[日本語] English
万見
- PDB-7bvr: DgpB-DgpC complex apo -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 7bvr
タイトルDgpB-DgpC complex apo
要素
  • AP_endonuc_2 domain-containing protein
  • DgpB
キーワードLYASE (リアーゼ) / C-deglycosylation / sugar phosphate isomerase/epimerase
機能・相同性Domain of unknown function DUF6379 / Domain of unknown function (DUF6379) / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / metal ion binding / : / DUF6379 domain-containing protein / Xylose isomerase-like TIM barrel domain-containing protein
機能・相同性情報
生物種human intestinal bacterium PUE (バクテリア)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.6 Å
データ登録者Mori, T. / He, H. / Abe, I.
資金援助1件
組織認可番号国
Not funded
引用ジャーナル: Nat Commun / 年: 2021
タイトル: C-Glycoside metabolism in the gut and in nature: Identification, characterization, structural analyses and distribution of C-C bond-cleaving enzymes.
著者: Takahiro Mori / Takuto Kumano / Haibing He / Satomi Watanabe / Miki Senda / Toshio Moriya / Naruhiko Adachi / Sanae Hori / Yuzu Terashita / Masato Kawasaki / Yoshiteru Hashimoto / Takayoshi ...著者: Takahiro Mori / Takuto Kumano / Haibing He / Satomi Watanabe / Miki Senda / Toshio Moriya / Naruhiko Adachi / Sanae Hori / Yuzu Terashita / Masato Kawasaki / Yoshiteru Hashimoto / Takayoshi Awakawa / Toshiya Senda / Ikuro Abe / Michihiko Kobayashi /
要旨: C-Glycosides, in which a sugar moiety is linked via a carbon-carbon (C-C) bond to a non-sugar moiety (aglycone), are found in our food and medicine. The C-C bond is cleaved by intestinal microbes and ...C-Glycosides, in which a sugar moiety is linked via a carbon-carbon (C-C) bond to a non-sugar moiety (aglycone), are found in our food and medicine. The C-C bond is cleaved by intestinal microbes and the resulting aglycones exert various bioactivities. Although the enzymes responsible for the reactions have been identified, their catalytic mechanisms and the generality of the reactions in nature remain to be explored. Here, we present the identification and structural basis for the activation of xenobiotic C-glycosides by heterocomplex C-deglycosylation enzymes from intestinal and soil bacteria. They are found to be metal-dependent enzymes exhibiting broad substrate specificity toward C-glycosides. X-ray crystallographic and cryo-electron microscopic analyses, as well as structure-based mutagenesis, reveal the structural details of these enzymes and the detailed catalytic mechanisms of their remarkable C-C bond cleavage reactions. Furthermore, bioinformatic and biochemical analyses suggest that the C-deglycosylation enzymes are widely distributed in the gut, soil, and marine bacteria.
履歴
登録2020年4月11日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02021年4月14日Provider: repository / タイプ: Initial release
改定 2.02021年11月17日Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description / Structure summary
カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_2 / pdbx_audit_support / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_ls_restr / refine_ls_shell / reflns / software / struct_conf / struct_conn / struct_mon_prot_cis / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.occupancy / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_ls_restr.dev_ideal / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _reflns.B_iso_Wilson_estimate / _software.name / _software.version / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_mon_prot_cis.pdbx_omega_angle / _struct_sheet.number_strands
解説: Occupancy of atoms on special symmetry positions / Provider: author / タイプ: Coordinate replacement
改定 2.12022年10月26日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 2.22023年11月29日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

