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- PDB-8ym4: Structure of Caspase-8/cFLIP death effector domain assembly -

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基本情報

登録情報
データベース: PDB / ID: 8ym4
タイトルStructure of Caspase-8/cFLIP death effector domain assembly
要素
  • CASP8 and FADD-like apoptosis regulator subunit p43
  • Caspase-8
キーワードAPOPTOSIS / FADD / Caspase-8 / cFLIP / death effector domain
機能・相同性
機能・相同性情報


negative regulation of myoblast fusion / skeletal myofibril assembly / caspase-8 / death effector domain binding / FasL/ CD95L signaling / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / skeletal muscle atrophy / TRAIL signaling / CD95 death-inducing signaling complex / regulation of skeletal muscle satellite cell proliferation ...negative regulation of myoblast fusion / skeletal myofibril assembly / caspase-8 / death effector domain binding / FasL/ CD95L signaling / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / skeletal muscle atrophy / TRAIL signaling / CD95 death-inducing signaling complex / regulation of skeletal muscle satellite cell proliferation / ripoptosome / Defective RIPK1-mediated regulated necrosis / Apoptotic execution phase / TRAIL-activated apoptotic signaling pathway / Activation, myristolyation of BID and translocation to mitochondria / TRIF-mediated programmed cell death / Microbial modulation of RIPK1-mediated regulated necrosis / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TLR3-mediated TICAM1-dependent programmed cell death / regulation of necroptotic process / Caspase activation via Death Receptors in the presence of ligand / positive regulation of extracellular matrix organization / positive regulation of macrophage differentiation / self proteolysis / positive regulation of glomerular mesangial cell proliferation / response to cobalt ion / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / death-inducing signaling complex / skeletal muscle tissue regeneration / CLEC7A/inflammasome pathway / negative regulation of necroptotic process / response to anesthetic / negative regulation of hepatocyte apoptotic process / regulation of tumor necrosis factor-mediated signaling pathway / tumor necrosis factor receptor binding / death receptor binding / positive regulation of hepatocyte proliferation / natural killer cell activation / negative regulation of cellular response to transforming growth factor beta stimulus / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / negative regulation of cardiac muscle cell apoptotic process / execution phase of apoptosis / regulation of innate immune response / Apoptotic cleavage of cellular proteins / pyroptotic inflammatory response / response to testosterone / : / B cell activation / positive regulation of proteolysis / macrophage differentiation / response to tumor necrosis factor / extrinsic apoptotic signaling pathway via death domain receptors / Caspase-mediated cleavage of cytoskeletal proteins / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / skeletal muscle tissue development / negative regulation of reactive oxygen species biosynthetic process / extrinsic apoptotic signaling pathway / negative regulation of canonical NF-kappaB signal transduction / cellular response to nitric oxide / cysteine-type peptidase activity / cellular response to epidermal growth factor stimulus / cellular response to dexamethasone stimulus / regulation of cytokine production / protein maturation / proteolysis involved in protein catabolic process / T cell activation / enzyme activator activity / positive regulation of interleukin-1 beta production / negative regulation of extrinsic apoptotic signaling pathway / Regulation of NF-kappa B signaling / apoptotic signaling pathway / cellular response to estradiol stimulus / Regulation of TNFR1 signaling / wound healing / NOD1/2 Signaling Pathway / protein processing / positive regulation of neuron projection development / Regulation of necroptotic cell death / cellular response to insulin stimulus / cellular response to mechanical stimulus / positive regulation of NF-kappaB transcription factor activity / positive regulation of neuron apoptotic process / response to estradiol / lamellipodium / peptidase activity / heart development / cell body / protease binding / scaffold protein binding / angiogenesis / cellular response to hypoxia / response to lipopolysaccharide / response to ethanol / mitochondrial outer membrane / positive regulation of canonical NF-kappaB signal transduction / cytoskeleton / positive regulation of ERK1 and ERK2 cascade
類似検索 - 分子機能
Caspase-8 / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Death effector domain / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. ...Caspase-8 / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Death effector domain / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Death-like domain superfamily
類似検索 - ドメイン・相同性
SELENIUM ATOM / CASP8 and FADD-like apoptosis regulator / Caspase-8
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 / 単波長異常分散 / 解像度: 2.34 Å
データ登録者Lin, S.-C. / Yang, C.-Y.
資金援助 台湾, 1件
組織認可番号国
Other government 台湾
引用ジャーナル: Nat Commun / 年: 2024
タイトル: Reverse hierarchical DED assembly in the cFLIP-procaspase-8 and cFLIP-procaspase-8-FADD complexes.
著者: Chao-Yu Yang / Yi-Chun Tseng / Yi-Fan Tu / Bai-Jiun Kuo / Li-Chung Hsu / Chia-I Lien / You-Sheng Lin / Yin-Ting Wang / Yen-Chen Lu / Tsung-Wei Su / Yu-Chih Lo / Su-Chang Lin /
要旨: cFLIP, a master anti-apoptotic regulator, targets the FADD-induced DED complexes of procaspase-8 in death receptor and ripoptosome signaling pathways. Several tumor cells maintain relatively high ...cFLIP, a master anti-apoptotic regulator, targets the FADD-induced DED complexes of procaspase-8 in death receptor and ripoptosome signaling pathways. Several tumor cells maintain relatively high levels of cFLIP in achieving their immortality. However, understanding the three-dimensional regulatory mechanism initiated or mediated by elevated levels of cFLIP has been limited by the absence of the atomic coordinates for cFLIP-induced DED complexes. Here we report the crystal plus cryo-EM structures to uncover an unconventional mechanism where cFLIP and procaspase-8 autonomously form a binary tandem DED complex, independent of FADD. This complex gains the ability to recruit FADD, thereby allosterically modulating cFLIP assembly and partially activating caspase-8 for RIPK1 cleavage. Our structure-guided mutagenesis experiments provide critical insights into these regulatory mechanisms, elucidating the resistance to apoptosis and necroptosis in achieving immortality. Finally, this research offers a unified model for the intricate bidirectional hierarchy-based processes using multiprotein helical assembly to govern cell fate decisions.
