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- PDB-7c72: Structure of a mycobacterium tuberculosis puromycin-hydrolyzing p... -

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基本情報

登録情報
データベース: PDB / ID: 7c72
タイトルStructure of a mycobacterium tuberculosis puromycin-hydrolyzing peptidase
要素Prolyl oligopeptidase
キーワードHYDROLASE / Prolyl oligopeptidase / tuberculosis / acyl aminopeptidase
機能・相同性D-MALATE
機能・相同性情報
生物種Mycobacterium tuberculosis (結核菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.00004456732 Å
データ登録者Ruiz-Carrillo, D. / Zhao, Y.H. / Feng, Q. / Zhou, X. / Zhang, Y. / Jiang, J. / Lukman, M.
資金援助 中国, 1件
組織認可番号
Other private 中国
引用ジャーナル: Proteins / : 2021
タイトル: Mycobacterium tuberculosis puromycin hydrolase displays a prolyl oligopeptidase fold and an acyl aminopeptidase activity.
著者: Zhao, Y. / Feng, Q. / Zhou, X. / Zhang, Y. / Lukman, M. / Jiang, J. / Ruiz-Carrillo, D.
履歴
登録2020年5月22日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02021年3月24日Provider: repository / タイプ: Initial release
改定 1.12021年5月19日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
改定 1.22023年11月29日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: Prolyl oligopeptidase
B: Prolyl oligopeptidase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)151,3155
ポリマ-150,9962
非ポリマー3183
00
1
A: Prolyl oligopeptidase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)75,8164
ポリマ-75,4981
非ポリマー3183
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint0 kcal/mol
Surface area25210 Å2
手法PISA
2
B: Prolyl oligopeptidase


分子量 (理論値)分子数
合計 (水以外)75,4981
ポリマ-75,4981
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area25670 Å2
手法PISA
単位格子
Length a, b, c (Å)183.950, 183.950, 146.310
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALALEULEU(chain 'A' and (resid 5 through 26 or resid 28...AA5 - 2625 - 46
12LEULEULEULEU(chain 'A' and (resid 5 through 26 or resid 28...AA28 - 5648 - 76
13GLYGLYASPASP(chain 'A' and (resid 5 through 26 or resid 28...AA58 - 7078 - 90
14THRTHRTHRTHR(chain 'A' and (resid 5 through 26 or resid 28...AA7393
15VALVALILEILE(chain 'A' and (resid 5 through 26 or resid 28...AA75 - 8695 - 106
16THRTHRTHRTHR(chain 'A' and (resid 5 through 26 or resid 28...AA88108
17GLYGLYPROPRO(chain 'A' and (resid 5 through 26 or resid 28...AA91 - 112111 - 132
18PROPROPROPRO(chain 'A' and (resid 5 through 26 or resid 28...AA114 - 119134 - 139
19PROPROPROPRO(chain 'A' and (resid 5 through 26 or resid 28...AA121 - 136141 - 156
110THRTHRGLUGLU(chain 'A' and (resid 5 through 26 or resid 28...AA139 - 146159 - 166
111ARGARGVALVAL(chain 'A' and (resid 5 through 26 or resid 28...AA177 - 199197 - 219
112GLYGLYASPASP(chain 'A' and (resid 5 through 26 or resid 28...AA201 - 241221 - 261
113THRTHRPROPRO(chain 'A' and (resid 5 through 26 or resid 28...AA244 - 247264 - 267
114THRTHRLEULEU(chain 'A' and (resid 5 through 26 or resid 28...AA249 - 254269 - 274
115GLUGLUGLUGLU(chain 'A' and (resid 5 through 26 or resid 28...AA256 - 266276 - 286
116SERSERPROPRO(chain 'A' and (resid 5 through 26 or resid 28...AA268 - 291288 - 311
117ALAALATHRTHR(chain 'A' and (resid 5 through 26 or resid 28...AA293 - 383313 - 403
118VALVALARGARG(chain 'A' and (resid 5 through 26 or resid 28...AA386 - 390406 - 410
