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- PDB-7orb: Crystal structure of the L452R mutant receptor binding domain of ... -

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基本情報

登録情報
データベース: PDB / ID: 7orb
タイトルCrystal structure of the L452R mutant receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-75 and COVOX-253 Fabs
要素
  • (COVOX-253 Fab ...) x 2
  • (COVOX-75 Fab ...) x 2
  • Spike protein S1
キーワードVIRAL PROTEIN / SARS-CoV-2 B.1.1.7 variant / B.1.351 variant / P.1 variant / B.1.617 variant / antibody / receptor-binding-domain / spike / neutralisation / VIRAL PROTEIN/IMMUNE SYSTEM
機能・相同性
機能・相同性情報


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
類似検索 - 分子機能
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
類似検索 - ドメイン・相同性
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Spike glycoprotein
類似検索 - 構成要素
生物種Severe acute respiratory syndrome coronavirus 2 (ウイルス)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.5 Å
データ登録者Zhou, D. / Ren, J. / Stuart, D.I.
資金援助 英国, 中国, 2件
組織認可番号国
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 英国
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 中国
引用ジャーナル: Cell / 年: 2021
タイトル: Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum.
著者: Liu, C. / Ginn, H.M. / Dejnirattisai, W. / Supasa, P. / Wang, B. / Tuekprakhon, A. / Nutalai, R. / Zhou, D. / Mentzer, A.J. / Zhao, Y. / Duyvesteyn, H.M.E. / Lopez-Camacho, C. / Slon-Campos, ...著者: Liu, C. / Ginn, H.M. / Dejnirattisai, W. / Supasa, P. / Wang, B. / Tuekprakhon, A. / Nutalai, R. / Zhou, D. / Mentzer, A.J. / Zhao, Y. / Duyvesteyn, H.M.E. / Lopez-Camacho, C. / Slon-Campos, J. / Walter, T.S. / Skelly, D. / Johnson, S.A. / Ritter, T.G. / Mason, C. / Costa Clemens, S.A. / Gomes Naveca, F. / Nascimento, V. / Nascimento, F. / Fernandes da Costa, C. / Resende, P.C. / Pauvolid-Correa, A. / Siqueira, M.M. / Dold, C. / Temperton, N. / Dong, T. / Pollard, A.J. / Knight, J.C. / Crook, D. / Lambe, T. / Clutterbuck, E. / Bibi, S. / Flaxman, A. / Bittaye, M. / Belij-Rammerstorfer, S. / Gilbert, S.C. / Malik, T. / Carroll, M.W. / Klenerman, P. / Barnes, E. / Dunachie, S.J. / Baillie, V. / Serafin, N. / Ditse, Z. / Da Silva, K. / Paterson, N.G. / Williams, M.A. / Hall, D.R. / Madhi, S. / Nunes, M.C. / Goulder, P. / Fry, E.E. / Mongkolsapaya, J. / Ren, J. / Stuart, D.I. / Screaton, G.R.
履歴
登録2021年6月4日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02021年7月7日Provider: repository / タイプ: Initial release
改定 1.12021年7月21日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22021年8月18日Group: Database references / カテゴリ: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.32024年1月31日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entity_branch_descriptor / pdbx_initial_refinement_model

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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
R: Spike protein S1
H: COVOX-253 Fab heavy chain
L: COVOX-253 Fab light chain
A: COVOX-75 Fab heavy chain
B: COVOX-75 Fab light chain
X: Spike protein S1
C: COVOX-253 Fab heavy chain
D: COVOX-253 Fab light chain
E: COVOX-75 Fab heavy chain
F: COVOX-75 Fab light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)243,81344
ポリマ－237,77910
非ポリマー6,03334
水7,512417
1
R: Spike protein S1
H: COVOX-253 Fab heavy chain
L: COVOX-253 Fab light chain
A: COVOX-75 Fab heavy chain
B: COVOX-75 Fab light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)121,70520
ポリマ－118,8905
非ポリマー2,81515
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
2
X: Spike protein S1
C: COVOX-253 Fab heavy chain
D: COVOX-253 Fab light chain
E: COVOX-75 Fab heavy chain
F: COVOX-75 Fab light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)122,10824
ポリマ－118,8905
非ポリマー3,21819
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)93.239, 149.425, 115.040
Angle α, β, γ (deg.)90.000, 92.025, 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 "B" and (resid 1 through 3 or resid 5...
d_2ens_1(chain "D" and (resid 1 through 3 or resid 5...
d_3ens_1(chain "L" and (resid 1 through 3 or resid 5...
d_1ens_2(chain "C" and (resid 1 through 45 or resid 47 through 224 or resid 300 through 401))
d_2ens_2(chain "H" and (resid 1 through 45 or resid 47 through 224 or resid 300 through 401))
d_1ens_3(chain "R" and (resid 333 through 345 or resid 347 through 516 or resid 600 through 702))
d_2ens_3(chain "X" and (resid 333 through 345 or resid 347 through 516 or resid 600 through 702))