-
集合体

登録構造単位
A: AP_endonuc_2 domain-containing protein
B: DgpB
C: AP_endonuc_2 domain-containing protein
D: DgpB
E: AP_endonuc_2 domain-containing protein
F: DgpB
G: AP_endonuc_2 domain-containing protein
H: DgpB
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)219,85621
ポリマ－218,0768
非ポリマー1,78013
水7,440413
1
A: AP_endonuc_2 domain-containing protein
B: DgpB
C: AP_endonuc_2 domain-containing protein
E: AP_endonuc_2 domain-containing protein
F: DgpB
G: AP_endonuc_2 domain-containing protein
H: DgpB
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)203,55619
ポリマ－202,0147
非ポリマー1,54112
水1267
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area9330 Å2
ΔGint-41 kcal/mol
Surface area36500 Å2
手法PISA
2
A: AP_endonuc_2 domain-containing protein
B: DgpB
D: DgpB
E: AP_endonuc_2 domain-containing protein
F: DgpB
G: AP_endonuc_2 domain-containing protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)164,95216
ポリマ－163,5576
非ポリマー1,39410
水1086
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area9100 Å2
ΔGint-39 kcal/mol
Surface area37160 Å2
手法PISA
単位格子
Length a, b, c (Å)86.516, 156.721, 158.931
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
要素

-
タンパク質 , 2種, 8分子 ACEGBDFH

#1: タンパク質
AP_endonuc_2 domain-containing protein


分子量: 38457.039 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) human intestinal bacterium PUE (バクテリア)
遺伝子: dgpC / 発現宿主: Escherichia coli BL21 (大腸菌) / 参照: UniProt: A0A3Q9WXL1
#2: タンパク質
DgpB


分子量: 16062.067 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) human intestinal bacterium PUE (バクテリア)
遺伝子: dgpB / 発現宿主: Escherichia coli BL21 (大腸菌) / 参照: UniProt: A0A3Q9WUX0

-
非ポリマー , 4種, 426分子

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


分子量: 92.094 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C3H8O3
#4: 化合物
ChemComp-MN / MANGANESE (II) ION


分子量: 54.938 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Mn / タイプ: SUBJECT OF INVESTIGATION
#5: 化合物
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES / HEPES


分子量: 238.305 Da / 分子数: 5 / 由来タイプ: 合成 / 式: C8H18N2O4S / コメント: pH緩衝剤*YM
#6: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 413 / 由来タイプ: 天然 / 式: H2O

-
詳細

研究の焦点であるリガンドがあるかY

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 2.47 Å3/Da / 溶媒含有率: 50.21 %
結晶化温度: 313 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 100 mM Tris (pH 8.5), 24% PEG4000

-
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: Photon Factory / ビームライン: BL-1A / 波長: 1.1 Å
検出器タイプ: DECTRIS EIGER2 X 4M / 検出器: PIXEL / 日付: 2019年11月10日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1.1 Å / 相対比: 1
反射解像度: 2.6→46.89 Å / Num. obs: 67240 / % possible obs: 100 % / 冗長度: 7.1 % / Biso Wilson estimate: 38.07 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.115 / Net I/σ(I): 13.3
反射 シェル解像度: 2.6→2.66 Å / 冗長度: 6.6 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 4482 / CC1/2: 0.821 / % possible all: 100

-
解析

ソフトウェア
名称バージョン分類
PHENIX1.19.2_4158精密化
XDSデータ削減
Aimless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: 7DRD