履歴
登録2024年3月8日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02024年10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
C: Caspase-8
B: Caspase-8
D: Caspase-8
H: CASP8 and FADD-like apoptosis regulator subunit p43
G: CASP8 and FADD-like apoptosis regulator subunit p43
F: CASP8 and FADD-like apoptosis regulator subunit p43
K: CASP8 and FADD-like apoptosis regulator subunit p43
I: CASP8 and FADD-like apoptosis regulator subunit p43
J: CASP8 and FADD-like apoptosis regulator subunit p43
A: Caspase-8
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)217,60411
ポリマ－217,52510
非ポリマー791
水91951
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • 根拠: gel filtration, light scattering
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)82.266, 167.448, 179.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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 2 through 4 or resid 6...
d_2ens_1(chain "B" and (resid 2 through 4 or resid 6...
d_3ens_1(chain "C" and (resid 2 through 4 or resid 6...
d_4ens_1(chain "D" and (resid 2 through 4 or resid 6...
d_1ens_2(chain "F" and (resid 2 through 10 or resid 12...
d_2ens_2(chain "G" and (resid 2 through 10 or resid 12...
d_3ens_2(chain "H" and (resid 2 through 10 or resid 12...
d_4ens_2(chain "I" and (resid 2 through 10 or resid 12...
d_5ens_2(chain "J" and (resid 2 through 10 or resid 12...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ASPASPSERSERAJ2 - 42 - 4
d_12ens_1ASNASNTHRTHRAJ6 - 816 - 81
d_13ens_1LYSLYSLYSLYSAJ8383
d_14ens_1GLUGLUGLUGLUAJ85 - 8785 - 87
d_15ens_1GLUGLUALAALAAJ89 - 9689 - 96
d_16ens_1ILEILESERSERAJ98 - 11398 - 113
d_17ens_1SERSERLEULEUAJ115 - 117115 - 117
d_18ens_1SERSERLEULEUAJ119 - 124119 - 124
d_19ens_1GLUGLUGLUGLUAJ127127
d_110ens_1LEULEULEULEUAJ133133
d_111ens_1ASPASPLYSLYSAJ136 - 161136 - 161
d_112ens_1VALVALALAALAAJ163 - 165163 - 165
d_113ens_1ILEILEASNASNAJ167 - 168167 - 168
d_114ens_1SERSERSERSERAJ170 - 182170 - 182
d_21ens_1ASPASPSERSERBB2 - 42 - 4
d_22ens_1ASNASNTHRTHRBB6 - 816 - 81
d_23ens_1LYSLYSLYSLYSBB8383
d_24ens_1GLUGLUGLUGLUBB85 - 8785 - 87
d_25ens_1GLUGLUALAALABB89 - 9689 - 96
d_26ens_1ILEILESERSERBB98 - 11398 - 113
d_27ens_1SERSERLEULEUBB115 - 117115 - 117
d_28ens_1SERSERLEULEUBB119 - 124119 - 124
d_29ens_1GLUGLUGLUGLUBB127127
d_210ens_1LEULEULEULEUBB133133
d_211ens_1ASPASPLYSLYSBB136 - 161136 - 161
d_212ens_1VALVALALAALABB163 - 165163 - 165
d_213ens_1ILEILEASNASNBB167 - 168167 - 168
d_214ens_1SERSERSERSERBB170 - 182170 - 182
d_31ens_1ASPASPSERSERCA2 - 42 - 4
d_32ens_1ASNASNTHRTHRCA6 - 816 - 81
d_33ens_1LYSLYSLYSLYSCA8383
d_34ens_1GLUGLUGLUGLUCA85 - 8785 - 87
d_35ens_1GLUGLUALAALACA89 - 9689 - 96
d_36ens_1ILEILESERSERCA98 - 11398 - 113
d_37ens_1SERSERLEULEUCA115 - 117115 - 117
d_38ens_1SERSERLEULEUCA119 - 124119 - 124
d_39ens_1GLUGLUGLUGLUCA127127
d_310ens_1LEULEULEULEUCA133133
d_311ens_1ASPASPLYSLYSCA136 - 161136 - 161
d_312ens_1VALVALALAALACA163 - 165163 - 165
d_313ens_1ILEILEASNASNCA167 - 168167 - 168
d_314ens_1SERSERSERSERCA170 - 182170 - 182
d_41ens_1ASPASPSERSERDC2 - 42 - 4
d_42ens_1ASNASNTHRTHRDC6 - 816 - 81
d_43ens_1LYSLYSLYSLYSDC8383
d_44ens_1GLUGLUGLUGLUDC85 - 8785 - 87
d_45ens_1GLUGLUALAALADC89 - 9689 - 96
d_46ens_1ILEILESERSERDC98 - 11398 - 113
d_47ens_1SERSERLEULEUDC115 - 117115 - 117
d_48ens_1SERSERLEULEUDC119 - 124119 - 124
d_49ens_1GLUGLUGLUGLUDC127127
d_410ens_1LEULEULEULEUDC133133
d_411ens_1ASPASPLYSLYSDC136 - 161136 - 161
d_412ens_1VALVALALAALADC163 - 165163 - 165
d_413ens_1ILEILEASNASNDC167 - 168167 - 168
d_414ens_1SERSERSERSERDC170 - 182170 - 182
d_11ens_2SERSERGLUGLUFF2 - 105 - 13
d_12ens_2ALAALALYSLYSFF12 - 1815 - 21
d_13ens_2MSEMSEVALVALFF20 - 2823 - 31
d_14ens_2VALVALVALVALFF33 - 3736 - 40
d_15ens_2ASPASPLEULEUFF39 - 4442 - 47
d_16ens_2GLUGLULEULEUFF46 - 7249 - 75
d_17ens_2MSEMSEARGARGFF74 - 7677 - 79
d_18ens_2ALAALALEULEUFF78 - 8481 - 87
d_19ens_2ASNASNALAALAFF86 - 9889 - 101
d_110ens_2ILEILEGLYGLYFF100 - 101103 - 104
d_111ens_2ASPASPASPASPFF103 - 105106 - 108
d_112ens_2SERSERMSEMSEFF107 - 116110 - 119
d_113ens_2ASPASPMSEMSEFF118 - 120121 - 123
d_114ens_2SERSERVALVALFF130 - 136133 - 139
d_115ens_2LEULEUGLUGLUFF138 - 153141 - 156
d_116ens_2CYSCYSGLNGLNFF155 - 169158 - 172
d_117ens_2TYRTYRLYSLYSFF171 - 172174 - 175
d_118ens_2SERSERVALVALFF174 - 175177 - 178
d_21ens_2SERSERGLUGLUGE2 - 105 - 13
d_22ens_2ALAALALYSLYSGE12 - 1815 - 21
d_23ens_2MSEMSEVALVALGE20 - 2823 - 31
d_24ens_2VALVALVALVALGE33 - 3736 - 40
d_25ens_2ASPASPLEULEUGE39 - 4442 - 47
d_26ens_2GLUGLULEULEUGE46 - 7249 - 75
d_27ens_2MSEMSEARGARGGE74 - 7677 - 79
d_28ens_2ALAALALEULEUGE78 - 8481 - 87
d_29ens_2ASNASNALAALAGE86 - 9889 - 101
d_210ens_2ILEILEGLYGLYGE100 - 101103 - 104
d_211ens_2ASPASPASPASPGE103 - 105106 - 108
d_212ens_2SERSERMSEMSEGE107 - 116110 - 119
d_213ens_2ASPASPMSEMSEGE118 - 120121 - 123
d_214ens_2SERSERVALVALGE130 - 136133 - 139
d_215ens_2LEULEUGLUGLUGE138 - 153141 - 156
d_216ens_2CYSCYSGLNGLNGE155 - 169158 - 172
d_217ens_2TYRTYRLYSLYSGE171 - 172174 - 175
d_218ens_2SERSERVALVALGE174 - 175177 - 178
d_31ens_2SERSERGLUGLUHD2 - 105 - 13
d_32ens_2ALAALALYSLYSHD12 - 1815 - 21
d_33ens_2MSEMSEVALVALHD20 - 2823 - 31
d_34ens_2VALVALVALVALHD33 - 3736 - 40
d_35ens_2ASPASPLEULEUHD39 - 4442 - 47
d_36ens_2GLUGLULEULEUHD46 - 7249 - 75
d_37ens_2MSEMSEARGARGHD74 - 7677 - 79
d_38ens_2ALAALALEULEUHD78 - 8481 - 87
