYGLYHH6 - 156 - 15
d_82METMETASNASNHH17 - 3817 - 38
d_83TYRTYRARGARGHH52 - 5652 - 56
d_84GLYGLYPHEPHEHH58 - 6158 - 61
d_85TYRTYRPROPROHH63 - 7663 - 76
d_86PHEPHEALAALAHH79 - 8979 - 89
d_87TYRTYRTRPTRPHH91 - 10491 - 104
d_91ASNASNGLYGLYKI6 - 156 - 15
d_92METMETASNASNKI17 - 3817 - 38
d_93TYRTYRARGARGKI52 - 5652 - 56
d_94GLYGLYPHEPHEKI58 - 6158 - 61
d_95TYRTYRPROPROKI63 - 7663 - 76
d_96PHEPHEALAALAKI79 - 8979 - 89
d_97TYRTYRTRPTRPKI91 - 10491 - 104
d_101ASNASNGLYGLYAB6 - 156 - 15
d_102METMETASNASNAB17 - 3817 - 38
d_103TYRTYRARGARGAB52 - 5652 - 56
d_104GLYGLYPHEPHEAB58 - 6158 - 61
d_105TYRTYRPROPROAB63 - 7663 - 76
d_106PHEPHEALAALAAB79 - 8979 - 89
d_107TYRTYRTRPTRPAB91 - 10491 - 104
d_111ASNASNGLYGLYDK6 - 156 - 15
d_112METMETASNASNDK17 - 3817 - 38
d_113TYRTYRARGARGDK52 - 5652 - 56
d_114GLYGLYPHEPHEDK58 - 6158 - 61
d_115TYRTYRPROPRODK63 - 7663 - 76
d_116PHEPHEALAALADK79 - 8979 - 89
d_117TYRTYRTRPTRPDK91 - 10491 - 104
d_121ASNASNGLYGLYCA6 - 156 - 15
d_122METMETASNASNCA17 - 3817 - 38
d_123TYRTYRARGARGCA52 - 5652 - 56
d_124GLYGLYPHEPHECA58 - 6158 - 61
d_125TYRTYRPROPROCA63 - 7663 - 76
d_126PHEPHEALAALACA79 - 8979 - 89
d_127TYRTYRTRPTRPCA91 - 10491 - 104

NCS oper:
IDCodeMatrixベクター
1given(0.883115793546, -0.0361855938348, -0.467757520504), (-0.445168617494, 0.250086009265, -0.859815032416), (0.148092529143, 0.96754720338, 0.204746213746)27.6309509732, -10.2216068821, 56.025745986
2given(0.615875300275, 0.516553410837, -0.594869891879), (-0.76131662038, 0.58448819664, -0.280660919122), (0.202718075279, 0.62573646349, 0.753232540597)5.08341311285, -21.8409328621, 17.5723166454
3given(-0.0959565160458, -0.976374706402, -0.193609864744), (0.353236830581, -0.215249845171, 0.91043464657), (-0.930599854153, 0.0189720017808, 0.365546131971)-40.9123145478, -25.7240812759, -13.5112764021
4given(0.816326592914, -0.549029350487, -0.179381342411), (0.362641513836, 0.728913697303, -0.580668540845), (0.449557589352, 0.408964049994, 0.794132469849)15.5335606778, 13.9867839104, 48.5034198315
5given(0.648064406664, -0.740904778885, 0.176274313048), (0.565926310993, 0.623382130449, 0.539557346315), (-0.509646873179, -0.249909639795, 0.823289278806)-23.6763126795, -2.93975302801, -12.3824767867
6given(0.0213030027928, -0.0939440117526, -0.99534953897), (-0.0527415961833, -0.994294790719, 0.0927156576871), (-0.998380942378, 0.050521201531, -0.0261362218352)13.941009051, -35.4829799236, 17.5465690994
7given(0.30375018365, -0.897873026935, -0.318684567298), (0.952540114382, 0.293239714696, 0.0817178084499), (0.020078755565, -0.32838163351, 0.94433169297)-0.90831651122, 13.8412604978, 24.6714710426
8given(-0.130002233259, 0.233545483407, -0.963616068011), (-0.962375459333, -0.263598791696, 0.0659481030098), (-0.238606149589, 0.935933856743, 0.259026873473)-14.0004112376, -45.2475353021, 16.8563390285
9given(-0.458436812351, -0.423726325851, -0.781211680572), (-0.432778607255, -0.661320631236, 0.612664426749), (-0.776233448251, 0.618959629929, 0.119794032966)-34.3755024213, -49.3010169924, 2.99520750483
10given(0.51742769429, 0.173044054859, -0.838047931958), (-0.626738244104, -0.590169156094, -0.508821717867), (-0.58263861403, 0.788515137631, -0.196916538584)27.3057998217, -33.7228245702, 40.8238207979