7drd


解像度: 2.6→46.89 Å / SU ML: 0.3184 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 23.5926
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2494 2008 2.99 %
Rwork0.1907 65141 -
obs0.1924 67149 99.95 %
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: 40.48 Å2
精密化ステップサイクル: LAST / 解像度: 2.6→46.89 Å
タンパク質核酸リガンド溶媒全体
原子数14649 0 103 413 15165
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.002915072
X-RAY DIFFRACTIONf_angle_d0.642720365
X-RAY DIFFRACTIONf_chiral_restr0.04442175
X-RAY DIFFRACTIONf_plane_restr0.00432617
X-RAY DIFFRACTIONf_dihedral_angle_d14.19165588
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.670.33681430.23744605X-RAY DIFFRACTION99.98
2.67-2.740.29241380.22124569X-RAY DIFFRACTION100
2.74-2.820.25241450.21364600X-RAY DIFFRACTION100
2.82-2.910.27751350.22264591X-RAY DIFFRACTION100
2.91-3.010.29861440.21794628X-RAY DIFFRACTION100
3.01-3.130.31461460.21694603X-RAY DIFFRACTION100
3.13-3.280.26271390.19834618X-RAY DIFFRACTION99.96
3.28-3.450.2531460.19484636X-RAY DIFFRACTION100
3.45-3.660.25551360.19294638X-RAY DIFFRACTION100
3.66-3.950.25011460.18614651X-RAY DIFFRACTION100
3.95-4.340.20971470.16914674X-RAY DIFFRACTION99.98
4.34-4.970.22391430.16374685X-RAY DIFFRACTION100
4.97-6.260.27261500.19124731X-RAY DIFFRACTION100
6.26-46.890.19821500.17234912X-RAY DIFFRACTION99.47
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)
11.106521128170.537920362197-0.2664784968190.993860154544-0.2004976736640.595836838056-0.06982325471090.1044101964130.343061558914-0.0257769274950.05184696497740.181383551356-0.261517879421-0.02911095878270.01642049053750.3833212320490.0148924359575-0.02879597445790.2107377814330.05387006732260.3532981266019.6247917856221.054607715451.7079228313
21.868412521291.629662391540.7572898018191.599264312451.162950898032.43204734736-0.07364098982280.0210122249666-0.1008228209160.1360014108470.01218092664390.222019574999-0.1536912072040.01272557673220.04780185938430.469068197114-0.0436221814136-0.176989620070.4764475766610.2562178017790.664039414076-4.6176606350326.364205124224.4100163002
32.23653030393-0.198361905467-0.5165607577011.779687950030.5884592989033.1389737626-0.02606789632830.3492092445780.67177866421-0.2168620127970.05036853563150.0191290031279-0.655439821720.169592346377-0.02152768090280.499858211182-0.0932838285107-0.1065278037050.3183110517560.1334654272640.51125108745613.115505633432.820896064138.2943302553
41.29186771877-0.0254204855622-0.145533852543.5038942938-0.04439108615081.937513042130.05100088475130.3626386391360.105341015923-0.503016100339-0.100660884211-0.330391311327-0.05590392023920.06774086984960.003536815259070.271207355011-0.0376947592817-0.03440733421590.3147907486650.01636634248030.2299586917486.72009349669-5.269570117335.7705869554
53.00475679286-1.470465237760.4578548325098.0969025783-5.173380140633.39943462756-0.02846518198180.4394540037850.02037779318130.3279554399590.131848063466-0.5891677184310.1346455708710.0102764625624-0.09227642219190.3588266496540.0358024173685-0.02760333485260.190528055208-0.04324177020620.215883692125.84713804492-15.442600067539.3090502078
61.791960576710.968005491029-0.5149224240895.074647859791.711060607741.36056693874-0.116291558530.09866735433860.0400734742005-0.06350633751380.00677815008839-0.0548930853234-0.0894513477448-0.04738785887730.09721169831970.2961502010240.0060108942779-0.03683196504650.2503173132530.04204660922990.274479394717-0.206499309192-2.4338713112641.7502140867
70.355731124920.09641726726860.1876180740660.6396546066960.9097815176411.31819180576-0.0147702761091-0.0259124171874-0.08945744126140.2498096290450.0734255605615-0.08897213712590.2501140644630.0087810367996-0.04265798418580.3082088748760.00380789948619-0.01909226666930.226985294850.03403427598990.2761065633252.90254733788-3.2295430088748.1334309007