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel seq-ID
d_11ens_1ASPGLNB1 - 3
d_12ens_1THRPROB5 - 8
d_13ens_1SERSERB12
d_14ens_1SERSERB14
d_15ens_1GLYGLYB16
d_16ens_1THRTHRB20
d_17ens_1CYSGLNB23 - 27
d_18ens_1SERSERB31
d_19ens_1LEUGLYB33 - 41
d_110ens_1ALAPROB43 - 44
d_111ens_1LEUTYRB46 - 49
d_112ens_1SERSERB52 - 53
d_113ens_1GLYGLYB57
d_114ens_1PROPROB59
d_115ens_1ARGSERB61 - 76
d_116ens_1LEULEUB78
d_117ens_1PROALAB80 - 84
d_118ens_1TYRGLNB86 - 90
d_119ens_1SERSERB93
d_120ens_1PROPROB95
d_121ens_1THRGLYB97 - 99
d_122ens_1GLYLEUB101 - 125
d_123ens_1SERSERB127 - 162
d_124ens_1THRALAB164 - 193
d_125ens_1GLUGLYB195 - 212
d_21ens_1ASPGLND1 - 3
d_22ens_1THRPROD5 - 8
d_23ens_1SERSERD12
d_24ens_1SERSERD14
d_25ens_1GLYGLYD16
d_26ens_1THRTHRD20
d_27ens_1CYSGLND23 - 27
d_28ens_1SERSERD31
d_29ens_1LEUGLYD34 - 42
d_210ens_1ALAPROD44 - 45
d_211ens_1LEUTYRD47 - 50
d_212ens_1SERSERD53 - 54
d_213ens_1GLYGLYD58
d_214ens_1PROPROD60
d_215ens_1ARGSERD62 - 77
d_216ens_1LEULEUD79
d_217ens_1PROALAD81 - 85
d_218ens_1TYRGLND87 - 91
d_219ens_1SERSERD94
d_220ens_1PROPROD96
d_221ens_1THRGLYD98 - 100
d_222ens_1GLYLEUD102 - 126
d_223ens_1SERSERD128 - 163
d_224ens_1THRALAD165 - 194
d_225ens_1GLUGLYD196 - 213
d_31ens_1ASPGLNL1 - 3
d_32ens_1THRPROL5 - 8
d_33ens_1SERSERL12
d_34ens_1SERSERL14
d_35ens_1GLYGLYL16
d_36ens_1THRTHRL20
d_37ens_1CYSGLNL23 - 27
d_38ens_1SERSERL31
d_39ens_1LEUGLYL34 - 42
d_310ens_1ALAPROL44 - 45
d_311ens_1LEUTYRL47 - 50
d_312ens_1SERSERL53 - 54
d_313ens_1GLYGLYL58
d_314ens_1PROPROL60
d_315ens_1ARGSERL62 - 77
d_316ens_1LEULEUL79
d_317ens_1PROALAL81 - 85
d_318ens_1TYRGLNL87 - 91
d_319ens_1SERSERL94
d_320ens_1PROPROL96
d_321ens_1THRGLYL98 - 100
d_322ens_1GLYLEUL102 - 126
d_323ens_1SERSERL128 - 163
d_324ens_1THRALAL165 - 194
d_325ens_1GLUGLYL196 - 213
d_11ens_2GLNLEUC1 - 45
d_12ens_2TRPLYSC47 - 219
d_13ens_2FUCFUCK
d_14ens_2NAGNAGK
d_15ens_2NAGNAGK
d_21ens_2GLNLEUH1 - 45
d_22ens_2TRPLYSH47 - 219
d_23ens_2FUCFUCI
d_24ens_2NAGNAGI
d_25ens_2NAGNAGI
d_11ens_3THRTHRR2 - 14
d_12ens_3PHEGLUR16 - 185
d_13ens_3FUCFUCG
d_14ens_3NAGNAGG
d_15ens_3NAGNAGG
d_16ens_3BMABMAG
d_21ens_3THRTHRX1 - 13
d_22ens_3PHEGLUX15 - 184
d_23ens_3FUCFUCJ
d_24ens_3NAGNAGJ
d_25ens_3NAGNAGJ
d_26ens_3BMABMAJ

NCSアンサンブル:
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixベクター
1given(0.0397443543125, -0.518278706158, -0.85428775541), (0.747466356071, 0.582803875273, -0.318800391324), (0.663109668789, -0.625880839865, 0.410559059635)-12.1821581268, -20.0873455804, 54.8038184461
2given(-0.0393972562223, 0.516699011843, 0.855260186939), (-0.744731461299, -0.58584409381, 0.319627514928), (0.66620035031, -0.624346721709, 0.407882660012)-34.3094949044, 20.6326702404, 54.8004206694
3given(-0.999997752018, -0.00159666361347, 0.00139521475503), (0.00160143085217, -0.999992861141, 0.0034224387721), (0.00138974031133, 0.00342466541847, 0.999993170121)-46.6559008608, 0.390092394799, 0.0603829155069
4given(-0.999937821641, 0.00996265634159, 0.00500982348177), (-0.0099409797036, -0.999941198109, 0.00433327218936), (0.00505269979633, 0.00428320020005, 0.99997806197)-47.0432028268, 0.237541580187, -0.0638984804296

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要素

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タンパク質 , 1種, 2分子 RX

#1: タンパク質 Spike protein S1


分子量: 23194.926 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Severe acute respiratory syndrome coronavirus 2 (ウイルス)
遺伝子: S, 2 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P0DTC2

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抗体 , 4種, 8分子 HCLDAEBF

#2: 抗体 COVOX-253 Fab heavy chain


分子量: 24371.400 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#3: 抗体 COVOX-253 Fab light chain


分子量: 23256.641 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#4: 抗体 COVOX-75 Fab heavy chain


分子量: 24821.846 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#5: 抗体 COVOX-75 Fab light chain


分子量: 23244.861 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)

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糖 , 4種, 4分子

#6: 多糖 alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 1056.964 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#7: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 570.542 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#8: 多糖 alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 894.823 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#9: 多糖 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 732.682 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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非ポリマー , 7種, 447分子