11given(-0.135207691315, -0.676769391966, -0.723672626474), (0.776431804908, -0.526104200605, 0.34694094949), (-0.615526224085, -0.514973358733, 0.596598614865)-1.92512645384, -11.7489198746, 12.262737398

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要素

#1: タンパク質
BTB/POZ domain-containing protein KCTD15 / Potassium channel tetramerization domain-containing protein 15


分子量: 13914.711 Da / 分子数: 12 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: KCTD15 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q96SI1
#2: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 89 / 由来タイプ: 天然 / 式: H2O

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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: 2.67 Å3/Da / 溶媒含有率: 53.85 %
結晶化温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 17.5% PEG3350, 0.3M Potassium thiocyanate

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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: Diamond / ビームライン: I03 / 波長: 0.976254 Å
検出器タイプ: DECTRIS EIGER2 XE 16M / 検出器: PIXEL / 日付: 2022年9月25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: 0.976254 Å / 相対比: 1
反射解像度: 2.25→77.99 Å / Num. obs: 85815 / % possible obs: 100 % / 冗長度: 27.28 % / Biso Wilson estimate: 65.83 Å2 / CC1/2: 0.9945 / Net I/σ(I): 14.8
反射 シェル解像度: 2.25→2.29 Å / Num. unique obs: 4227 / CC1/2: 0.3134

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
xia2データ削減
DIALSデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.25→46.75 Å / SU ML: 0.4154 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 31.5775
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2854 4173 4.87 %
Rwork0.2462 81511 -
obs0.2481 85684 99.96 %
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: 80.17 Å2
精密化ステップサイクル: LAST / 解像度: 2.25→46.75 Å
タンパク質核酸リガンド溶媒全体
原子数9447 0 0 89 9536
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00879707
X-RAY DIFFRACTIONf_angle_d1.245513208
X-RAY DIFFRACTIONf_chiral_restr0.06661451
X-RAY DIFFRACTIONf_plane_restr0.01071692
X-RAY DIFFRACTIONf_dihedral_angle_d5.33171319
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2BX-RAY DIFFRACTIONTorsion NCS0.721969067886
ens_1d_3BX-RAY DIFFRACTIONTorsion NCS0.694980204249
ens_1d_4BX-RAY DIFFRACTIONTorsion NCS0.722008776791
ens_1d_5BX-RAY DIFFRACTIONTorsion NCS0.684362197104
ens_1d_6BX-RAY DIFFRACTIONTorsion NCS0.786362172258
ens_1d_7BX-RAY DIFFRACTIONTorsion NCS0.683614545139
ens_1d_8BX-RAY DIFFRACTIONTorsion NCS0.687425743132
ens_1d_9BX-RAY DIFFRACTIONTorsion NCS0.695232064626
ens_1d_10BX-RAY DIFFRACTIONTorsion NCS0.668798610313
ens_1d_11BX-RAY DIFFRACTIONTorsion NCS0.707290485422
ens_1d_12BX-RAY DIFFRACTIONTorsion NCS0.755282571216
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.280.39531350.38012657X-RAY DIFFRACTION99.47
2.28-2.30.40821190.3682689X-RAY DIFFRACTION99.79
2.3-2.330.34361260.34782704X-RAY DIFFRACTION99.96
2.33-2.360.34691360.33932709X-RAY DIFFRACTION100
2.36-2.390.3231150.31712655X-RAY DIFFRACTION99.93
2.39-2.420.32131460.30922683X-RAY DIFFRACTION100
2.42-2.460.35531500.30542664X-RAY DIFFRACTION100
2.46-2.50.36681380.29882716X-RAY DIFFRACTION100
2.5-2.530.30511460.32644X-RAY DIFFRACTION100
2.53-2.580.32961370.30382696X-RAY DIFFRACTION100
2.58-2.620.35531380.3132702X-RAY DIFFRACTION100
2.62-2.670.42681260.35292681X-RAY DIFFRACTION100