119GLUGLULEULEU(chain 'A' and (resid 5 through 26 or resid 28...AA392 - 393412 - 413
120PROPROPROPRO(chain 'A' and (resid 5 through 26 or resid 28...AA397 - 413417 - 433
121GLYGLYPROPRO(chain 'A' and (resid 5 through 26 or resid 28...AA415 - 433435 - 453
122GLYGLYARGARG(chain 'A' and (resid 5 through 26 or resid 28...AA435 - 490455 - 510
123GLNGLNLEULEU(chain 'A' and (resid 5 through 26 or resid 28...AA492 - 568512 - 588
124GLYGLYGLUGLU(chain 'A' and (resid 5 through 26 or resid 28...AA570 - 579590 - 599
125ALAALASERSER(chain 'A' and (resid 5 through 26 or resid 28...AA581 - 614601 - 634
126PHEPHELEULEU(chain 'A' and (resid 5 through 26 or resid 28...AA617 - 621637 - 641
127LYSLYSPHEPHE(chain 'A' and (resid 5 through 26 or resid 28...AA624 - 640644 - 660
128LYSLYSTHRTHR(chain 'A' and (resid 5 through 26 or resid 28...AA642 - 660662 - 680
129GLYGLYILEILE(chain 'A' and (resid 5 through 26 or resid 28...AA662 - 671682 - 691
130LEULEUVALVAL(chain 'A' and (resid 5 through 26 or resid 28...AA673 - 675693 - 695
21ALAALALEULEU(chain 'B' and (resid 5 through 26 or resid 28...BB5 - 2625 - 46
22LEULEULEULEU(chain 'B' and (resid 5 through 26 or resid 28...BB28 - 5648 - 76
23GLYGLYASPASP(chain 'B' and (resid 5 through 26 or resid 28...BB58 - 7078 - 90
24THRTHRTHRTHR(chain 'B' and (resid 5 through 26 or resid 28...BB7393
25VALVALILEILE(chain 'B' and (resid 5 through 26 or resid 28...BB75 - 8695 - 106
26THRTHRTHRTHR(chain 'B' and (resid 5 through 26 or resid 28...BB88108
27GLYGLYPROPRO(chain 'B' and (resid 5 through 26 or resid 28...BB91 - 112111 - 132
28PROPROPROPRO(chain 'B' and (resid 5 through 26 or resid 28...BB114 - 119134 - 139
29PROPROPROPRO(chain 'B' and (resid 5 through 26 or resid 28...BB121 - 136141 - 156
210THRTHRGLUGLU(chain 'B' and (resid 5 through 26 or resid 28...BB139 - 146159 - 166
211ARGARGVALVAL(chain 'B' and (resid 5 through 26 or resid 28...BB177 - 199197 - 219
212GLYGLYASPASP(chain 'B' and (resid 5 through 26 or resid 28...BB201 - 241221 - 261
213THRTHRPROPRO(chain 'B' and (resid 5 through 26 or resid 28...BB244 - 247264 - 267
214THRTHRLEULEU(chain 'B' and (resid 5 through 26 or resid 28...BB249 - 254269 - 274
215GLUGLUGLUGLU(chain 'B' and (resid 5 through 26 or resid 28...BB256 - 266276 - 286
216SERSERPROPRO(chain 'B' and (resid 5 through 26 or resid 28...BB268 - 291288 - 311
217ALAALATHRTHR(chain 'B' and (resid 5 through 26 or resid 28...BB293 - 383313 - 403
218VALVALARGARG(chain 'B' and (resid 5 through 26 or resid 28...BB386 - 390406 - 410
219GLUGLULEULEU(chain 'B' and (resid 5 through 26 or resid 28...BB392 - 393412 - 413
220PROPROPROPRO(chain 'B' and (resid 5 through 26 or resid 28...BB397 - 413417 - 433
221GLYGLYPROPRO(chain 'B' and (resid 5 through 26 or resid 28...BB415 - 433435 - 453
222GLYGLYARGARG(chain 'B' and (resid 5 through 26 or resid 28...BB435 - 490455 - 510
223GLNGLNLEULEU(chain 'B' and (resid 5 through 26 or resid 28...BB492 - 568512 - 588
224GLYGLYGLUGLU(chain 'B' and (resid 5 through 26 or resid 28...BB570 - 579590 - 599
225ALAALASERSER(chain 'B' and (resid 5 through 26 or resid 28...BB581 - 614601 - 634
226PHEPHELEULEU(chain 'B' and (resid 5 through 26 or resid 28...BB617 - 621637 - 641