#10: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 16 / 由来タイプ: 合成 / 式: C3H8O3
#11: 化合物
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / ジエチレングリコ-ル


分子量: 106.120 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C4H10O3
#12: 化合物
ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Cl
#13: 化合物 ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / トリス(ヒドロキシメチル)メチルアンモニウム


分子量: 122.143 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C4H12NO3 / コメント: pH緩衝剤*YM
#14: 化合物 ChemComp-PO4 / PHOSPHATE ION / ホスファ-ト


分子量: 94.971 Da / 分子数: 3 / 由来タイプ: 合成 / 式: PO4
#15: 化合物 ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / ビストリス


分子量: 209.240 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C8H19NO5 / コメント: pH緩衝剤*YM
#16: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 417 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかN

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.37 Å3/Da / 溶媒含有率: 63.48 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 0.1 M BIS-TRIS pH 6.5 and 16% (w/v) PEG 10000

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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: 0.97628 Å
検出器タイプ: DECTRIS EIGER2 XE 16M / 検出器: PIXEL / 日付: 2021年4月30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: 0.97628 Å / 相対比: 1
反射解像度: 2.5→75 Å / Num. obs: 108845 / % possible obs: 99.8 % / 冗長度: 28.1 % / Biso Wilson estimate: 54.63 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.3 / Rpim(I) all: 0.058 / Net I/σ(I): 5.6
反射 シェル解像度: 2.5→2.58 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 5144 / CC1/2: 0.609

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19_4092精密化
GDA1.19_4092データ収集
xia2データ削減
xia2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
開始モデル: 7BEN