d_39ens_2ASNASNALAALAHD86 - 9889 - 101
d_310ens_2ILEILEGLYGLYHD100 - 101103 - 104
d_311ens_2ASPASPASPASPHD103 - 105106 - 108
d_312ens_2SERSERMSEMSEHD107 - 116110 - 119
d_313ens_2ASPASPMSEMSEHD118 - 120121 - 123
d_314ens_2SERSERVALVALHD130 - 136133 - 139
d_315ens_2LEULEUGLUGLUHD138 - 153141 - 156
d_316ens_2CYSCYSGLNGLNHD155 - 169158 - 172
d_317ens_2TYRTYRLYSLYSHD171 - 172174 - 175
d_318ens_2SERSERVALVALHD174 - 175177 - 178
d_41ens_2SERSERGLUGLUIH2 - 105 - 13
d_42ens_2ALAALALYSLYSIH12 - 1815 - 21
d_43ens_2MSEMSEVALVALIH20 - 2823 - 31
d_44ens_2VALVALVALVALIH33 - 3736 - 40
d_45ens_2ASPASPLEULEUIH39 - 4442 - 47
d_46ens_2GLUGLULEULEUIH46 - 7249 - 75
d_47ens_2MSEMSEARGARGIH74 - 7677 - 79
d_48ens_2ALAALALEULEUIH78 - 8481 - 87
d_49ens_2ASNASNALAALAIH86 - 9889 - 101
d_410ens_2ILEILEGLYGLYIH100 - 101103 - 104
d_411ens_2ASPASPASPASPIH103 - 105106 - 108
d_412ens_2SERSERMSEMSEIH107 - 116110 - 119
d_413ens_2ASPASPMSEMSEIH118 - 120121 - 123
d_414ens_2SERSERVALVALIH130 - 136133 - 139
d_415ens_2LEULEUGLUGLUIH138 - 153141 - 156
d_416ens_2CYSCYSGLNGLNIH155 - 169158 - 172
d_417ens_2TYRTYRLYSLYSIH171 - 172174 - 175
d_418ens_2SERSERVALVALIH174 - 175177 - 178
d_51ens_2SERSERGLUGLUJI2 - 105 - 13
d_52ens_2ALAALALYSLYSJI12 - 1815 - 21
d_53ens_2MSEMSEVALVALJI20 - 2823 - 31
d_54ens_2VALVALVALVALJI33 - 3736 - 40
d_55ens_2ASPASPLEULEUJI39 - 4442 - 47
d_56ens_2GLUGLULEULEUJI46 - 7249 - 75
d_57ens_2MSEMSEARGARGJI74 - 7677 - 79
d_58ens_2ALAALALEULEUJI78 - 8481 - 87
d_59ens_2ASNASNALAALAJI86 - 9889 - 101
d_510ens_2ILEILEGLYGLYJI100 - 101103 - 104
d_511ens_2ASPASPASPASPJI103 - 105106 - 108
d_512ens_2SERSERMSEMSEJI107 - 116110 - 119
d_513ens_2ASPASPMSEMSEJI118 - 120121 - 123
d_514ens_2SERSERVALVALJI130 - 136133 - 139
d_515ens_2LEULEUGLUGLUJI138 - 153141 - 156
d_516ens_2CYSCYSGLNGLNJI155 - 169158 - 172
d_517ens_2TYRTYRLYSLYSJI171 - 172174 - 175
d_518ens_2SERSERVALVALJI174 - 175177 - 178

NCSアンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
1given(0.297224349727, 0.949168570785, -0.103618097666), (-0.945999947946, 0.307449700535, 0.102755925025), (0.129390047593, 0.067481152002, 0.989294955869)-131.684149855, 113.861122183, 1.66087517656
2given(-0.797678789651, 0.600202550804, -0.0588680435385), (-0.59114245822, -0.75882478512, 0.273378015901), (0.119411651989, 0.252867244809, 0.960103647463)-67.5284642935, 265.374585957, -12.680137953
3given(-0.836647545273, -0.529489874343, 0.140218964324), (0.546261290771, -0.787775078158, 0.284620850321), (-0.0402428526921, 0.314723528197, 0.948329907578)95.5972649437, 257.772822467, -6.82560358174
4given(0.267244914575, 0.963506743629, -0.0153267940327), (-0.956766685663, 0.267203057781, 0.114891405757), (0.114794010464, -0.0160399779885, 0.993259812067)-136.101233243, 116.967907542, 14.3348979407
5given(-0.820124020261, 0.571642422589, 0.0249305452607), (-0.560989956515, -0.811890208578, 0.161630931152), (0.112635962641, 0.118571623553, 0.98653631966)-67.6914247316, 275.494054735, 8.31535258376
6given(-0.0411151114303, -0.996801852678, 0.0685245511414), (0.996301323147, -0.0357220075549, 0.0781512103045), (-0.0754534366871, 0.0714842966903, 0.99458371906)159.782420183, 147.909737554, 16.7390693618
7given(0.922934148933, -0.383981772436, 0.027396261958), (0.382132345495, 0.922443700528, 0.0554300449521), (-0.0465556361681, -0.0406892835234, 0.998086647014)60.2117586442, 10.9294735912, 47.068659998

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要素

#1: タンパク質
Caspase-8 / CASP-8 / Apoptotic cysteine protease / Apoptotic protease Mch-5 / CAP4 / FADD-homologous ICE/ced-3- ...CASP-8 / Apoptotic cysteine protease / Apoptotic protease Mch-5 / CAP4 / FADD-homologous ICE/ced-3-like protease / FADD-like ICE / FLICE / ICE-like apoptotic protease 5 / MORT1-associated ced-3 homolog / MACH


分子量: 22339.715 Da / 分子数: 4 / 変異: F122G, L123G / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CASP8, MCH5 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q14790, caspase-8
#2: タンパク質
CASP8 and FADD-like apoptosis regulator subunit p43 / cFLIP


分子量: 21361.031 Da / 分子数: 6 / 変異: H7G / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CFLAR, CASH, CASP8AP1, CLARP, MRIT / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: O15519
#3: 化合物 ChemComp-SE / SELENIUM ATOM / セレン


分子量: 78.960 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Se / タイプ: SUBJECT OF INVESTIGATION
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 51 / 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
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: 2.83 Å3/Da / 溶媒含有率: 56.61 %
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
詳細: 0.1 M MES pH 6.5, 0.08 M sodium chloride, 0.2 M Potassium Thiocyanate, 10 % PEG 4000, 0.01 M TCEP

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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: NSRRC / ビームライン: BL13B1 / 波長: 0.97942 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2016年4月3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: 0.97942 Å / 相対比: 1
反射解像度: 2.34→30 Å / Num. obs: 102320 / % possible obs: 97.9 % / 冗長度: 7.6 % / Biso Wilson estimate: 35.59 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 22.935
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.34-2.426.80.35890960.8870.970.1470.3891.08388
2.42-2.527.10.36196030.9170.9780.1450.3911.14493.1