227LYSLYSPHEPHE(chain 'B' and (resid 5 through 26 or resid 28...BB624 - 640644 - 660
228LYSLYSTHRTHR(chain 'B' and (resid 5 through 26 or resid 28...BB642 - 660662 - 680
229GLYGLYILEILE(chain 'B' and (resid 5 through 26 or resid 28...BB662 - 671682 - 691
230LEULEUVALVAL(chain 'B' and (resid 5 through 26 or resid 28...BB673 - 675693 - 695

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要素

#1: タンパク質 Prolyl oligopeptidase


分子量: 75498.156 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Mycobacterium tuberculosis (結核菌)
遺伝子: CNE19725.1 / プラスミド: pet28a+ / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
#2: 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: 2 / 由来タイプ: 合成 / : C3H8O3
#3: 化合物 ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / D-りんご酸


分子量: 134.087 Da / 分子数: 1 / 由来タイプ: 合成 / : C4H6O5
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: 4.87 Å3/Da / 溶媒含有率: 74.73 % / 解説: diamond shaped crystals with a hexagonal symmetry
結晶化温度: 287.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7
詳細: 0.1 M BIS-TRIS propane pH 7, 2.4 M DL-Malic acid pH 7.0 20 % (v/v) glycerol

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データ収集

回折平均測定温度: 120 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: SSRF / ビームライン: BL18U1 / 波長: 0.97853 Å
検出器タイプ: DECTRIS PILATUS3 X CdTe 1M / 検出器: PIXEL / 日付: 2018年12月12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: 0.97853 Å / 相対比: 1
反射解像度: 3→46.4897392546 Å / Num. obs: 56249 / % possible obs: 99.9 % / 冗長度: 19.5 % / Biso Wilson estimate: 111.913128818 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.2407 / Rpim(I) all: 0.0564 / Rrim(I) all: 0.2473 / Net I/σ(I): 7.97
反射 シェル解像度: 3→3.107 Å / 冗長度: 19.5 % / Rmerge(I) obs: 3.358 / Mean I/σ(I) obs: 0.86 / Num. unique obs: 5581 / CC1/2: 0.297 / CC star: 0.676 / Rpim(I) all: 0.7807 / Rrim(I) all: 3.448 / % possible all: 100

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解析

ソフトウェア
名称バージョン分類
PHENIX1.12_2829精密化
XDSデータ削減
XSCALEデータスケーリング
BALBES位相決定
精密化構造決定の手法: 分子置換
開始モデル: 3AZO
解像度: 3.00004456732→46.4897392546 Å / SU ML: 0.436494325758 / 交差検証法: FREE R-VALUE / σ(F): 1.35974463903 / 位相誤差: 24.7533958124
Rfactor反射数%反射Selection details
Rfree0.218114150504 2004 3.56361696452 %0.05
Rwork0.17714709451 ---
obs0.178582720641 56235 99.9306962363 %-
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso mean: 134.932464909 Å2
精密化ステップサイクル: LAST / 解像度: 3.00004456732→46.4897392546 Å
タンパク質核酸リガンド溶媒全体
原子数10055 0 21 0 10076
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.0079219333995110367
X-RAY DIFFRACTIONf_angle_d1.2217622512214180
X-RAY DIFFRACTIONf_chiral_restr0.06445658883721508
X-RAY DIFFRACTIONf_plane_restr0.008488522929591889
X-RAY DIFFRACTIONf_dihedral_angle_d10.24154112436057
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.00004456732-3.07510.3561828288441360.3400787303193831X-RAY DIFFRACTION100
3.0751-3.15820.3788658263981480.3121695086443885X-RAY DIFFRACTION100
3.1582-3.25110.3236372963811400.2912050399033850X-RAY DIFFRACTION100
3.2511-3.3560.2793864592421440.2495191156083886X-RAY DIFFRACTION100
3.356-3.47590.2598715569811440.2291026507493834X-RAY DIFFRACTION99.9497487437
3.4759-3.6150.2591104926321360.2128190152193887X-RAY DIFFRACTION99.9751491054
3.615-3.77950.2244043126051410.2044687491943836X-RAY DIFFRACTION99.9246231156