7ben


解像度: 2.5→73.67 Å / SU ML: 0.4227 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 27.743
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2513 5504 5.08 %
Rwork0.2128 102853 -
obs0.2148 108357 99.31 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 65.47 Å2
精密化ステップサイクル: LAST / 解像度: 2.5→73.67 Å
タンパク質核酸リガンド溶媒全体
原子数16134 0 391 417 16942
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.002416908
X-RAY DIFFRACTIONf_angle_d0.559522981
X-RAY DIFFRACTIONf_chiral_restr0.04292608
X-RAY DIFFRACTIONf_plane_restr0.0042915
X-RAY DIFFRACTIONf_dihedral_angle_d12.28016118
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2DX-RAY DIFFRACTIONTorsion NCS1.50051822445
ens_1d_3LX-RAY DIFFRACTIONTorsion NCS1.46293208506
ens_2d_2HX-RAY DIFFRACTIONTorsion NCS0.288943806319
ens_3d_2XX-RAY DIFFRACTIONTorsion NCS0.47660012684
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.36941390.35462805X-RAY DIFFRACTION80.75
2.53-2.550.37371990.3543418X-RAY DIFFRACTION99.81
2.55-2.590.40121910.34283428X-RAY DIFFRACTION99.92
2.59-2.620.38871600.33513456X-RAY DIFFRACTION99.94
2.62-2.650.34972000.31683422X-RAY DIFFRACTION99.92
2.65-2.690.34161750.30093459X-RAY DIFFRACTION99.92
2.69-2.730.33892040.28813402X-RAY DIFFRACTION99.92
2.73-2.770.32111910.283402X-RAY DIFFRACTION99.94
2.77-2.810.30281880.26673470X-RAY DIFFRACTION99.97
2.81-2.860.32261700.26053454X-RAY DIFFRACTION99.92
2.86-2.910.26791490.25113471X-RAY DIFFRACTION99.92
2.91-2.960.3091640.24823447X-RAY DIFFRACTION100
2.96-3.020.30391610.2493487X-RAY DIFFRACTION99.97
3.02-3.080.29461840.24663433X-RAY DIFFRACTION100
3.08-3.150.26331850.24613443X-RAY DIFFRACTION99.94
3.15-3.220.31312030.24363432X-RAY DIFFRACTION100
3.22-3.30.30152080.23183409X-RAY DIFFRACTION100
3.3-3.390.26821550.22393472X-RAY DIFFRACTION99.97
3.39-3.490.24051800.21413466X-RAY DIFFRACTION99.97
3.49-3.60.23451690.21143475X-RAY DIFFRACTION100
3.6-3.730.26481870.20273466X-RAY DIFFRACTION100
3.73-3.880.24492110.20013387X-RAY DIFFRACTION99.97
3.88-4.060.22891620.18873486X-RAY DIFFRACTION100
4.06-4.270.20882100.17613436X-RAY DIFFRACTION99.97
4.27-4.540.20181920.16093442X-RAY DIFFRACTION100
4.54-4.890.20062230.1593432X-RAY DIFFRACTION100
4.89-5.380.18881920.15643453X-RAY DIFFRACTION100
5.38-6.160.23051740.18123472X-RAY DIFFRACTION100
6.16-7.760.21711890.20743500X-RAY DIFFRACTION100
7.76-73.670.23971890.21123528X-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)
13.43248610052-0.551010083041-1.41904373014.01421050387-1.212987988536.47272491390.0451275731220.567677831022-0.256494285935-0.634625187929-0.434891231056-0.296203242130.253376063550.8755324237780.4338804973160.472731552482-0.07777631963140.06886801728840.6236939214750.08023611491290.82792963688420.91636.04524.121
21.708210954130.853409046077-0.1774812182874.68234747979-1.407799409664.21536641988-0.00113883210788-0.2547912586110.5377248832140.2455989945-0.385313082668-0.350826608405-0.6354849713510.5590579702640.2689812374280.577198212429-0.195056326455-0.06247138630850.506966873407-0.0188928150020.82928179883315.38143.64530.061
31.007217433730.5514921576580.03339933497641.85128731167-1.729406878322.284462925030.207278006976-0.273781973053-0.1808750897410.251030494811-0.218452109926-0.0101883272679-0.1289240235480.4088417223150.1717164146330.475930591094-0.136403064580.0413782599350.436381653-0.06885331261050.6632181818285.08324.15340.214
43.005452263811.28300625297-0.2832721108883.66255782589-0.0007897231371192.86118062108-0.5298825672240.4512484705690.4370976032940.2045671166220.03936310897450.331758902179-0.6402302311450.2750364149260.202322958180.503793648336-0.0456065393654-0.01957730860590.315925273277-0.03809917674550.7804351315566.38436.75726.274
58.260623699361.456621790441.376865270551.489928021940.02643050421174.82727801923-0.208252466080.3514445153391.05232816409-0.1898974832290.3801064624330.0249711847953-0.95144275894-0.104085180946-0.1699178086050.602437762452-0.09665760030860.1434322426580.3686879602810.09816367521140.771317503517-27.4428.48438.669
63.76133061804-1.94856938173-0.01996589927741.01749538314-0.1846824818735.54751220074-0.157510442327-0.007128493396071.04991643606-0.4016577865330.1592922209730.0811106151807-0.308940017785-0.02901394725320.05752259671950.449079061656-0.06619109860230.1316433927560.3412302855960.01123547368050.677195383298-19.04322.47842.947
76.37757423153-0.7791408658780.8337259199480.833708560943-0.7844593617514.16743100830.05560373014720.3573454526190.405041110712-0.0352949316663-0.0174446550262-0.04065573267-0.205967495239-0.1961365731-0.07759289002940.481157352274-0.1006857808040.1011405141010.309785967337-0.003172950325150.54408027019-18.32922.69339.96
83.93832626005-1.19375272688-0.3748224803251.560742498271.44167448483.954927203960.1362522910320.1625816931721.345294415110.1110938752420.2627700235550.508635748271-0.3324705843470.248982537782-0.4289935953520.566553674127-0.07132096053650.09793985118250.464016889380.05496021080170.948947769312-51.22623.90447.147
94.11321359201-1.3586952207-0.01401564123213.650533171781.815675170497.17493470723-0.01891043776880.001620866890850.850156385840.205663324438-0.1570214947930.538382554763-0.872555091112-0.5009619626580.05917744759760.6417510193020.005925147604540.1424179034120.468252118985-0.08702500656521.02330500504-55.76328.90651.734