2.67-2.720.39761310.32372715X-RAY DIFFRACTION100
2.72-2.780.35741370.30692691X-RAY DIFFRACTION100
2.78-2.840.34461630.30652672X-RAY DIFFRACTION100
2.84-2.90.4031570.28182678X-RAY DIFFRACTION100
2.9-2.970.35561310.28292726X-RAY DIFFRACTION100
2.97-3.050.28241110.2672728X-RAY DIFFRACTION100
3.05-3.140.32651190.26472740X-RAY DIFFRACTION100
3.14-3.250.28521480.26772683X-RAY DIFFRACTION100
3.25-3.360.35551520.29422712X-RAY DIFFRACTION100
3.36-3.50.30281450.25912702X-RAY DIFFRACTION100
3.5-3.660.26121380.23222733X-RAY DIFFRACTION100
3.66-3.850.28921450.22692715X-RAY DIFFRACTION100
3.85-4.090.271370.22842753X-RAY DIFFRACTION100
4.09-4.40.25751160.22292772X-RAY DIFFRACTION100
4.4-4.850.2441230.19622793X-RAY DIFFRACTION100
4.85-5.550.24841530.21482774X-RAY DIFFRACTION100
5.55-6.990.28461730.23132792X-RAY DIFFRACTION100
6.99-46.750.23661820.22352932X-RAY DIFFRACTION99.68
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)
10.202960572334-0.0768948887243-0.107792051915-0.0428520894576-0.02802261737830.0458310254092-0.2562988794860.169952361379-0.3416051567691.05425259236-0.01130396688790.310263989129-0.4854895920370.1453461087780.001355706578850.925425938-0.1033287859170.05958853885380.5514129707210.02717685031550.684594537902-10.3162602109-52.79900030093.89730001491
20.151113896753-0.4036997748820.02837838751690.633879566388-0.0501049180348-0.07460450388420.233356769281.27540948330.453000480288-1.34204286779-0.1117289689320.712125208250.5846283316950.173379869620.005260931518550.941175486621-0.152327560885-0.1999602192751.02422368836-0.1812096674460.891871220955-13.0194533897-56.4264011544-26.9941727688
30.0690403692186-0.1085407395730.006520004586280.116404190805-0.01282048014180.1754647449151.135559884490.0386127963474-0.1035097632250.171392416566-1.72171719449-0.568935814460.8611565951890.8691917268760.004036079264581.21156706899-0.170056669493-0.3499972140211.153357833940.1111952649330.93237376473-19.6978297939-57.9398893605-31.7291912063
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491.824264423190.358096016797-2.583485804242.892312428430.3594206599584.00759803753-0.1408030741310.05204403140410.4473267800020.916979558609-0.50687720405-1.04142758407-1.56246469394-1.29373991715-1.5405869791.281373141260.273059328617-0.5131712701050.538575967256-0.3352349950150.92072324326545.885610011219.162621679732.7826082768
500.1622574969870.105330601956-0.03394029709240.1196674977920.02562532603020.168710984181-0.6050450743840.5871752004420.37670705520.269536656279-1.99501785479-1.11978353238-0.6175098078820.131569265602-0.009604851748471.03997586403-0.135142254401-0.1917667619271.135287408310.08757736894971.0644007637156.947943318716.665789302926.147145148
510.2586238552960.056518296515-0.2981613112120.3896347786090.1831374209180.639374143948-0.5722547367540.553290332951-0.4431138114720.8439769158120.0968030843507-0.5869278380940.00315460426592-0.0706601775167-0.01070868732720.5881949756780.102223221955-0.1253502820180.624736560719-0.128348915810.88347477315949.24023466288.6581091475531.1508390399
521.219804926040.132896250501-0.4351274418310.46608815068-0.1877169648370.327537917145-0.1902247945010.5257450397790.380544425861.2072972729-0.2256807751060.151537165273-1.01499491854-2.53334891568-0.0753006678280.7807225595160.296368729551-0.2038751018490.969145892287-0.2244156378370.5954288096837.013200917813.669420398331.0879001404