3.7795-3.97860.2349403075881440.1813805133543886X-RAY DIFFRACTION99.97519226
3.9786-4.22780.2022799743391400.1747144329973858X-RAY DIFFRACTION99.9250187453
4.2278-4.55390.1998904730031490.154710666693885X-RAY DIFFRACTION99.9504459861
4.5539-5.01170.1915716790621440.1494639109433871X-RAY DIFFRACTION99.9502116007
5.0117-5.73580.19285998121470.1572492461623892X-RAY DIFFRACTION100
5.7358-7.22210.2531184928621470.1923335396853876X-RAY DIFFRACTION99.8263027295
7.2221-46.48973925460.1808486550451440.1424019902613954X-RAY DIFFRACTION99.5626822157
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.880298349023.073698271280.4848875249317.028634657693.030863817121.51244054423-0.270582392844-0.3545513342140.9999473544070.0756862132009-0.1474721807631.11818276555-0.577561860099-0.2768755569430.6231070543431.032657192570.140638753713-0.3004614340230.8481581562030.09603678412241.29842434872-25.0535966124-65.15762570891.18721676066
28.95935121623-1.958678979590.8478382194697.94861336773-0.9540739229058.570759430530.1972996113030.1013647614530.623754405245-0.169657510165-0.2515448217481.285589161040.286308952009-1.344360125450.1583421370830.752769521049-0.0157162722111-0.08223093200510.632551633029-0.1342558078880.821021974486-32.3199970353-84.0893404557-1.29707268048
33.47858243598-3.268407309672.305581420494.37605561216-3.656702612923.501766306720.29704529628-2.125717157681.603275606630.1555662502220.0268456738756-0.2642016768780.89455650373-2.46205740631-0.1746817921041.0970939024-0.01385525969760.1488331126821.03922582186-0.118944589921.20804995641-36.1756786028-92.38531171544.29750281532
44.85156318577-4.145105195722.827431080417.47310364478-7.509215722558.08223912180.2453615470490.118775850969-0.3877923139130.304107627263-0.1107895995060.2983252306511.40548358192-0.610045218144-0.142995399860.781766442874-0.08967288539570.01074813118560.668156004815-0.09364864784270.931617526757-23.6854585397-96.53323044280.35380312087
57.45928542426-2.192716733912.540119696237.4576172202-1.888486246423.26054331208-0.308123478214-1.370990861060.452825946191.05942363785-0.1284879704580.653032083830.611366929458-0.5271971910.4826417499560.816580717364-0.0303057386426-0.05964889530210.490615744569-0.02482851339250.7703621907-20.6308499838-98.23317303126.40363223101
68.245143486721.04127073337-1.352003493474.700460212390.5812884157842.40596301036-0.0674442754044-0.163589430661-0.5349247999930.177080378202-0.327096055420.1600925109560.412201785484-0.3599876441420.4030529955720.7309056288450.0228440119304-0.07142212221030.51432678409-0.04872344762630.655713862603-15.6700870863-99.0421348379-7.22606181615
74.706676965-3.915937293144.306758611268.69795682045-4.420743288945.34711874278-0.3113346506541.33259811795-0.116022868683-0.782958568074-0.174745225923-0.3476212317990.6475398974511.280957322480.3928254339120.8430677998190.06680360568230.03676621629970.7216482404750.09440370017210.855448493528-8.70078790567-90.5890408323-17.3712766649
84.712648533545.432607637094.547391744026.749686042236.053672063665.936745446440.2692445693630.628796446099-0.2049187886960.2730501656870.0465157988239-1.459564798070.452598857612-0.357269815689-0.3967330322791.119648215160.205273114153-0.107297398280.998221444864-0.01783083444960.790901751993-5.83394357086-89.8380604825-20.2350162363