107.34978004025-0.737189609273-2.092215143212.94897914553-0.4699187038780.6947666107680.0883225228502-0.365937382122-0.106836687740.298767207582-0.125975186389-0.241506496871-0.02802201960930.0699263458401-0.03386372225420.495005630875-0.0461763054058-0.04256979155040.4432946902590.009043160522480.391262349456-21.9375.25157.688
114.12690417133-1.376419303380.1851570557772.21875314221-0.06802822563294.18335506008-0.0160566922131-0.7189615192130.4686125144470.7271155760980.01968345981770.0141685855118-0.310698244787-0.118438191759-0.03921211536050.5667974374-0.2164986759850.1049315725040.492454837562-0.1390218270430.504734438132-17.87415.05960.102
127.89090366664-0.191306732031-0.06926817310611.08426259614-0.4594123075760.225898160498-0.0531788517941-0.5154172389480.9555604529260.1767324024490.03290136727270.206734430313-0.295209747321-0.05857133274260.07119315578170.503026995655-0.07837874662010.1171875107260.457870092588-0.1446889628180.681490673364-37.12113.82755.451
136.958870968690.4191650274242.833918158621.26052300555-0.8342258341096.91872658354-0.0355117171521-0.1229822904890.09095204573590.1219354656260.2399619686780.466384706039-0.0499908496596-0.31159784747-0.1946014110670.4261640110330.004851358829160.1258758884120.44321395017-0.06566351495080.787698189491-56.1118.90451.102
142.524025034812.041043170770.7694839024242.915250057982.160347226832.57411513980.222831076459-0.2957605768510.2248710100190.217266898379-0.07862407349540.739067526531-0.128860124167-0.852871008477-0.248854530990.3107893816860.07569627401450.06772498916340.418768835908-0.01034980667290.651248556989-17.7847.9322.609
156.11118807182.578938808544.208083967075.243013040842.382474630982.95807147360.430872117811-1.016401208570.3222035660640.867752045865-0.8151423123091.187023079680.600410369716-1.03102244330.3904737493140.450592025604-0.0889793880460.1044857930660.489367050467-0.166272038930.633992455699-16.07510.53616.14
165.00445623321-0.12305397339-0.09533461863043.659987776791.838466320657.69341296552-0.0441981410182-0.113435505030.407233199708-0.202577932691-0.2854520954330.895930771091-0.57134830774-0.4526290925280.1249232517110.340945015524-0.0128911404908-0.02620474045990.308595472663-0.1093847885110.612664167319-13.3417.4088.196
171.016163127191.512864389822.719815489031.593924831582.881916685276.748299788660.0141694436222-0.04701417407750.110303390943-0.0249218786814-0.00212418777690.0501676897897-0.281996452955-0.2448174895330.1096565958320.2772178655180.03797480421310.003074448431720.350460247295-0.04897977597140.516404204573-9.66412.3146.493
184.88929928322-1.06002770704-1.049388682014.423950631730.6560766672733.87839345140.1575616325740.699398710083-0.307503122562-0.274461066287-0.151630248305-0.7180563925580.4869866480510.3920276058610.01069969240470.3222895431910.0703501321653-0.02736132335330.4253691039-0.1072753412810.479426199175-4.006-10.314-17.602
192.0216292242-4.48491193094-5.779770010676.380467451542.915105108633.07482926849-0.06859367532490.293514203598-2.1186424244-0.0146936413123-0.4429031853130.00831190268836-0.02841553307290.115224904356-0.3112328181140.5440712806730.0744842488886-0.04123803374220.599390773058-0.1182798309460.373808802172-12.677-13.381-17.665
201.19162207863-0.033142533754-1.212924622164.676735800180.8347880122663.890694125080.1128996629930.398216297664-0.236216958184-0.3576459617990.003244755139890.0992698444435-0.2232418144450.598784614732-0.1566027850350.301500552811-0.083229069877-0.05599123473330.453987483578-0.01897843669310.52559649352813.4599.3194.106
212.66357201699-1.37278703517-0.6795255204745.429528714740.844958730433.445837213410.104341486977-0.1059056746090.1562218139360.01238135336570.0709340865927-0.727665756978-0.2954908212180.529653593061-0.189278346210.295648634988-0.05000312961890.002344843300690.417798488262-0.08498443509760.4849870840318.43410.82812.898
226.02592048694-4.98046275962-0.9782816706145.21187756786-0.692237790582.978113900540.1629292491620.531136185106-0.2208806866050.275116665739-0.2974267582150.8196740335290.4016721847280.1545401959210.03724739624960.442439601701-0.0245876618415-0.07854644510920.393998528047-0.1603893849820.6422127686129.0553.3448.564
234.55571499177-0.13281223137-0.6529765450313.279071540222.016049279882.39511125767-0.20191746549-0.0322262611286-0.1426780281110.1815417271330.5905923625090.07537631157880.06754438458630.889403300012-0.3557778301640.3485672981770.00307268204344-0.08801699580860.46250431619-0.02535461566550.347344216958.5947.4811.399
249.30070736139-3.681576253823.022032732535.46289025056-0.2611272349829.017059064660.6382334054841.83635116444-1.04410808721-0.750652013744-0.179671808158-0.1067327043760.6954562001440.0167993766862-0.199545478770.422727078216-0.02064449440910.09134777449790.889664914607-0.2056214999830.467417337004-2.842-7.726-28.775
255.03959223161-1.347760095952.055189380473.727726247810.3493615258428.03558354617-0.08362037105930.6770956326981.06366036923-0.1767977766750.346424838337-0.7762823655690.18367977190.642124403557-0.1555022086440.3525014910160.01311284567290.06588904124880.743316642532-0.07097516755480.5721523767898.205-1.746-19.95