530.615571262703-0.1518555509140.06759418244824.572166464830.5936181283683.26815285104-0.165948030607-0.7819476416430.1667510851390.716869751402-0.576996549702-0.1726473438170.568580761813-2.12975440915-0.5716720036370.6807768319220.1399479394290.01528431450551.46782951214-0.1553686134860.33481472846130.03813344299.4653687482834.2891295493
541.28853947124-1.48839750861-1.530512063772.238864301360.593908992384.60915745167-1.2688305056-1.024324038990.5130812757161.170218579880.47040433682-1.773298909381.21011690955-0.53250988499-0.02014607684231.187844313770.593084146181-0.3894411801970.542157764417-0.4197488449710.81288084947539.21505437216.9683773835940.7232203479
556.13017051194-1.24358063383-1.652255374133.279557858271.202570857710.792617557474-0.127049515937-0.456722720783-0.5017797130150.866239901120.206597215872-0.242854880848-1.28003816158-0.874770134570.1548346559491.058038871870.460385784628-0.127626502620.936799237397-0.1970079403250.51596241098236.208517653414.389733662441.970049602
564.230815166690.960064647619-3.516697025310.385027885355-0.8213157436772.910734171-0.808782126837-0.0965301387775-0.222086965674-0.363981309589-0.3750442504560.194592727648-0.724838543636-0.738705613055-3.261149814671.040269371570.644137207698-0.07617151925771.66738162893-0.08054357812260.27675422374325.73015216878.1769620349243.4810668224
574.294106991882.175595554153.301676908561.585922836731.744751239752.76506707187-0.721858358823-0.1523826026550.742508293918-0.4475791532690.4450667814830.724231893339-1.253079365980.5505831072820.01988695742720.525662450346-0.0155589314332-0.03106624986230.805402574222-0.2172901834080.68905639251855.6396340322-13.979320203916.4125082429
580.01048878314450.1027558590990.01733874112230.6520217926680.3664221249990.1455604884780.3815656137490.3191345512960.467001557827-0.645288626352-0.4350785633060.4572120838250.04325608761920.7647521179080.001499896609760.7263796977920.00683750913706-0.1702985033560.759387539487-0.1301035167490.78293241656552.2538704347-15.403119365518.0244409331
590.0345476875626-0.128629825433-0.08715366319770.939042384153-0.2287555008250.6983086575050.08302819592370.248651854604-1.528808319220.812882503242-0.7392539479490.4148297060340.5399306127720.879881283468-0.0106124694450.7847719107080.21204511891-0.2894582800180.895132707874-0.193675153430.9334381823453.8895462488-29.429874729320.2338779249
600.7429257254710.0954418480845-0.420927204470.1746301192010.05863258709610.146876157286-0.2696957115980.784430120653-0.480396915598-0.5040118280830.849047231161-0.3527856319060.301707441391.320191953970.02913098858850.92251960797-0.133481306323-0.1931131887951.11545012185-0.3012009563450.70769267939256.0152066667-21.214912723510.4680987863
610.450394032502-0.2546059549810.2681384313990.4654014030490.0007446030731590.3459952726650.435865270211-0.08260569010510.0670883254163-0.0656098706601-0.1607836230780.491241342940.378274100940.407844045185-0.001085434583020.629443875634-0.0812278671844-0.04932413990980.64866526724-0.1372589068610.61401246265545.6527407661-18.492384344917.5964705034