2.52-2.647.50.322102060.9450.9860.1280.3481.31898.4
2.64-2.7780.287103330.9670.9920.1110.3081.379100
2.77-2.958.10.197104090.9860.9970.0750.2111.569100
2.95-3.1880.141103670.9930.9980.0530.1511.45799.9
3.18-3.497.90.093104290.9960.9990.0350.0991.527100
3.49-47.80.069104620.9970.9990.0260.0741.67999.9
4-5.037.40.063105550.9970.9990.0250.0682.17499.7
5.03-307.10.061108600.99810.0240.0656.30399.4

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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
HKL-2000データスケーリング
HKL-2000データ削減
AutoSol位相決定
精密化構造決定の手法: 単波長異常分散 / 解像度: 2.34→29.84 Å / SU ML: 0.3065 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 27.7255
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2525 5078 4.97 %
Rwork0.2056 97136 -
obs0.2079 102214 97.73 %
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: 50.24 Å2
精密化ステップサイクル: LAST / 解像度: 2.34→29.84 Å
タンパク質核酸リガンド溶媒全体
原子数14515 0 1 51 14567
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.005214660
X-RAY DIFFRACTIONf_angle_d0.707119625
X-RAY DIFFRACTIONf_chiral_restr0.04252275
X-RAY DIFFRACTIONf_plane_restr0.00572497
X-RAY DIFFRACTIONf_dihedral_angle_d12.58435889
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2JAX-RAY DIFFRACTIONTorsion NCS0.695680935389
ens_1d_3JAX-RAY DIFFRACTIONTorsion NCS0.627431882538
ens_1d_4JAX-RAY DIFFRACTIONTorsion NCS0.782926668295
ens_2d_2FFX-RAY DIFFRACTIONTorsion NCS0.769646270061
ens_2d_3FFX-RAY DIFFRACTIONTorsion NCS0.918943846628
ens_2d_4FFX-RAY DIFFRACTIONTorsion NCS0.962889956458
ens_2d_5FFX-RAY DIFFRACTIONTorsion NCS1.05246734813
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.370.32561300.27652780X-RAY DIFFRACTION84.08
2.37-2.40.29911300.26022888X-RAY DIFFRACTION87.81
2.4-2.430.33661610.25672939X-RAY DIFFRACTION89.62
2.43-2.460.33011650.26472924X-RAY DIFFRACTION90.72
2.46-2.490.32641630.25153083X-RAY DIFFRACTION92.93
2.49-2.530.33521760.25833065X-RAY DIFFRACTION95.24
2.53-2.560.29931640.25373211X-RAY DIFFRACTION97.15
2.56-2.60.30241650.25073203X-RAY DIFFRACTION98.05
2.6-2.640.29292030.25023272X-RAY DIFFRACTION99.83
2.64-2.680.31451660.24083244X-RAY DIFFRACTION99.91
2.68-2.730.28881570.23883308X-RAY DIFFRACTION99.94
2.73-2.780.30361700.22933287X-RAY DIFFRACTION99.94
2.78-2.830.291560.22143319X-RAY DIFFRACTION99.94
2.83-2.890.26431590.2273268X-RAY DIFFRACTION99.94
2.89-2.950.28451750.23513325X-RAY DIFFRACTION99.97
2.95-3.020.31222060.25683222X-RAY DIFFRACTION99.97
3.02-3.10.31031820.24293276X-RAY DIFFRACTION99.91
3.1-3.180.28841810.23213315X-RAY DIFFRACTION99.97
3.18-3.270.27651840.22223297X-RAY DIFFRACTION99.97
3.27-3.380.24631750.21233277X-RAY DIFFRACTION99.94
3.38-3.50.27121690.21923321X-RAY DIFFRACTION99.97
3.5-3.640.27581870.20673312X-RAY DIFFRACTION99.97
3.64-3.810.20291810.18553325X-RAY DIFFRACTION99.94
3.81-4.010.21831930.16773276X-RAY DIFFRACTION99.88
4.01-4.260.18991300.16333378X-RAY DIFFRACTION99.83
4.26-4.580.20431750.16113348X-RAY DIFFRACTION99.69
4.58-5.040.22021550.16863363X-RAY DIFFRACTION99.43
5.04-5.770.24671580.19833392X-RAY DIFFRACTION99.64
5.77-7.250.25531760.22733377X-RAY DIFFRACTION98.97
7.25-29.840.19111860.16823541X-RAY DIFFRACTION99.33
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)
1-0.0106952710843-0.01881879552440.005406423379640.0680755007763-0.02501647737820.02093955793920.126207343993-0.190805438270.001990445816190.0109864808585-0.0315470751428-0.03457746157510.00587601115198-0.299887419506-2.02365910538E-70.1439643854830.0101762397423-0.009093554791760.1012149039340.0002953101672480.181382336037.12489751722134.6169340882.0614232342
20.01054539715250.1098093974650.03858315508580.0228871734913-0.0710092491977-0.005477879993280.05110399788650.0497300517137-0.0307874213604-0.01919808981230.00117297271495-0.02565150530540.04171546406940.0972830128367.53219918072E-80.125788388236-0.000534841092387-0.000689285720870.1136835270060.005733295771820.11279838994415.5127794006132.06486295776.8081897472
30.0249024816045-0.01905763717660.05532789243090.08473352421570.0129705569388-0.006012821215250.0125151552439-0.1888338963-0.0510118716913-0.0004078677988940.1109230971320.01486834130620.0445902962038-0.0160267595963-1.59781651982E-80.151148066512-0.00487724497443-0.01185784020850.2396345032770.03066131213850.1724035118913.7429797635123.89316386789.9824913638
40.0258702848769-0.02372423637830.09683081376180.0471070602734-0.008348472359580.05756836452680.114597825888-0.145150772333-0.00936279585399-0.00539470983925-0.1628620501340.0412744912394-0.077080932799-0.03370245499826.67693258048E-90.176280631375-0.0204914770489-0.0005409489539080.0957147591808-0.04224871884530.1380287054327.4767650012146.43561316490.326698308
50.06834434987980.02051213674380.01750834967490.0219307919706-0.0125075765850.02797119232810.04146756787930.0361053241411-0.220290199380.185374241319-0.0768065400945-0.228119229458-0.01181405177270.1750280824924.51606544985E-80.185156735576-0.00326571136331-0.03623320367510.236462778794-0.02744625004050.19863675324433.7755795979135.4284989795.9450948807
60.008455672173880.01453340151610.002355349685170.00582282715663-0.003889872680490.01174740526240.1084093915190.0685085727145-0.09952191258170.0898230056162-0.056809366195-0.06624163921010.0593009838011-0.0105655517158-3.23714307451E-60.14822770140.008439139199590.006990264499130.136156260496-0.01099380300620.15964829045732.3166813402135.78235271564.2838188042