263.490993536422.409123022782.517062397316.94536634096-0.7408012443056.82103769095-0.05843301619151.030380635731.13844658322-0.9395306815920.116685605686-0.513296130033-0.7700105051741.462864067060.2059617025240.557263271469-0.03701201063250.09736089644250.8767926370310.2138105336160.9337971207215.0884.469-25.389
274.57386620486-0.2565888531160.656676479512.03083363427-0.2853446174393.264789410170.1314474783741.201560796940.028266833689-0.2384456474350.269913183461-0.22770009432-0.3980648281190.759324506834-0.3038205604110.4283391897670.05400219374180.09168713893321.04528304628-0.1317946878360.606375471476.941-3.859-24.553
282.369515542781.476743883970.2897570789835.664964808521.916937715762.92978937971-0.032421181610.131641232101-0.130949358324-0.681176377369-0.4208192528910.848645959071-0.0563637449109-0.6533791463390.5372928101960.526635548565-0.1059299792480.07332520954680.563976281442-0.0948195017560.924331432866-67.221-40.08624.015
293.105088805751.249230175580.3419405591353.963551955651.810425741552.96301681684-0.0056970075981-0.120906561327-0.8185169054980.350507911287-0.3821316582710.2106603714230.661120948693-0.4709873474180.1810607189180.583522815677-0.2106712880.131732136860.47129296964-0.02676930231170.850590121014-59.753-42.98432.38
303.008572824381.5040500025-0.9914895798862.031345650460.3644064741522.470466662620.279224217167-0.2852423292720.03620201410850.121680924064-0.2611401847340.1093764919220.290340151097-0.5523874635310.01910533524820.384499224578-0.05767492505940.07128475576090.321783842830.04540935632850.686687378021-53.501-25.939.248
312.41232508793-0.221422782937-0.2148712615380.1742385609030.1381067952854.50255521786-0.261926050929-0.0903043891346-0.07432320268180.0450834065999-0.1335430880740.4650063972790.2229111207160.171150186430.1521994686770.37301491614-0.1013489295160.0777246559840.2705020626740.03174731411080.696022230585-50.518-29.19233.116
326.631687367671.29369529032-0.7173585590292.4597347062-0.1901073135614.60654412614-0.254763140590.294467838146-0.851382750213-0.1407505604730.08983388922520.3880874047670.776839650056-0.1697839932720.1198271589180.459412990567-0.08428002900890.01602921234830.26821829741-0.05546462164380.63411061496-25.15-27.13741.14
338.247602310391.59541961584-0.7822697701924.84380378599-1.694144296854.81656593703-0.06924948542070.5212780309240.0125736501903-0.02891836476450.01994216315910.288585949269-0.01667344216750.355803412447-0.06541281331140.442585051002-0.102246231268-0.01614400409210.354960786778-0.01064656861040.436440841461-28.985-19.85437.529
345.836160227550.7855793399810.6485020130271.444506133820.1160572242410.655809570679-0.01848660915330.551701899149-0.1940428943230.1342609932620.0820272387206-0.171313638976-0.04788535031610.1309630560380.1036424777310.476865154951-0.0885251671019-0.000909503406750.34428297946-0.007086881984620.539869920794-16.147-22.68343.918
357.494306147991.20428353813-1.042424368572.41553035248-1.031258009465.16319894166-0.0908882728098-0.545105533277-1.246046058490.1224976023830.122497475068-0.4923113032010.705203755987-0.286924161227-0.03518755979990.509505148821-0.0191150827763-0.0008035572259840.4791386629120.110239742170.7862628653436.25-25.79150.255
363.661764179250.6459416792362.637282497052.9346483115-1.006295363712.50776591516-0.385266566918-0.731950127724-0.5954119730250.3118830093660.8788177127280.122145183853-0.78324959292-0.260179459746-0.135558146280.4903106621810.02373252565440.04032842117640.652899432044-0.06647889040050.537117315116-20.719-5.66659.023
374.926958547761.34178626986-0.5567098185512.415631116710.6137039419841.968098333850.303876880098-0.348046114908-0.04450503034930.27262429158-0.2740169832240.1631801606940.07940524011330.0226955308235-0.07657542951080.396793027339-0.1083527522860.03789396298690.3666480549660.0348953569370.369397181313-27.634-12.08956.038
385.381483826550.9366938182090.2609562615431.908371681180.5230841600592.354882186530.0833471995094-0.874966824771-0.6454058748460.8593174358130.1467348557220.7076624171930.138189875643-0.200242677833-0.05590574508610.648750252926-0.1044123850290.0746658287620.616893558630.06235737427940.470835327319-30.926-12.58563.37
397.212186451320.909162927448-0.936966532621.940344002620.6105277497470.6459727901080.312027451054-0.732521936174-1.704338274150.432568688677-0.253070468040.2880336478090.5149630460390.777715373760.07775549835530.556832694324-0.103970022874-0.01539532005730.5440174125520.1564508599670.648077795529-20.923-14.34162.202
406.85124497135-0.0576310000377-0.8102246960311.225229003110.5743908985140.947684991496-0.0360978338448-0.589942379066-0.4060892423350.1996093657260.05285977088440.157600191858-0.03673915278310.3027658847290.05522857847920.447881386126-0.165392629412-0.009128063027160.4499982630350.06941014065530.430278133551-17.784-9.22556.476
417.886146852710.393000163892-1.354008737883.046952203770.4908794407383.199593001050.093819459440.488672407233-1.8267111995-0.1700512075690.387648676188-0.7671013503880.5547038783220.4294346940440.2209252646330.459053541677-0.04737456813790.08330805876990.701883018713-0.1029981998781.2151679085116.134-18.13846.147