94.81655673544-0.635310621035-2.086805223393.61213254434-1.245150623229.31999994446-0.2793345927460.1771091943270.5089973784710.484745899412-0.0828091263956-0.9390349089470.1394896523391.475864273050.2611669325470.8400472224920.133368496595-0.1632988407170.8687559468750.03556077120931.17630691474-7.89705374346-81.9103279488-15.016581057
108.107719436032.96944599577-1.744951001196.495887107873.440902580217.56324120699-0.1777930574371.197071710621.32151319672-0.690196634066-0.1447144817650.378994326138-0.8936710641780.4812793346430.5798210411490.8507100309120.125797648134-0.2904042435951.017067119780.2645090219391.11110131973-14.6492232164-77.0058171571-22.9784592814
117.4739613841-2.92783196601-5.150201559753.457095933651.445278385743.591400045730.1281191632970.3318103476710.679761213699-0.51886144802-0.2865889170520.327490649081-0.115608510878-0.7424367925740.1421508950310.7637650449280.0838130869038-0.3059134650570.7997719596120.148582230570.95455573224-23.5975401073-70.2252837336-15.3300628641
127.87150773467-2.030789878761.459949269848.269316614190.1297691501677.495036636040.5957865278670.6359232870080.517966391217-0.452929289045-0.4056137663741.01088069458-0.558084789633-0.05842918913660.1889250836211.150062866370.0111385489211-0.4163260226170.976843323260.0898229513531.4747336471-17.5625658511-55.5769285701-4.20637000237
139.32142078716-8.588030419764.307015707598.09957433415-3.194963758519.36783261112-0.5304983050013.024282688242.59830727049-1.18539919789-3.11866100018-2.23745105153-0.1617057206932.515464173792.55219616611.48962377193-0.0746773934130.05341714893681.433115580880.5356785639091.797562293899.3707935576-65.8483948639-4.22591732182
142.01452638451-2.89958897629-2.299247573014.719626893164.801227856935.940069903320.07661878194540.03315915589851.16882925848-1.474035704910.110234989059-0.124820190941-0.893271603193-0.441336826927-0.1617366325790.9883772671-0.0231662556311-0.3556175328050.8495775152460.04468527046331.53456731037-6.3355024919-54.09668062422.05882747664
151.99105771785-1.47552777885-2.769711523945.880513863641.53748914373.31935444843-0.2559570552310.4710846047680.640932950198-0.436788169780.0641121789610.103832489913-0.3710000524530.1286527924840.1706596719430.725827977345-0.0299353965638-0.4201445557610.613284204946-0.002937250592971.13775213563-2.4166579465-66.07230806814.94471274153
169.238704230421.56148517444-6.907567575576.395894783232.475599040798.40862683022-0.4971348349-0.852360327596-0.6982457660430.131684118375-0.0840396814987-0.6182273984081.344693119150.1149031536490.5175420230570.9512780946430.177821513006-0.3041013244930.7437653688990.07335855759430.765376210591-2.24026386736-86.539629113310.6826309223
175.41890257674-5.6847629453-1.124107100785.958962955151.032424737045.057870152-1.04682152002-1.458596020480.7613041244451.244926711960.519573226733-1.654412745370.1965726155561.788812114450.09199801930091.261369402750.254551670244-0.4051513829141.0926431028-0.06900516697731.230778161957.39774646132-82.580919917915.5759548217