70.0125258609343-0.003353040445050.0219383052886-0.000325429613921-0.008501592052340.007094215061370.0176561790342-0.0928376979059-0.04848140831440.127151525771-0.0305041620157-0.01496710865450.100105602587-0.0334979849011-7.04621814489E-70.10519476833-0.0256324473670.0228369252450.143270064210.04244451292630.20410578462829.6756901034152.00530937869.7089138298
80.07865687570940.0396615744896-0.003769922001920.108604838683-0.0138096337880.03989830236940.01430205077570.25586092496-0.01767488611840.0571343863314-0.0727849232660.0518269290653-0.07581878640870.1587353470062.15797612373E-80.135002591468-0.0094193983440.001314015077710.1884593141870.02348336273240.18121840119935.7653532981147.95915205763.1616492457
90.003071778124020.000266440466104-0.001027480005570.00756637246969-0.00114039657193-0.006892204418820.08772140496520.0390833597399-0.1257910872490.05818991672070.0177465725562-0.0798745422-0.004825436742010.09561277235622.84098831366E-60.215582785637-0.0155777480056-0.02082664330470.4113540868520.01274890286880.27820876753448.6301943985144.09318591174.5735287207
100.06008559808460.009087972308510.09538180512260.0649288753744-0.06197403395490.0702974305028-0.09259221941550.1622738530370.07721520068130.194198643599-0.00549550352879-0.0467314632912-0.1439731159560.1234759683926.63755269797E-80.224875812529-0.00265711985429-0.01915132379360.185282078383-0.03793468881340.26672338979831.7493376463164.66188198174.6369178432
11-0.00189196431992-0.0184684466154-0.02419512560480.05183525399290.06573775050370.0155067002145-0.07081709162540.07192139185030.09873221548980.3549564535280.267204955101-0.146653643445-0.2448663150390.00194839462155-1.27812225012E-80.389952138052-0.0844212406135-0.1347292055020.21850066481-0.07340829216390.34699910770938.1408017527169.35350903775.488946157
120.01580320976450.001307231761560.0110781338270.0414299374667-0.01760248626250.0319226611191-0.04315098099950.2479950617430.0889063800991-0.00757052171914-0.0371861682974-0.311607537322-0.0783126574104-0.02867339328171.96057928068E-70.1010114495370.2067702763950.0611560619465-0.705475946473-0.1586874114590.176242356289-6.30273282715151.2976633191.2306315337
130.0007243029053440.0006022075255760.00839555250240.005043965495460.003674529950330.000391530129439-0.0489789852930.1254630631750.148722046064-0.134147751371-0.024346017581-0.0669156325755-0.01583207966470.124628325862-5.46095210653E-70.2759410969610.02188202954620.06288795545260.2423597614720.03480223441370.247919948553-8.42021450233150.07684936485.3558308425
140.01333574714620.0221857918235-0.009099505914990.0149313347732-0.006654747087870.00910548821567-0.07324588062040.2434696535030.0114532011362-0.08409548340710.0432728031565-0.001282112688580.1090190491630.032972140366-1.72572672587E-70.247852786980.04678740021170.02192119881490.286484723167-0.0281164874350.228008596878-16.706808318146.07633120291.8850864992
150.00857376875573-0.018390689395-0.01882763419060.00780707682776-0.00262009258327-0.00339619552417-0.0394467657817-0.111670882096-0.01260965740680.29546891854-0.04046887528270.1075694862980.0442105897346-0.1998099878911.79276310243E-70.3960534051180.06972529126320.04584803927220.309324217282-0.05492964878860.324270896417-20.0171988583152.427222069102.102216784
160.0179721551409-0.0162861028758-0.02436044140340.01407756178840.02923914531690.0278097536229-0.0100140294826-0.149611377941-0.04956444988680.0814568534642-0.1670324507070.1305013922680.0876915593069-0.0391890591683-2.4729956474E-80.154412341614-0.02112019552570.01867300387140.132108352254-0.04582712759250.235328751491-10.9092227399139.825034237103.712527376
170.000964418759740.002714619898270.009538246573170.00415470237944-0.005463210723340.00590565811926-0.00161829665946-0.06377638666160.03317508233770.0602481942354-0.0382382321451-0.002607395117910.06611644085980.06534045413446.93039585661E-70.2639620862-0.07883016641190.008723633551620.590556071532-0.04438036672880.3266011093488.56014708086145.7501911111.668524143
180.01018208903060.00339667150676-0.01476448474770.00414594524171-0.00330053717597-0.00187254652454-0.0336672769389-0.07475498739530.0362243657851-0.0785296678249-0.0008380229786860.0770618782138-0.119089388323-0.01842432468727.41887177716E-70.415190807317-0.02171156578350.01758111859480.615265319971-0.04889661544090.39419368338613.7720387647141.923480274103.04560623
190.000960198085815-0.00642883113307-0.00989766169996-0.002916838457480.01032628400080.004935059045750.0285301658048-0.03235760843080.06205872241210.01729381481260.0356826022302-0.06760950650920.01500721670730.1572454558971.67690306068E-60.243791910123-0.06130569806640.04108745214760.224484679964-0.05084090564390.2157314859595.62375029611138.653054823100.229617095
200.017697481549-0.01473889021830.006001500792320.0108087843514-0.007908725510090.0110373547686-0.0529853960654-0.2487865431540.00366914840754-0.0990064252051-0.186031635293-0.1278512127690.1611708279650.0628621374085-2.62681054585E-80.261635878355-0.00319953715648-0.01837872514160.2928316919060.004073186567850.2347920568063.37468808408132.882587564109.745800885