428.031605004620.331122618444-3.559509287293.674498741041.010361645117.235419375140.179772269556-0.1394483100640.3451670141030.4694707848530.1814900398-0.216900266158-0.251399656845-0.00382049200118-0.2824089451380.442411853018-0.1136478301860.04188293556350.6555258847260.07821533015010.5310256710626.629-8.19852.953
437.822389005571.92683039154-2.66114216972.58336011733-0.1328000633217.07029772151-0.233213699434-0.220713809781-0.08203227668980.3937110172180.329887305564-0.2937606686520.16776562223-0.482385860858-0.178689237790.5270611154140.134138230089-0.02045059577850.4947959553240.02025741935750.6554614553082.884-10.09252.947
447.58758832529-0.307617327748-1.912189868742.267786010691.592764990013.871074335750.1937625731190.826157888617-0.592505626681-0.09665890601380.0518488315518-0.865778848177-0.536711349910.100397608829-0.1722276812580.507332006597-0.06561705374540.06332299695030.630843191579-0.01128223290990.80128280693315.565-8.59344.108
457.77277220811-0.062843400434-2.330622720343.112516652951.182589625285.085905312410.665985991084-1.363882404280.13731936216-0.4645122812680.0384950854634-0.793579769371-0.9605255545391.67265872145-0.3105570139710.517154622357-0.0745196485584-0.1201691198530.9463800826420.02990789205180.74163636533515.455-5.43355.741
463.10916966552.288556171670.8513476374722.67737135893-1.539007697825.617056851930.235716981198-0.1917617841340.3030688680370.0682905737889-0.0743108973855-0.887372833099-0.3893442507890.14792666293-0.3454146615920.3087446497240.0426014270093-0.07827390292590.333796797441-0.06648530615290.657982882092-28.885-7.6072.63
474.34481125731.47199845342-3.217910848256.09923690041-0.245453535322.471761955440.460362942254-1.08332528377-0.02682735666560.803346281252-0.455300974822-0.851055165284-0.6602497472581.845849223540.008711102081890.457819083332-0.13525066028-0.07908825701470.6268893880310.09647792136030.507544831078-30.63-10.1916.172
484.17505996111-0.565572184868-0.8295665464524.12397406286-0.916720398937.33413675689-0.0904806893406-0.17314376009-0.671536063572-0.00116620877174-0.132568402472-0.473025813590.4911074042360.4364791390240.1795352728060.324136460115-0.01452545769550.04547852151630.3493605643940.1161946915130.536090904595-35.294-18.2587.274
493.674387801460.311856260078-1.338746902962.2427446659-2.549185387268.305734500580.141999290146-0.117672217931-0.4519802862510.0491910442287-0.331592242081-0.744271107080.1357546066940.3044044471170.1920076986350.292573433442-0.00552327634277-0.007911049576360.2961280847790.0905552007480.523024598486-31.267-13.3185.452
502.763519763760.758905765327-2.422487474441.7900375641-0.2622180606883.27907973047-0.000307151595420.128659655030.3328214144250.07995016460360.1682146511710.147958787498-0.319697643373-0.545884783294-0.04746007228020.3382295715670.0218029280495-0.05884161054920.3039561429310.04343599064420.543026955866-41.435-13.42517.754
513.55817602642-0.897882588669-0.1624155921942.847345660510.06348793412772.19436609159-0.09613203558930.447060922490.360034086404-0.05358363869160.1402275729610.46074731922-0.0827351249019-0.2283593778730.004273159242690.3143671516940.05514166688940.01835248860120.4342773102110.1231642855850.433754331269-39.4186.315-16.939
523.46133701381-0.05477481315620.7807364144713.920231700381.33491998674.27672092181-0.01948358061240.4268826825420.929011551274-0.011871348632-0.5181846722710.607331795694-0.978891866357-0.557915308440.1602543128750.4557345381390.1529369336620.05899294835030.5082355248660.1078262998170.863295181032-46.30616.316-18.933
534.88255763942-5.103748765412.511601418145.30547460958-2.615509879242.174552484730.06205104307360.6507643052660.6425764079260.448646490271-0.4261787115410.0837426535893-0.415419518990.0647253981980.2818514485930.3975415922970.004138548683650.004495699619420.3800927101780.04688529885070.400470309281-33.32111.485-14.445
547.20590329911-4.2353163446-1.248442628886.251366261121.063535901180.2490286224650.3957757750450.6906502698481.17360368643-0.601870083034-0.3568635311320.1846541789160.4484749530620.306735371648-0.2123276610370.540861672109-0.00594781701639-0.05600855630470.5566408247740.2550121688020.384063471529-34.76815.429-21.229
550.755103023797-0.991780897810.9532535041846.52078813496-0.590369709233.279342718960.04449888466940.264256082001-0.279281135673-0.0440108468059-0.104309886770.7287238544690.36978615208-0.7262194760620.1788853140720.339205969631-0.1095117405840.0779008757680.484371215890.06133209316510.538852745511-60.141-9.1294.096
564.29032106071-1.116745253370.3042158657213.29802467978-1.394253761325.403218942250.0168087135638-0.186154489957-0.1912405308440.03071754565190.2641083104050.5438373119660.112673916596-0.779776631774-0.2755643484970.291461300656-0.01002478634840.02722752288840.3553268726660.06566624895210.48837735881-55.1-10.58612.865
575.80535602784-2.92697294150.9297365119135.00690957153-1.586032866474.959132845350.3015233677460.5019990010750.441663422520.318465546507-0.234744636497-0.240165098411-0.490029257153-0.241519325953-0.05994656279940.424977883616-0.006059387685260.1170182453750.4882092943810.1844181820570.668217318911-55.74-3.1188.486
583.75512858549-0.4190884204761.200864901261.8862396195-2.093933575984.2772504801-0.09300001901660.1969586144920.115412264042-0.1655768652720.4720400955870.182804953810.123224937245-1.0642948731-0.3756635245150.376733060294-0.0320607733820.1056855864160.4677861859530.03825977655210.57678456682-55.257-7.3031.337