184.985322134411.992538087450.9350546389625.930628032411.633289458287.123900334320.025058198657-0.362310461337-0.009885703359130.53796656227-0.09470126576720.373691777520.291787590572-0.21122392258-0.01497704687030.9263253995510.122415691265-0.246604384830.652272485614-0.1393793371121.00371812857-7.97761153752-72.244841513621.302719218
193.50183418994-3.77737100638-1.444992037555.5144657163-0.5585979234953.81567110348-0.176352345501-1.308232869762.1717168557-0.889446979925-0.5694844275760.967512476995-1.14829778317-0.5782896334460.4810703227591.114358313330.180543454592-0.3057960238680.876415885964-0.278469627271.70716527056-15.7483953289-58.192339213315.3551161881
202.53441098622-2.45124222663-0.8754505479779.89177289763-2.109972614371.468510988281.995371222270.682945586735-0.897968352924-0.972181717801-0.7864872849242.567706865020.37530117512-1.18932376519-1.328411529961.082882124080.0887780097127-0.443883152481.33329516229-0.3954357283361.07438615078-12.1990315031-58.343156191126.4197850395
212.563736782051.42004547293-0.557339814254.04337685362-3.186105898823.39341817431-0.961998056301-0.6754604882090.04917945370691.312791785740.142727454687-1.47162190529-0.902099423602-1.0138085131.286513765471.331254584970.360065595384-0.3583356809761.12234923726-0.03387834634861.14873687024-37.3397906011-54.767484731-14.6689258361
228.36405200871-1.80839774268-3.367529607877.437840334970.1835756094038.05572297036-0.2239643817010.3226399828031.849538712890.0604108373613-0.787694065069-1.150611453150.7298967823190.8425403477990.5322021488850.9824976935970.0731742750022-0.2632737572041.733139758450.728746093121.85009257387-17.9236123117-56.0586522467-34.9391769592
232.06054457834-3.50328639684-0.9437404380255.925852834680.8266752046867.14700218065-0.420205029526-0.207100644490.309865241982-0.1542199485290.180105553997-0.565415912260.03831083561851.11857987667-0.03691238531180.909165517855-0.156496905051-0.1900730077791.669063277180.5768292388841.87993452911-14.5948335546-51.4556450107-37.5734937364
245.074946544550.1701088813222.606542531450.547422434151.227171839695.434369649960.2574581372931.092102349410.727198184107-1.72200602222-0.05810602907930.1680528838850.2228941467290.464618783023-0.1896763588941.35295682109-0.03909618944460.09779727554312.029445448410.8321379058282.18754531217-7.3006115333-49.3685492604-42.1517590932
256.79503758225-7.214947528832.398804862847.71615622896-2.570318576750.8559479016270.2962131968380.2235661033270.633535074649-0.857282439377-1.08796584974-3.24642941486-0.4368877197531.729362842831.660039293641.075535807030.04939333129820.2676939537052.255463079321.126496959012.80708829998-10.8985883389-43.6165146982-48.9270136699
265.62246191872-1.055673106886.932229072242.37759420876-2.190303810468.947778552230.906740388139-1.4490717906-2.14465514925-1.14566707608-1.11992761933-1.980057710230.3480780158040.6563533081450.5690215099141.239178918080.1895357703560.2677171783452.167502112271.283518849262.10713297177-16.7380581227-41.9458818591-53.9383691024
274.92346743995-5.079663305026.306694270425.34951013393-6.313926795728.23353638938-1.24101330638-1.815787123830.734034842668-0.1345018565340.852529486408-2.04669520647-0.4092049073870.2215127538661.788463581391.25668401606-0.02046548668020.3737444782331.900811184520.4494715367112.39409356334-6.38208316915-40.3963375649-55.6073368889