210.001284856216550.00897693482541-0.01202189886650.01336027098110.009058769292370.003985954687770.0648094869955-0.0828869020292-0.0248682572330.0269070792239-0.02158032264320.07255118355480.110819526516-0.057480155933.3874048181E-70.260770771355-0.06928028767540.02101328007510.172829781074-0.007872745890770.173577285415-8.57506406716132.607070787112.590144803
220.01345613387230.002937100114360.008314040077280.01113070771350.009479361006270.00891884257513-0.00418667309372-0.02469355041910.0214065807488-0.05899425677680.00147979578787-0.1163424849340.03808601607410.0602694664385-1.83949314353E-70.34322672471-0.002491746045980.02861080857980.3114712591250.1384175061570.381763056419.6199024147168.44679062823.5123802627
230.02496421205540.02501778084940.01967830973360.0128843498786-0.004869941084190.01155217684350.09378731791420.1487724512620.0191001513201-0.103487039840.0342093855260.096346143751-0.0739776050767-0.04140617157873.53367959558E-80.245925699226-0.05052314608860.001440883957280.3061085118260.1316697740780.31165820065313.0616397094174.23057996518.2586868611
24-0.0570782952480.0898207992180.0227247832475-0.01668238894890.004210283798640.01649048788580.2025072141480.03931093756360.01277525436930.0486307206917-0.01154463736840.116840723602-0.1072761580010.339944368499-5.54341054835E-80.0588273391214-0.6666166726920.360750758138-1.940103053551.58160283821-0.42689871831513.4650545452177.9294299831.2733942584
25-0.00586292255321-0.001434529757260.00297178846316-0.002061195118470.0004090798355150.006594210836210.09963057406610.1581611379250.0604886674085-0.05017642139850.0902844017392-0.04102998735-0.0772030331217-0.0250436577583-2.89392178836E-60.361584063944-0.03787414358170.01549426129640.4418440367030.07288399043820.372413765058-9.3419606914163.20534574133.5591329354
260.02465703385140.04776028083180.04191938199590.00757742344089-0.01968615904110.04417587856690.1091886320880.4312382277060.104800251050.0419545366945-0.00955121199862-0.0921986300860.0627927956925-0.355683122847-6.97523594306E-90.207136897688-0.08527597638370.00815011433031-0.6197573252330.4619344953810.255728309965-2.76525115513174.89525540235.1471905165
270.0302508835175-0.00342062488244-0.007721094733380.01094380531080.01364791223020.01814940978640.01589274638060.119756063362-0.027477512310.002341268805660.01609289311290.008111228372-0.02742308618490.09070103309193.0375913114E-70.293669096299-0.0525737048480.09168740774480.3432431138870.1218620988640.321528217877-5.31799612916163.3076850610.8417830969
280.06850632403780.1020661763660.007041925764660.133296059819-0.0252570336370.0190621529437-0.02514669428150.1361417967980.0531578544878-0.0817650062142-0.149571238123-0.0171819420325-0.02960703733940.0306783384375-1.40785642757E-80.2845231898980.01982374486460.009686895705960.2803539289970.07885286471680.244703632736-14.3315528126163.91583675410.9877896376
29-0.002444925403090.020087563644-0.02724102442260.0206188599099-0.02712853991710.01821643953490.0110551143778-0.06391336530440.1829254831690.025256452397-0.06256802739160.002783071502010.05436889725550.09577198958071.67660356171E-70.2836890209360.0261299150813-0.04851888870930.2150538143160.009523284698560.252562842489-14.4495383224151.93641169723.1289841591
30-0.000178706139814-0.005909926958030.001254918418870.0006146348053680.00333382387540.003300148206-0.02827763067980.05756221858510.0365724886387-0.0804747200507-0.0300195331897-0.0242954422044-0.0026968897782-0.0268624826045-1.97749244757E-60.7699145831030.155920078702-0.2673555456610.446286538974-0.02895135816810.165560133241-8.20270641222134.9430956623.0027073734
310.02342960578-0.02593372351950.02111156096610.0565836280959-0.01811158711250.03322123730440.02731701905710.149151709844-0.01712011707340.0593278458338-0.0581736278869-0.05529294585040.107463747282-0.0638522722503-2.18854610547E-70.2975503400910.00967056560684-0.03095962356560.205865622347-0.02202137997090.173834004491-14.0817160357142.87220588223.3015759188
320.001906370344690.000666411092379-0.003562110955290.00968504679231-0.003786331553930.002848745227390.0226682703455-0.02054616058190.1893071409490.0356470439394-0.1153477893860.133045705865-0.0420772789736-0.06436912762943.55838799885E-70.235477308968-0.0693993436822-0.02992605228860.279095546329-0.001699149519210.283607590381-24.9990688984150.80830814928.6583001931
330.0246490421549-0.0213187786411-0.00389546246636-0.009669743496180.0232151571050.00972861336471-0.02763281284060.0936607706967-0.0915418028532-0.07139718912990.141657045537-0.130641392332-0.2827736746950.1649070185843.41548135264E-80.293259841498-0.0133958621295-0.02393109238230.366887777507-0.0868824971460.226279165674-6.45806303573135.481420832-1.16876020174
340.0811100831193-0.01855910716520.03910763637180.04465575085610.02759746149730.0274136492072-0.1073061279430.2775012303720.0002456536249740.01872265128670.127147128843-0.00561101483214-0.0844762865648-0.2270717047911.5335749637E-80.215376803737-0.016906277969-0.02566864325550.416582874695-0.1031736240040.160324057862-15.8851052566130.5044512041.49751747283
350.01625306294590.00623976880198-0.0176930355083-0.02024453840480.01973183236880.00434760026548-0.0313476478264-0.129066863466-0.08492363739790.0248395072865-0.02508946770810.0936620899550.005458658873530.05268422695326.75455409218E-80.2329535943410.0369544402166-0.03859119083640.333715837428-0.1214536948120.2973457698780.329937725949126.42284665310.946600481