88.681365224474.32131088091-6.467366812246.05760227791-9.157652852292.01538931901-0.10415585478-0.1704330193750.124983902334-0.249295702182-0.19513966719-0.7607952758810.3416231829490.3726244793290.2993404859410.457954150817-0.009244055617110.009120698038930.299194882927-0.03030931963640.3494402798283.84019655308-21.091939939933.0456218969
91.58666370586-2.107902566770.01319579281155.728686498561.97267540661.42618909138-0.03853531344030.3090537262180.166455690585-0.2366087230270.01708123891340.0681898391562-0.236609762708-0.1452281664480.01416822439540.305888322471-0.05293427190510.00221941524530.2875726450690.06143074838630.250710085845-1.450281829891.8599209303937.2344221333
100.5460832820821.433187656611.365796263727.935266129050.9862287730235.013751656950.1739455720360.0918627897460.282402083428-0.490500022331-0.6549236788490.658043382897-0.672394656584-0.6392655061610.4325358438470.2719752773150.0223418183957-0.09215846102660.332992254634-0.01968636944480.411609361352-7.7992117920312.100962403641.3993549844
112.334654921632.9504491848-0.6716181917314.77862821962.066234685018.150092505710.1408990548620.365092904963-0.312209744492-0.7439746280220.00847093665194-0.5904168912120.227951569434-0.213098043036-0.1186128348670.3949629282750.02169177443850.02961378295790.271424045305-0.02793743875470.2845080192667.30788735374-10.382540724228.4246832505
122.208745681581.82972178788-0.2400502765642.931129169190.6928744149242.20682149407-0.1212098487430.151202247846-0.246424408639-0.05913398299730.0498677506355-0.1267762340610.0506123541749-0.2497879238190.09682486366580.3102384203440.0545397035490.02727126624240.227579810768-0.04230845395090.25827821865824.3315358406-24.239083496939.7236147756
132.65795880625-0.1452962259510.6187607156850.4860254914380.277551374810.8075094015920.1105649440340.01054481959960.0912680773257-0.0192460321247-0.0688799264979-0.100324166010.1470170466930.0740624350555-0.04295067234070.2926822442540.0295782608298-0.00602439292550.2355393677110.01119969252450.28621854195132.1482129317-21.342312531853.5131750178
142.34581021809-0.966497811807-0.3248926773031.594495025161.095723039524.106078221780.1701698177110.179597416607-0.0753573065678-0.22550761027-0.151484693092-0.2770992149510.3827616719920.322646574899-0.001482760913390.3391789780110.07838012630560.03847908245680.2403876709210.005546212651710.35112863222441.1583002834-35.365226765153.6071632892
154.224592666951.62328375051-0.4462811407293.38169678296-0.196439126784.18098101485-0.1272365486470.3595089755150.0106594248835-0.712491714806-0.163791787222-0.9897087800690.2861852694310.9321921569040.2501330449030.666121042050.1658272541290.1868514645640.5789311088820.0928358751640.55461581735349.8911644157-33.532734710621.7864788862
164.172841180171.76130558750.635012286566.58751697057-1.747626399513.37735226273-0.393191879874-0.1138741796070.0259215413401-0.823582700220.0268820732537-0.9281791932360.2934963064450.7726536561520.3550132098430.5308956772060.1649750935670.1647737692430.5294392035580.01262698152870.51537338338149.7564882302-31.779240053626.2833352502
171.47463569146-0.953999251377-0.2189734099592.51952132895-0.8767821049162.646849227090.04351289012270.26445280788-0.485548836345-0.350276136291-0.1469969145770.05615685713850.9473523662930.3101190493560.09703788459770.5353744520530.06582560157650.06029913130420.293830814588-0.06269129105990.44839166914334.4440953018-41.83580747137.5920425222
185.085136693582.42061900247-2.208419728447.51869996115-1.476913326614.14850761349-0.0725176667490.1132323071380.0758419816525-0.1741785613210.0883426916685-0.1961061814710.0238066770250.251928354448-0.04414872451680.422954583780.03116392368970.03351999740010.23449662976-0.05756342257690.31366041931330.9609209337-32.177279300138.6205427139