289.38269373816-2.773335384420.381058466693.432771464781.882164276294.27691492213-0.1249568792470.5830861907830.614938344705-1.80414342257-0.307322933476-0.3184315739311.355732587161.721092966790.6032511940331.714360828520.609276072444-0.01919864759532.128892454690.6511846666571.5908110957-27.8890217962-45.7536634815-58.3014440605
292.682252113931.44452509608-0.3954918478462.75985130070.2384395684250.1714622117950.159829061939-0.0154341425954-0.6493209942-0.629567735612-1.19176996033-0.656383360157-0.9657789154742.038400068410.528020665951.834484439660.414846625629-0.1052673498452.200474605070.7466198637421.12692850317-28.3529257095-48.5232548376-63.4304968483
302.182355925411.26249553477-1.592953829963.2314561179-2.411339520542.491737447650.2826360261681.37037603254-0.0706630966367-1.82801488657-0.7101812717210.1425667048160.5268944698090.2124261540870.346321640981.761421189860.455267682751-0.3911542811721.795992801420.1031739818751.16761460481-35.2792734472-57.8752514398-57.4253834971
311.849595406020.711615785357-0.6333098553365.00558024810.2649736267970.259692090019-0.0727244746909-0.766946682764-0.185761810266-0.8538203078820.767257384711.57417110036-0.409420955247-1.626526835340.3804009788421.524434247721.61094294536-0.9111474213852.369428699070.4031636562540.676714301914-27.4688304285-59.3753423566-50.205924325
322.410690101762.092986378590.2098914872116.046884560683.28916526769.850370231590.0452003440170.429389496643-0.148047944624-1.13605422681-0.425688853265-0.06063454110731.524173704950.4006732296990.2396428401581.352598084050.39772664815-0.334008205111.125453697190.07848889214931.26310679391-31.8698061942-66.9346559731-44.6213629088
334.50789373622-1.62538377362-2.057311428165.69150441446-4.19112484786.355104422540.0542314940299-0.902439949991-1.09144940922-0.577101712183-1.06761740616-0.387815830382-0.09474455165771.160711169330.7904481655240.9163599172950.210889602571-0.3852436942651.079173565520.2104064513761.457065127-27.6656433734-66.0644530445-29.0811293452
348.009958973484.336918579341.872319374128.16655423553-1.781181156939.69498804579-0.553422329573-0.485165489036-0.793803019923-0.4943565773760.2271897783110.238990067440.000198337810099-1.378315732450.2086033669121.03115864020.174632718369-0.267103490381.08504950554-0.103223195771.43073336171-51.863804436-55.4274444384-32.7011888781
352.78087105008-0.9547268554030.7796998696244.79383298788-1.721597645254.79426506735-0.4477274380620.07227485174330.312014489936-0.1178556775020.293725279163-0.0599937604293-0.27782076743-0.1417450144750.2254545277930.8757704144010.126677014365-0.4544449874230.9289278354180.004866544116851.22109282236-46.1378727371-44.9711854562-30.5917335917
364.18940449989-0.9476826014692.158792387570.757706310235-2.365382448627.15824848204-0.186719465788-0.4194404080820.7625892143831.1720086429-0.0468897849885-0.843464999145-1.96233534956-0.6024341231640.261528584971.552517348990.165759257937-0.7174508607790.940583926245-0.003356250431971.53042027667-46.5768477908-28.9942193365-33.5931784701