360.0821071251333-0.05000195034320.06633695484010.01671722925430.006902873311810.0693202357150.0139597601692-0.00828806833716-0.137141344149-0.01761526139620.04745856399010.0790202564763-0.03281466620610.268959321937.09878343407E-90.2185972884310.0401805965593-0.0205041382010.493409429637-0.0884793304540.2102692467718.02188855182122.63965752911.3422683675
370.072879707502-0.009805435784960.00606332722890.0412043975943-0.02562062242340.04355672982960.04869369665180.06054162146470.02495125562960.0508205952194-0.03846168886920.01396387027550.009899654742810.02479051337031.37646801198E-70.199881052275-0.039709126871-0.01403272902850.2539059797530.05438736483050.21797940896-10.9096051229154.8390090449.7965669553
380.03892985320270.01110982787980.02558400562520.0247768938481-0.03920435502480.00428936627691-0.01988978313410.0553596919026-0.0225761949178-0.009564345572810.08103195339440.0769010948858-0.11853305555-0.14602850369-2.98194260902E-70.2120797120590.00864283625920.01898945126040.1910906256860.03390434895950.210430186242-21.9042025964159.62858643755.9361566247
390.07166277776750.0356325668426-0.002554406273220.05688064133550.01078298364180.059287986890.0466724289689-0.008255512849450.0633593639841-0.0003680758629930.00423767806947-0.08030673694790.0549728279063-0.00181146233892-1.29463311935E-70.16602698662-0.00843168479688-0.01853609389970.2169132253260.02548179035480.177049301688-7.28299182584141.49918647463.6112401526
400.00711810605756-0.064864464683-0.01191962284180.0453957627616-0.06002619848850.0283932537302-0.0511890133505-0.195098087847-0.0828821472210.09251247962680.04564431868760.03695544264030.2225082596-0.2233258163791.62854531805E-70.161283681096-0.002720770833030.01443272607370.2308086051490.03815033738110.193142155412-15.9635521829136.6319220769.6388951833
410.0190535199893-0.0152169261586-0.001625668202450.029326236714-0.01291111956670.0296083551247-0.02075057394620.181920879047-0.09573075931920.011750750677-0.01801546916160.0352885582193-0.08225536220490.0597347976764-8.02101282365E-80.2639815209340.020845728278-0.002850195391710.433295630647-0.07618673461650.22837167665425.1603317184134.50461991325.5237034038
420.03071212978970.0612436104468-0.04137909942040.0893952417245-0.005345096214560.00549742179815-0.2973023203460.2498152775570.119566985506-0.03638486878880.0581434542117-0.0927989331231-0.1101502787810.209263528564-3.78763169431E-80.1460126399590.08982116003620.1302161429710.29153947422-0.293715731076-0.14449922231930.5187220296127.32129877628.4244977669
430.08523677907320.145870571541-0.03766092639380.07619830567870.005326264136920.0862530504781-0.08408537277850.0951903502435-0.00377465260162-0.02700702229060.07591431162910.0311957735114-0.03256134818620.1464276208691.10572659879E-80.198841536242-0.06169849091010.01247726013210.363559069555-0.01048739342570.19478910911537.2876249794149.71123203336.649532563
440.00516364459033-0.00551530779315-6.98177119277E-50.001033431641010.002753083632690.00831298638830.2841860246330.04513641848320.14789873837-0.1214334534280.1378835261110.1469457115520.0223479486296-0.01769599901312.81303425467E-60.3193876829240.0849693601192-0.163230758550.276562655553-0.01500556381890.220253687927-8.11417372434133.94857946737.4650834635
450.02049471136250.01712281109990.003233594571830.0372218748503-0.00766240335720.009815767170830.1406969247660.04115221432690.008081446353670.05254704059770.07695566817170.166951861560.1648018801240.118768528073-2.66417188728E-90.2582200624750.0998758026527-0.05732101406620.219262456568-0.04043434219160.1315903554896.94861282769131.92308000941.3083451326
460.1127908558770.0274773504867-0.0216884046670.08166652903220.0250170790331-0.003319460656480.163988052689-0.0136237949164-0.263040660166-0.223322251548-0.218280702520.275705322988-0.1073837355840.05796572588032.67602432153E-80.2699397525540.0632080657645-0.05990474860940.157702925466-0.05927819219130.266981812328-4.53217739853125.17649705943.6969056466
470.03443751549-0.01883124636820.03212127122290.0156017268943-0.01428729432550.005811648248990.18787199426-0.00385896509480.0269944554326-0.0405652962358-0.3167884238840.0190371992485-0.01526929736240.158310009227-1.12412120174E-70.1515403421450.0773525516001-0.02527619190280.039759287666-0.1052803776010.11781466900512.5869708355128.46101606552.8200712794
48-0.0135264227950.007965565235220.0006607856252370.02232115100660.0010553221675-0.01666385879530.09007452514270.01284986933210.0453125037659-0.1709099606230.0244012537382-0.06960414190090.06890472578910.05538988454412.98257685996E-70.2674724220820.06195204910120.05158533383180.400778225703-0.0403118458440.1407366708425.8111892813136.68094483450.0043703185
490.0213794143833-0.03266670769810.003261664279940.006911873279620.03160753335870.03300250988680.3100545744460.1338969658040.1118239422330.0174011712489-0.1586265151410.05309145736960.1076867030880.2124395037072.93948639066E-80.1647027232180.09587604202490.0352843457736-0.0741056843229-0.372771790769-0.53146106740619.5418283394124.1576793554.154947287
500.02277675343280.004362344647680.03091961168540.05658958557910.0482863541551-0.0066697701374-0.115791312876-0.03456640336290.09951294023520.0822590467150.0880761809206-0.054553602945-0.07982067245530.2150987808591.87979921183E-70.215379271084-0.0714042868198-0.02164909396290.1645472751980.06851374283860.28030037214729.0354882849167.92118909650.4357155293