593.72745980306-3.15724389039-3.52041282375.19269552110.6631539962637.576550367130.194388731141.00988005270.890154143489-0.4874018027070.1169940089790.0329572354446-0.0069372465078-0.104496619187-0.2268931482530.461637636106-0.0198855698609-0.04240222668680.9091990790250.1661606428490.383946877062-43.8837.677-28.905
606.39906597376-0.979777772101-1.981588809814.084699111170.1553833751385.89129047225-0.145769604519-0.286330705225-0.392256610724-0.06082363719940.4097503038080.7056074669710.373738805944-0.019232391244-0.1641831168760.329286563203-0.0513141967737-0.08681628986980.7798964126730.1938497083080.592303416714-54.8661.707-20.078
616.808043157480.941212941331-2.751155456834.710212862890.9070379211434.96919549576-0.6683801211830.976830265449-0.585211369969-0.5957771551570.0389866619160.6027073087880.496957539206-0.3687538915040.5788506432820.515016149212-0.0733936750485-0.03117629004910.6901561052630.06529819401270.787970258233-51.732-4.587-25.436
625.203574017250.245581727377-0.7277906701551.99979524546-0.2795931691072.64955039979-0.01348645257961.31363082940.26547891739-0.3398826458060.1960552135740.1890529127940.355028076715-1.0283649926-0.2546926688630.4583912088090.00829364809757-0.04630267915650.9924955148710.2539523567210.623767444332-53.5963.694-24.698
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN R AND RESID 332:353 )R332 - 353
2X-RAY DIFFRACTION2( CHAIN R AND RESID 354:442 )R354 - 442
3X-RAY DIFFRACTION3( CHAIN R AND RESID 443:494 )R443 - 494
4X-RAY DIFFRACTION4( CHAIN R AND RESID 495:516 )R495 - 516
5X-RAY DIFFRACTION5( CHAIN H AND RESID 1:17 )H1 - 17
6X-RAY DIFFRACTION6( CHAIN H AND RESID 18:52 )H18 - 52
7X-RAY DIFFRACTION7( CHAIN H AND RESID 53:121 )H53 - 121
8X-RAY DIFFRACTION8( CHAIN H AND RESID 122:185 )H122 - 185
9X-RAY DIFFRACTION9( CHAIN H AND RESID 186:224 )H186 - 224
10X-RAY DIFFRACTION10( CHAIN L AND RESID 1:30 )L1 - 30
11X-RAY DIFFRACTION11( CHAIN L AND RESID 31:76 )L31 - 76
12X-RAY DIFFRACTION12( CHAIN L AND RESID 77:129 )L77 - 129
13X-RAY DIFFRACTION13( CHAIN L AND RESID 130:214 )L130 - 214
14X-RAY DIFFRACTION14( CHAIN A AND RESID 1:17 )A1 - 17
15X-RAY DIFFRACTION15( CHAIN A AND RESID 18:33 )A18 - 33
16X-RAY DIFFRACTION16( CHAIN A AND RESID 34:83 )A34 - 83
17X-RAY DIFFRACTION17( CHAIN A AND RESID 84:133 )A84 - 133
18X-RAY DIFFRACTION18( CHAIN A AND RESID 134:207 )A134 - 207
19X-RAY DIFFRACTION19( CHAIN A AND RESID 208:228 )A208 - 228
20X-RAY DIFFRACTION20( CHAIN B AND RESID 1:18 )B1 - 18
21X-RAY DIFFRACTION21( CHAIN B AND RESID 19:75 )B19 - 75
22X-RAY DIFFRACTION22( CHAIN B AND RESID 76:90 )B76 - 90
23X-RAY DIFFRACTION23( CHAIN B AND RESID 91:113 )B91 - 113
24X-RAY DIFFRACTION24( CHAIN B AND RESID 114:128 )B114 - 128
25X-RAY DIFFRACTION25( CHAIN B AND RESID 129:150 )B129 - 150
26X-RAY DIFFRACTION26( CHAIN B AND RESID 151:163 )B151 - 163
27X-RAY DIFFRACTION27( CHAIN B AND RESID 164:214 )B164 - 214
28X-RAY DIFFRACTION28( CHAIN X AND RESID 333:375 )X333 - 375
29X-RAY DIFFRACTION29( CHAIN X AND RESID 376:442 )X376 - 442
30X-RAY DIFFRACTION30( CHAIN X AND RESID 443:479 )X443 - 479
31X-RAY DIFFRACTION31( CHAIN X AND RESID 480:516 )X480 - 516
32X-RAY DIFFRACTION32( CHAIN C AND RESID 1:39 )C1 - 39
33X-RAY DIFFRACTION33( CHAIN C AND RESID 40:83 )C40 - 83
34X-RAY DIFFRACTION34( CHAIN C AND RESID 84:144 )C84 - 144
35X-RAY DIFFRACTION35( CHAIN C AND RESID 145:224 )C145 - 224
36X-RAY DIFFRACTION36( CHAIN D AND RESID 1:18 )D1 - 18
37X-RAY DIFFRACTION37( CHAIN D AND RESID 19:49 )D19 - 49
38X-RAY DIFFRACTION38( CHAIN D AND RESID 50:76 )D50 - 76
39X-RAY DIFFRACTION39( CHAIN D AND RESID 77:91 )D77 - 91
40X-RAY DIFFRACTION40( CHAIN D AND RESID 92:114 )D92 - 114
41X-RAY DIFFRACTION41( CHAIN D AND RESID 115:129 )D115 - 129
42X-RAY DIFFRACTION42( CHAIN D AND RESID 130:151 )D130 - 151
43X-RAY DIFFRACTION43( CHAIN D AND RESID 152:175 )D152 - 175
44X-RAY DIFFRACTION44( CHAIN D AND RESID 176:198 )D176 - 198
45X-RAY DIFFRACTION45( CHAIN D AND RESID 199:214 )D199 - 214
46X-RAY DIFFRACTION46( CHAIN E AND RESID 1:17 )E1 - 17
47X-RAY DIFFRACTION47( CHAIN E AND RESID 18:33 )E18 - 33
48X-RAY DIFFRACTION48( CHAIN E AND RESID 34:73 )E34 - 73
49X-RAY DIFFRACTION49( CHAIN E AND RESID 74:99 )E74 - 99
50X-RAY DIFFRACTION50( CHAIN E AND RESID 100:123 )E100 - 123
51X-RAY DIFFRACTION51( CHAIN E AND RESID 124:189 )E124 - 189
52X-RAY DIFFRACTION52( CHAIN E AND RESID 190:207 )E190 - 207
53X-RAY DIFFRACTION53( CHAIN E AND RESID 208:217 )E208 - 217
54X-RAY DIFFRACTION54( CHAIN E AND RESID 218:228 )E218 - 228
55X-RAY DIFFRACTION55( CHAIN F AND RESID 1:18 )F1 - 18
56X-RAY DIFFRACTION56( CHAIN F AND RESID 19:75 )F19 - 75
57X-RAY DIFFRACTION57( CHAIN F AND RESID 76:90 )F76 - 90
58X-RAY DIFFRACTION58( CHAIN F AND RESID 91:113 )F91 - 113
59X-RAY DIFFRACTION59( CHAIN F AND RESID 114:128 )F114 - 128
60X-RAY DIFFRACTION60( CHAIN F AND RESID 129:150 )F129 - 150
61X-RAY DIFFRACTION61( CHAIN F AND RESID 151:163 )F151 - 163
62X-RAY DIFFRACTION62( CHAIN F AND RESID 164:214 )F164 - 214

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万見について

-
お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://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