193.24606322282-1.77968694489-0.6251612560927.87317861896-4.938896764558.29098119838-0.09787564354280.195591500098-0.168491758566-0.6234978454220.373191500159-0.04242113890661.02358372971-0.177334203831-0.2444211189750.395099830720.0407280590322-0.02462320018280.32062921946-0.08046348129230.30493321754123.6366263874-36.022101506732.851840493
200.225364067616-0.02912162414740.4256273674812.688080845090.2488981103310.792548285942-0.0007027900641040.2011079851680.129442560261-0.4238243299390.0325317477756-0.209521915481-0.1142705386490.289867981828-0.03762482501290.331592233382-0.04191346347310.1079370901570.3610756988370.04949491883370.32651909915240.1017753143-1.4060676193639.9837677205
216.84086922123.45530803682-2.555453484096.6946167294-3.576897824349.89112687260.3132720707730.3689164220480.2138280239750.193257342051-0.217855926758-0.599677090336-0.7860109798580.371025179762-0.1204524318730.311420369204-0.03967119169960.02085345476060.3066233965280.03666005970240.30692442866945.68261412954.8449183586243.2650781197
221.708711208710.6223292764050.05209486940723.51278372497-0.3550328889471.510248817140.09025452074460.287319151960.105649134594-0.306333941747-0.151928424537-0.0016001422594-0.1751497228680.414110435660.06624275029890.286196191522-0.0231367406470.06658090992240.3199741882530.04547583190360.24860580830542.721506119-1.7391529741943.5939950567
234.50734369321-5.719480727772.961014454139.95592762479-3.660174533462.517333824620.2834872853950.6972309450550.129698055626-0.366903960698-0.619807316979-0.417335281680.04152169230840.5340797000830.3128985523280.3619336280350.03258064684880.1245249829670.43117621950.0152451912590.37655024903246.3279296955-8.4496622067637.4322259073
241.15392212975-0.5438190540090.6169214070010.179332750476-0.5902613542081.300029970910.0204620293301-0.00315974826926-0.04260846739370.00489538001776-0.04316187924930.01801173954470.07547896225060.01987215789650.02677401216470.246105447861-0.0210552896836-0.0004719380060910.1600133397420.01264727824970.290093925796.83031138508-18.205178548566.4466299893
251.907057397430.885417236516-0.1146173008941.29764019695-1.22185029762.29251437192-0.0241918330646-0.07425547853480.0507762472115-0.1001402533560.04264310878310.335352888075-0.0287393994322-0.221775956276-0.01235896848370.297138136962-0.0109588172173-0.003289202149410.230364603574-0.01174723448030.384603401747-8.38173237523-25.324731046961.2355923279
263.43753238242-1.46158349308-0.8216960362652.563189838061.203930309512.763145055220.223541636651-0.1208897142370.4645596986960.132748841305-0.1330421239330.109260531639-0.160779883395-0.381124139206-0.0851953025240.428090933167-0.05727974998620.1214921039580.3693992029870.001764214792540.33218685175-15.9556914583-21.104181344191.2447119528
271.327983190021.11652287987-0.1548983789651.269445621870.481608176233.17349965802-0.0116569601878-0.191961651283-0.3867864345250.119100781687-0.1450880185370.08281935622410.625090172879-0.04746304476450.1506076470760.366300000171-0.008016666825310.0261423348360.2098663020570.04581402168010.410589977759-5.19497377954-35.183431104676.6376009319
282.738978396471.253292724931.129782422423.827607398375.810001651169.023655076670.391938998941-0.104958270404-0.04298114526740.513751060796-0.102777209807-0.2613306658430.444638958142-0.470392021393-0.3032044767350.455608557272-0.01545039211540.06248028132850.2003626205420.08764237899620.3175188706451.85638576849-27.653165438576.3156998538