620.3756792560970.4445844813730.04022695654220.4262790019530.1132456036070.27735172468-0.4344319020080.2535441915051.006484586410.962206930928-0.6238009998550.3369872766480.189803823042-0.7049341320230.005211042435520.804394182925-0.04942525843750.08118267102361.0745775706-0.2222234521930.80556276166638.2845813328-20.183566019128.7011826233
630.727878446644-0.643624668751-0.05862768988670.7861448587030.4591863869170.3983452261220.533873919361.0349140941-0.24198041246-0.957438533978-0.9547584511220.292388745546-0.320601575705-0.356251239745-0.01128364794350.565789556472-0.160382169774-0.01500410585520.758833804859-0.1093517294430.70493901589139.4197379413-26.08137219516.7532831844
640.2401113167850.150363718445-0.6025356682270.565774093298-0.293761613641.380675863671.41194733752-0.437293267618-0.4395732887171.34557729187-1.44973529719-0.07663531882650.09252892353890.846463734692-0.04464906890161.09854431439-0.264048249609-0.1255305814720.7806249946720.0176393556280.58978605966340.3193538826-29.521159710925.6244900547
650.691622590640.213256990250.113151195970.215227082940.4220021187250.483245925756-0.3671241344570.809614704786-0.3507628067-0.1823781947550.130065798385-0.569200551644-0.0497326114146-0.0429842465839-0.0001351563089850.692153986313-0.1019356223370.08117177225830.647978559907-0.01632871065861.017496320015.05250746808-59.037326316-13.4946563543
660.5724184597530.08400154232490.09049666260720.01127455019080.1520375830880.9464661643290.03208149512090.739318748677-0.634618351214-0.00950376626278-0.3313704454710.0850671801160.550200370914-0.734569014439-0.002399679361980.758755729587-0.09155696562750.07496565469960.636859711955-0.1591768551270.80906621834-1.04329673356-63.0635796328-17.2570822716
670.5038659417110.608033977040.4010950431510.5088754302850.1979209463170.813107582799-0.183888355220.01784327009540.7031684413690.789757926212-0.146952860365-0.0855841885829-0.343749917209-0.06145081444410.0002651037509120.620970954523-0.0703507296022-0.0001712342701410.5547213804860.06945411657410.857857577115-2.43320196565-49.619184472-4.63256144844
680.04011497145970.1015375213450.02076433780540.1437447090950.06122440597640.388307479548-0.008296670878260.272519298238-0.0919822977194-0.990675759885-0.03972623905960.480172323989-0.112348489139-0.6217807509180.001729921891810.564360638541-0.1137667401350.01456458965030.587747613376-0.02591790454390.703217607454-10.355692219-57.4864786001-7.14908322735
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 'D' and (resid 95 through 110 )DK95 - 11086 - 101
22chain 'F' and (resid 4 through 31 )FL4 - 311 - 28
33chain 'F' and (resid 32 through 38 )FL32 - 3829 - 35
44chain 'F' and (resid 39 through 51 )FL39 - 5136 - 40
55chain 'F' and (resid 52 through 81 )FL52 - 8141 - 70
66chain 'F' and (resid 82 through 107 )FL82 - 10771 - 96
77chain 'C' and (resid 3 through 25 )CA3 - 251 - 23
88chain 'C' and (resid 26 through 39 )CA26 - 3924 - 37
99chain 'C' and (resid 40 through 51 )CA40 - 5138 - 43
1010chain 'C' and (resid 52 through 59 )CA52 - 5944 - 51
1111chain 'C' and (resid 60 through 70 )CA60 - 7052 - 62
1212chain 'C' and (resid 71 through 94 )CA71 - 9463 - 86
1313chain 'C' and (resid 95 through 111 )CA95 - 11187 - 103
1414chain 'A' and (resid 4 through 31 )AB4 - 311 - 28