376.51999382724.37356726048-5.618611997193.80427829982-4.353211722865.223842722130.5190534807410.1694093025572.29338784981-1.590196304861.423052163180.42863611524-1.68570620332.44416116907-1.459222245712.03725755534-0.540599060148-0.7538966237392.064769676860.3493112175012.49135795365-35.5405346645-27.7908346419-28.3524275186
386.04152077925-1.69830573443.658395590835.5657682999-5.960971674876.98000854216-1.03870265249-0.3686499764052.686690577393.412058909590.358058156333-0.812521378066-2.64415157953-0.1231450285711.447169746652.247104505380.0334902810378-0.6213443363660.879477365544-0.09378305016692.21909388443-45.3760416329-27.0675381697-19.1538552742
397.026831985941.20755122716-3.131409737926.42372609978-3.240828304818.54084069561-1.25001432646-0.4914429006551.681356199171.188077507810.229617144629-0.720073398583-1.78574875751-0.005539248304480.5204840914372.037898402490.121047374721-0.9738225081681.45147220735-0.08795100561421.81353103672-36.6245478794-41.7059073828-16.4613747758
401.971367472131.23175517302-2.804792085250.819343337962-2.222931419747.831641886972.692401400891.894598931-0.981465565423-2.53637221862-2.694924778831.850051439612.911200621094.03983351003-0.9293706986172.159229494430.245891732389-0.4648273793940.996358275186-0.3080866795081.17655274488-42.3731475293-35.2680431205-8.43399291229
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 4:51)
2X-RAY DIFFRACTION2(chain A and resid 52:107)
3X-RAY DIFFRACTION3(chain A and resid 108:124)
4X-RAY DIFFRACTION4(chain A and resid 125:153)
5X-RAY DIFFRACTION5(chain A and resid 169:184)
6X-RAY DIFFRACTION6(chain A and resid 185:251)
7X-RAY DIFFRACTION7(chain A and resid 252:277)
8X-RAY DIFFRACTION8(chain A and resid 278:289)
9X-RAY DIFFRACTION9(chain A and resid 290:310)
10X-RAY DIFFRACTION10(chain A and resid 311:346)
11X-RAY DIFFRACTION11(chain A and resid 347:391)
12X-RAY DIFFRACTION12(chain A and resid 392:408)
13X-RAY DIFFRACTION13(chain A and resid 409:416)
14X-RAY DIFFRACTION14(chain A and resid 417:447)
15X-RAY DIFFRACTION15(chain A and resid 448:551)
16X-RAY DIFFRACTION16(chain A and resid 552:576)
17X-RAY DIFFRACTION17(chain A and resid 577:587)
18X-RAY DIFFRACTION18(chain A and resid 588:640)
19X-RAY DIFFRACTION19(chain A and resid 641:668)
20X-RAY DIFFRACTION20(chain A and resid 669:675)
21X-RAY DIFFRACTION21(chain B and resid 4:27)
22X-RAY DIFFRACTION22(chain B and resid 28:48)
23X-RAY DIFFRACTION23(chain B and resid 49:87)
24X-RAY DIFFRACTION24(chain B and resid 88:112)
25X-RAY DIFFRACTION25(chain B and resid 113:140)
26X-RAY DIFFRACTION26(chain B and resid 141:184)
27X-RAY DIFFRACTION27(chain B and resid 185:198)
28X-RAY DIFFRACTION28(chain B and resid 199:239)
29X-RAY DIFFRACTION29(chain B and resid 240:262)
30X-RAY DIFFRACTION30(chain B and resid 263:308)
31X-RAY DIFFRACTION31(chain B and resid 309:315)
32X-RAY DIFFRACTION32(chain B and resid 316:371)
33X-RAY DIFFRACTION33(chain B and resid 372:403)
34X-RAY DIFFRACTION34(chain B and resid 404:425)
35X-RAY DIFFRACTION35(chain B and resid 426:571)
36X-RAY DIFFRACTION36(chain B and resid 572:605)
37X-RAY DIFFRACTION37(chain B and resid 606:615)
38X-RAY DIFFRACTION38(chain B and resid 616:632)
39X-RAY DIFFRACTION39(chain B and resid 633:667)
40X-RAY DIFFRACTION40(chain B and resid 668:675)

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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