293.280480785491.788425566961.412979270732.754033162273.187640203967.178255239080.165939686926-0.0568207784422-0.4564290292350.5601830602580.187967480405-0.008373424491690.6029415831380.370285724439-0.2755313343160.312415471825-0.0217966842405-0.05770411629190.2357823046230.09807474707980.4041232632647.03725385497-34.182298486581.66069086
307.441764815520.7377265060671.33071404926.87336562925-0.7884103287282.9822758363-0.187958613902-0.414577060113-0.00762831043030.1542407861850.397939836980.108167619658-0.0342558800386-0.966679660334-0.180556993040.336450354049-0.004572036408590.1316971307520.3939317606290.07019093122160.284009816859-0.781903368946-6.0285881039483.0347400987
312.355939134833.03814947313-1.223210215416.97394218051-1.720697740841.7534638118-0.164764334242-0.03452974283560.0273618392878-0.1899891441950.0616994951874-0.4852589060220.02228322900520.1682643706570.05954460562740.3766730238430.01803652583270.01782687509150.241029171768-0.01774108120040.3255080727314.309678899912.60394980278.4965974362
322.378505033481.75919598543-0.009881359538992.08755267226-0.2255020608361.637020173610.080777918505-0.1027735516070.3841235318240.485702897390.02223033866860.26436216793-0.380099497765-0.142742030691-0.1054627330710.3662764364270.04916500345430.05455374032050.1733842914-0.004590783012020.3238157831482.847770837323.895138865475.0171421171
330.8951400426120.5982779406682.007162244153.106269893731.977965879856.069990712580.0534915000454-0.1633649026580.369113699891-0.298613825365-0.1093679687180.0530437470778-0.805856265995-0.1967467025120.04287201955760.358082118752-0.01071437424590.06167033178810.227566694047-0.001490274971110.377353431351.7785737372810.293360468470.3767829918
342.157348866510.08789969121260.7916058712345.36786869163-1.344421607032.13523684230.1157151302240.0277868770229-0.0605352236285-0.224684592986-0.103153487763-0.243464470044-0.19194625045-0.05127363582960.007314733899270.2099934451430.02634688988740.08234790668840.1808402737280.001429730526070.2178779623025.845991914421.9327227897569.9872737025
353.7486872102-1.820988073372.882111970657.85357142191-7.739497909978.00664170567-0.00308589325699-0.2890706087250.4628323542310.96425630032-0.26180343507-0.552696587617-0.8002682253590.2526812485210.2457962291750.674880816076-0.0325767760628-0.02300518426010.253408652823-0.1318471478060.6274145766311.087602614420.296758241483.1192775557
363.391643473711.79144829132.934912231842.76412651111.973436417163.937407592610.0486023483149-0.317523316480.1544575186860.245527497533-0.09057413613060.23305830915-0.114454804759-0.3950156855640.05321678791410.2924926641340.03460939304430.1119459441590.241391343129-0.004379092694240.339804127565-5.85499987218-1.5091336276677.1833137933
375.351523742896.521817054315.3664420660310.00521756485.126765862836.40074463990.2468183681410.03133735789110.4766304603930.503352581608-0.543196732698-0.2215893727860.0481304180046-0.007468434877940.2596062407460.488504476229-0.0255945905201-0.0733867535280.3494874387230.02734194687320.28474438429311.04184178369.6280514317887.1544209381
380.71080454465-0.1793518574680.2364800069860.552759169124-0.2294656656050.8928953149510.03877409182360.01497827227750.2175731954330.097463928091-0.0797607067757-0.0895314966785-0.199289848850.09617299257220.03545904209030.366097253109-0.05010281791980.02316702930670.2423421258550.02368279238170.32076990574536.066916202511.140794088768.2033523445
390.538826468080.1972519519980.1029112619011.04336803561.236691786791.48420925377-0.06734956322820.07590713146680.10651520477-0.09027513469530.141007156057-0.268262845012-0.2247495333720.389165569639-0.05495243835690.430162830478-0.144874586734-0.01595980845390.4506373629070.08427005808820.45957958034351.546877980818.60328256964.4180586998