510.004540081740730.006403167406460.0220622929923-0.009946382718620.02041601407020.00249923303208-0.07898123741060.0206515484286-0.04322980039440.0432728129767-0.1067768604990.00856262409745-0.0448904217576-0.09593893202963.73653765164E-80.306545467851-0.0728612460512-0.02420636352520.1683749330440.06073925225880.34244268624919.2294199768169.82859537743.6515108742
520.008543884037220.00383290383173-0.004452991382930.04840231750950.05515592283950.0258171613533-0.194732184648-0.0136734212510.350791858411-0.0314110893032-0.0009912394056-0.217811504278-0.2009502448210.07894010825271.5350254142E-80.337497487255-0.126821493103-0.127168174196-0.0006044322946050.1120355282870.58657286020430.31989717180.80526038751.8018309163
530.0102984489827-0.0022081871257-0.02211123799730.0236623405393-0.01592115721720.0191336170113-0.0783391614748-0.1893713260280.1448860229620.1263874192550.2427495757740.105623944641-0.0462884432098-0.254485927576-9.86888501908E-80.4256407647080.0923124396333-0.0078229462590.4150822024320.01852592212060.4727338784429.18260946865175.31781054964.1924342722
542.18892621356E-50.004148063156550.003972927345150.0035518903879-0.00174557649793-0.00326268044958-0.07283620523590.0136520754789-0.0281144087937-0.0177152599745-0.165069038431-0.01489807673480.0208127769966-0.007703914072097.69878426394E-70.602796436447-0.0575587552830.0006091218428330.5640292775920.04893881295060.744511142534-0.0412810832501168.04058583558.511609212
550.002363538836940.010881449312-0.02287293852110.0130476252072-0.01168610398180.00753184456951-0.251352354737-0.388800166390.251875977958-0.2030197391640.264035538183-0.08312612735180.0309861706421-0.2759105997631.51763827332E-90.4129831643060.125760004525-0.04371414979320.19086094273-0.09869754049050.3795654918997.58883961306183.22682484161.0535695189
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 'C' and (resid 1 through 25 )CA1 - 251 - 25
22chain 'C' and (resid 26 through 68 )CA26 - 6826 - 68
33chain 'C' and (resid 69 through 101 )CA69 - 10169 - 101
44chain 'C' and (resid 102 through 149 )CA102 - 149102 - 149
55chain 'C' and (resid 150 through 184 )CA150 - 184150 - 184
66chain 'B' and (resid 1 through 13 )BB1 - 131 - 13
77chain 'B' and (resid 14 through 25 )BB14 - 2514 - 25
88chain 'B' and (resid 26 through 79 )BB26 - 7926 - 79
99chain 'B' and (resid 80 through 91 )BB80 - 9180 - 91
1010chain 'B' and (resid 92 through 138 )BB92 - 13892 - 138
1111chain 'B' and (resid 139 through 182 )BB139 - 182139 - 182
1212chain 'D' and (resid 2 through 40 )DC2 - 401 - 39
1313chain 'D' and (resid 41 through 50 )DC41 - 5040 - 49
1414chain 'D' and (resid 51 through 68 )DC51 - 6850 - 67
1515chain 'D' and (resid 69 through 88 )DC69 - 8868 - 87
1616chain 'D' and (resid 89 through 111 )DC89 - 11188 - 110
1717chain 'D' and (resid 112 through 123 )DC112 - 123111 - 122
1818chain 'D' and (resid 124 through 138 )DC124 - 138123 - 137
1919chain 'D' and (resid 139 through 149 )DC139 - 149138 - 148
2020chain 'D' and (resid 150 through 168 )DC150 - 168149 - 167
2121chain 'D' and (resid 169 through 185 )DC169 - 185168 - 184
2222chain 'H' and (resid 1 through 22 )HD1 - 221 - 22
2323chain 'H' and (resid 23 through 61 )HD23 - 6123 - 61
2424chain 'H' and (resid 62 through 114 )HD62 - 11462 - 114
2525chain 'H' and (resid 115 through 124 )HD115 - 124115 - 124
2626chain 'H' and (resid 125 through 175 )HD125 - 175125 - 175
2727chain 'G' and (resid 1 through 22 )GE1 - 221 - 22
2828chain 'G' and (resid 23 through 85 )GE23 - 8523 - 85
2929chain 'G' and (resid 86 through 114 )GE86 - 11486 - 114
3030chain 'G' and (resid 115 through 124 )GE115 - 124115 - 124
3131chain 'G' and (resid 125 through 161 )GE125 - 161125 - 161
3232chain 'G' and (resid 162 through 175 )GE162 - 175162 - 175
3333chain 'F' and (resid 2 through 36 )FF2 - 361 - 32
3434chain 'F' and (resid 37 through 85 )FF37 - 8533 - 81
3535chain 'F' and (resid 86 through 114 )FF86 - 11482 - 110
3636chain 'F' and (resid 115 through 175 )FF115 - 175111 - 169
3737chain 'K' and (resid 0 through 46 )KG0 - 461 - 47
3838chain 'K' and (resid 47 through 84 )KG47 - 8448 - 85
3939chain 'K' and (resid 85 through 140 )KG85 - 14086 - 141
4040chain 'K' and (resid 141 through 178 )KG141 - 178142 - 179
4141chain 'I' and (resid -1 through 36 )IH-1 - 361 - 35
4242chain 'I' and (resid 37 through 85 )IH37 - 8536 - 84
4343chain 'I' and (resid 86 through 175 )IH86 - 17585 - 168
4444chain 'J' and (resid 1 through 12 )JI1 - 121 - 12
4545chain 'J' and (resid 13 through 36 )JI13 - 3613 - 36
4646chain 'J' and (resid 37 through 85 )JI37 - 8537 - 85
4747chain 'J' and (resid 86 through 114 )JI86 - 11486 - 114
4848chain 'J' and (resid 115 through 130 )JI115 - 130115 - 128
4949chain 'J' and (resid 131 through 176 )JI131 - 176129 - 174
5050chain 'A' and (resid 1 through 25 )AJ1 - 251 - 25
5151chain 'A' and (resid 26 through 50 )AJ26 - 5026 - 50
5252chain 'A' and (resid 51 through 101 )AJ51 - 10151 - 101
5353chain 'A' and (resid 102 through 127 )AJ102 - 127102 - 127
5454chain 'A' and (resid 128 through 138 )AJ128 - 138128 - 138
5555chain 'A' and (resid 139 through 182 )AJ139 - 182139 - 182

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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