1515chain 'A' and (resid 32 through 59 )AB32 - 5929 - 49
1616chain 'A' and (resid 60 through 70 )AB60 - 7050 - 60
1717chain 'A' and (resid 71 through 91 )AB71 - 9161 - 81
1818chain 'A' and (resid 92 through 105 )AB92 - 10582 - 95
1919chain 'J' and (resid 3 through 15 )JC3 - 151 - 13
2020chain 'J' and (resid 16 through 51 )JC16 - 5114 - 44
2121chain 'J' and (resid 52 through 69 )JC52 - 6945 - 62
2222chain 'J' and (resid 70 through 81 )JC70 - 8163 - 74
2323chain 'J' and (resid 82 through 108 )JC82 - 10875 - 101
2424chain 'I' and (resid 4 through 15 )ID4 - 151 - 12
2525chain 'I' and (resid 16 through 31 )ID16 - 3113 - 28
2626chain 'I' and (resid 32 through 51 )ID32 - 5129 - 44
2727chain 'I' and (resid 52 through 69 )ID52 - 6945 - 62
2828chain 'I' and (resid 70 through 81 )ID70 - 8163 - 74
2929chain 'I' and (resid 82 through 109 )ID82 - 10975 - 102
3030chain 'B' and (resid 4 through 15 )BE4 - 151 - 12
3131chain 'B' and (resid 16 through 39 )BE16 - 3913 - 36
3232chain 'B' and (resid 40 through 51 )BE40 - 5137 - 43
3333chain 'B' and (resid 52 through 60 )BE52 - 6044 - 52
3434chain 'B' and (resid 61 through 70 )BE61 - 7053 - 62
3535chain 'B' and (resid 71 through 81 )BE71 - 8163 - 73
3636chain 'B' and (resid 82 through 111 )BE82 - 11174 - 103
3737chain 'E' and (resid 5 through 20 )EF5 - 201 - 16
3838chain 'E' and (resid 21 through 59 )EF21 - 5917 - 53
3939chain 'E' and (resid 60 through 108 )EF60 - 10854 - 102
4040chain 'G' and (resid 4 through 70 )GG4 - 701 - 61
4141chain 'G' and (resid 71 through 81 )GG71 - 8162 - 72
4242chain 'G' and (resid 82 through 107 )GG82 - 10773 - 98
4343chain 'H' and (resid 4 through 39 )HH4 - 391 - 36
4444chain 'H' and (resid 40 through 50 )HH40 - 5037 - 43
4545chain 'H' and (resid 51 through 70 )HH51 - 7044 - 63
4646chain 'H' and (resid 71 through 92 )HH71 - 9264 - 85
4747chain 'H' and (resid 93 through 107 )HH93 - 10786 - 100
4848chain 'K' and (resid 5 through 15 )KI5 - 151 - 11
4949chain 'K' and (resid 16 through 39 )KI16 - 3912 - 35
5050chain 'K' and (resid 40 through 51 )KI40 - 5136 - 42
5151chain 'K' and (resid 52 through 59 )KI52 - 5943 - 50
5252chain 'K' and (resid 60 through 70 )KI60 - 7051 - 61
5353chain 'K' and (resid 71 through 81 )KI71 - 8162 - 70
5454chain 'K' and (resid 82 through 91 )KI82 - 9171 - 80
5555chain 'K' and (resid 92 through 102 )KI92 - 10281 - 91
5656chain 'K' and (resid 103 through 107 )KI103 - 10792 - 96
5757chain 'L' and (resid 5 through 13 )LJ5 - 131 - 9
5858chain 'L' and (resid 14 through 25 )LJ14 - 2510 - 21
5959chain 'L' and (resid 26 through 31 )LJ26 - 3122 - 27
6060chain 'L' and (resid 32 through 51 )LJ32 - 5128 - 42
6161chain 'L' and (resid 52 through 69 )LJ52 - 6943 - 60
6262chain 'L' and (resid 70 through 81 )LJ70 - 8161 - 72
6363chain 'L' and (resid 82 through 93 )LJ82 - 9373 - 84
6464chain 'L' and (resid 94 through 104 )LJ94 - 10485 - 95
6565chain 'D' and (resid 3 through 31 )DK3 - 311 - 29
6666chain 'D' and (resid 32 through 59 )DK32 - 5930 - 50
6767chain 'D' and (resid 60 through 81 )DK60 - 8151 - 72
6868chain 'D' and (resid 82 through 94 )DK82 - 9473 - 85

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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://pdbjlvh1.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