402.84542424768-0.2544858872340.154827784543.50780023936-1.646488931886.20597364284-0.03114203639140.342605810273-0.316736675177-0.166008522063-0.150700030768-0.5358077483470.1935500897991.401896724710.150759204530.459607153497-0.0100870261903-0.002230408353860.646307521924-0.03825711181820.3612631280156.911253644113.03963095295.3369242642
411.400265031710.3232178776960.3613148397381.5673391738-0.6742347213452.986776876510.0879270819469-0.1773341313010.5715282785410.267204927848-0.100594660546-0.109925734665-1.030531000810.798389465307-0.02761903779620.64290110305-0.189540091569-0.03355069055860.390717056931-0.003859437538450.45403933091447.344499842627.487176472680.2123452431
422.38092924855-0.102341537780.4435624396923.98030697398-0.7104571009532.03340141958-0.202481447938-0.03213452813560.224443413180.3298826728080.3144090914360.226137920845-0.7109192075550.230335701423-0.1605298027280.549184994179-0.0924635600849-0.03650365433010.2872145948290.03419677940390.38124104566640.474721555520.027262997278.8757611977
436.772526144370.803102718182-0.4184280037872.007764046721.428631163756.360483558010.02726465652170.0489117253030.8118600585730.3057819224180.1569883000160.158358208968-1.05985148399-0.0362842015317-0.1750139832780.528374972294-0.04179818313580.05030909573310.2709424910420.008943290194890.34384897177934.807829302826.23004628984.3513409673
440.7109026090370.975796769310.5526329328023.588183416461.016676107431.92467838961-0.0497010588346-0.04439662975270.121530881480.077810296666-0.01100946296690.223310976757-0.221934569580.1154768589850.04844531583710.3062316921820.0267751163165-0.02138876692950.2598720258060.03097324182020.28102557819634.3443152226-12.341604624980.6616975747
451.08868287384-0.4187116435580.7303442282531.98029541090.5165520414112.037046849360.0110065548022-0.259406853079-0.129514612649-0.0158433791167-0.00893924617031-0.229483612526-0.132694468864-0.005539708870480.009005286228380.251929755896-0.0317314977798-0.007546956591060.2347534444290.05264627948330.21065246254836.4354892625-10.515881710775.5468457326
462.686121655331.48007944987-2.435915826042.75021920126-0.4457963442665.95139128965-0.0493999110635-0.0829746674571-0.08564380447330.0544881650953-0.0954202690410.002959594430140.2872960009410.3903598364670.1607809478630.2321734228550.0127655671754-0.03264401644990.1843896277810.009481731649210.24629721659342.2818916844-16.349106010572.048540077
471.99176745999-1.0246889415-0.6635320085793.441206608113.167564341632.900884114470.280372217977-0.04387071093820.198369554478-0.289005927279-0.2964509417620.106283564003-0.3054002441340.2187720111530.002872971595320.2443510082830.0376618861231-0.05885429810010.2220630681140.08528800216390.28274218955236.8573040346-9.2074027727870.4764496369
486.56239823987-0.609635005091-2.823936786883.449272937115.594844572569.621409787460.384205644459-0.2422517698190.07708075487630.618359824397-0.3586392682720.7146118584420.344052593791-0.146814569387-0.011901827390.560079449397-0.0364470860109-0.001988514854550.2453949108980.1157173563130.55868292883430.5328885335-28.174656931982.2311002787
492.730669875153.43231699797-1.494611791826.77172514724-2.726439658542.852845543330.268930974629-0.497518781571-0.003270341380960.699644628172-0.332892009653-0.11921687742-0.1448210292310.4587347942980.08900116990760.3366542359220.0465147340817-0.06162363583140.3585793632510.05341325579250.32873884593944.6257549872-8.9636246457779.7649109512
503.08442602682.53080065807-1.364618056165.57601954702-1.678067114715.516724318860.205269399307-0.562626865128-0.2116716481830.328660281561-0.30948201733-1.00258124657-0.4815208820121.059800473060.09762894694210.315775708023-0.0324445704449-0.1355939830760.418285615165-0.05243732712060.47035477588154.4535187438-1.7333430123276.3019522383
518.988862709666.50688138683-2.469397136098.27256983305-2.4177881892.010132596070.277467662438-0.86382756691-0.2305562513740.74748170892-0.4167179530810.2939057985370.312717170291-0.5279195176140.138382030120.411066669663-0.04225424559430.05460815147930.5703848468580.04316614111370.2980599811331.5218168927-17.28985253387.6228244377
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 177 )AA2 - 1771 - 176
22chain 'A' and (resid 178 through 245 )AA178 - 245177 - 244
33chain 'A' and (resid 246 through 324 )AA246 - 324245 - 323
44chain 'B' and (resid 3 through 25 )BE3 - 251 - 23
55chain 'B' and (resid 26 through 34 )BE26 - 3424 - 32
66chain 'B' and (resid 35 through 70 )BE35 - 7033 - 68
77chain 'B' and (resid 71 through 97 )BE71 - 9769 - 95
88chain 'B' and (resid 98 through 105 )BE98 - 10596 - 103
99chain 'B' and (resid 106 through 121 )BE106 - 121104 - 119
1010chain 'B' and (resid 122 through 133 )BE122 - 133120 - 131
1111chain 'B' and (resid 134 through 141 )BE134 - 141132 - 139
1212chain 'C' and (resid 2 through 34 )CI2 - 341 - 33
1313chain 'C' and (resid 35 through 108 )CI35 - 10834 - 107
1414chain 'C' and (resid 109 through 177 )CI109 - 177108 - 176
1515chain 'C' and (resid 178 through 222 )CI178 - 222177 - 221
1616chain 'C' and (resid 223 through 245 )CI223 - 245222 - 244
1717chain 'C' and (resid 246 through 289 )CI246 - 289245 - 288
1818chain 'C' and (resid 290 through 307 )CI290 - 307289 - 306
1919chain 'C' and (resid 308 through 324 )CI308 - 324307 - 323
2020chain 'D' and (resid 4 through 54 )DM4 - 541 - 51
2121chain 'D' and (resid 55 through 70 )DM55 - 7052 - 67
2222chain 'D' and (resid 71 through 121 )DM71 - 12168 - 118
2323chain 'D' and (resid 122 through 141 )DM122 - 141119 - 138
2424chain 'E' and (resid 2 through 107 )EP2 - 1071 - 106
2525chain 'E' and (resid 108 through 177 )EP108 - 177107 - 176
2626chain 'E' and (resid 178 through 245 )EP178 - 245177 - 244
2727chain 'E' and (resid 246 through 289 )EP246 - 289245 - 288
2828chain 'E' and (resid 290 through 307 )EP290 - 307289 - 306
2929chain 'E' and (resid 308 through 324 )EP308 - 324307 - 323
3030chain 'F' and (resid 3 through 12 )FT3 - 121 - 10
3131chain 'F' and (resid 13 through 25 )FT13 - 2511 - 23
3232chain 'F' and (resid 26 through 54 )FT26 - 5424 - 52
3333chain 'F' and (resid 55 through 80 )FT55 - 8053 - 78
3434chain 'F' and (resid 81 through 97 )FT81 - 9779 - 95
3535chain 'F' and (resid 98 through 105 )FT98 - 10596 - 103
3636chain 'F' and (resid 106 through 133 )FT106 - 133104 - 131
3737chain 'F' and (resid 134 through 142 )FT134 - 142132 - 140
3838chain 'G' and (resid 2 through 107 )GW2 - 1071 - 106
3939chain 'G' and (resid 108 through 177 )GW108 - 177107 - 176
4040chain 'G' and (resid 178 through 245 )GW178 - 245177 - 244
4141chain 'G' and (resid 246 through 289 )GW246 - 289245 - 288
4242chain 'G' and (resid 290 through 307 )GW290 - 307289 - 306
4343chain 'G' and (resid 308 through 324 )GW308 - 324307 - 323
4444chain 'H' and (resid 3 through 25 )HAA3 - 251 - 23
4545chain 'H' and (resid 26 through 43 )HAA26 - 4324 - 41
4646chain 'H' and (resid 44 through 80 )HAA44 - 8042 - 78
4747chain 'H' and (resid 81 through 97 )HAA81 - 9779 - 95
4848chain 'H' and (resid 98 through 105 )HAA98 - 10596 - 103
4949chain 'H' and (resid 106 through 121 )HAA106 - 121104 - 119
5050chain 'H' and (resid 122 through 133 )HAA122 - 133120 - 131
5151chain 'H' and (resid 134 through 141 )HAA134 - 141132 - 139

+
万見について

-
お知らせ

-
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

-
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

+
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

+
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

+
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。

-
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