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- PDB-6s7m: Structure of parasitic PEX14 in complex with a benzo[b]thiophene-... -

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基本情報

登録情報
データベース: PDB / ID: 6s7m
タイトルStructure of parasitic PEX14 in complex with a benzo[b]thiophene-7-carboxylic acid.
要素Peroxin 14
キーワードSIGNALING PROTEIN / PEX14 / PPI / PEX14/PEX5 / Trypanosomes / FBDD
機能・相同性
機能・相同性情報


glycosome membrane / peroxisomal importomer complex / protein import into peroxisome matrix, docking / protein targeting to vacuole / glycosome / post-transcriptional regulation of gene expression / signaling receptor binding
類似検索 - 分子機能
Peroxisome membrane anchor protein Pex14p, N-terminal / Peroxisomal membrane protein 14 / Pex14 N-terminal domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
類似検索 - ドメイン・相同性
1-benzothiophene-7-carboxylic acid / DI(HYDROXYETHYL)ETHER / Peroxisomal membrane protein PEX14
類似検索 - 構成要素
生物種Trypanosoma brucei brucei (トリパノソーマ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.75845964621 Å
データ登録者Hassaan, E. / Heine, A. / Klebe, G.
資金援助 ドイツ, 1件
組織認可番号国
European Commission ドイツ
引用ジャーナル: To Be Published
タイトル: Structure of parasitic PEX14 in complex with a benzo[b]thiophene-7-carboxylic acid.
著者: Hassaan, E. / Heine, A. / Klebe, G.
履歴
登録2019年7月5日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02020年7月15日Provider: repository / タイプ: Initial release
改定 1.12024年5月15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 / 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

ダウンロードとリンク

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集合体

登録構造単位
A: Peroxin 14
B: Peroxin 14
C: Peroxin 14
D: Peroxin 14
E: Peroxin 14
F: Peroxin 14
G: Peroxin 14
H: Peroxin 14
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)63,89016
ポリマ－62,6088
非ポリマー1,2818
水2,720151
1
A: Peroxin 14
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)8,1103
ポリマ－7,8261
非ポリマー2842
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Peroxin 14
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)8,0042
ポリマ－7,8261
非ポリマー1781
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: Peroxin 14
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)8,0042
ポリマ－7,8261
非ポリマー1781
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: Peroxin 14
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)8,1103
ポリマ－7,8261
非ポリマー2842
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
5
E: Peroxin 14
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)8,1823
ポリマ－7,8261
非ポリマー3562
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
6
F: Peroxin 14


分子量 (理論値)分子数
合計 (水以外)7,8261
ポリマ－7,8261
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
7
G: Peroxin 14


分子量 (理論値)分子数
合計 (水以外)7,8261
ポリマ－7,8261
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
8
H: Peroxin 14


分子量 (理論値)分子数
合計 (水以外)7,8261
ポリマ－7,8261
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)79.786, 39.712, 81.100
Angle α, β, γ (deg.)90.000, 90.082, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
41
51
61
71
81

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
11ARGARGVALVAL(chain A and ((resid 7 and (name N or name...AA7 - 119 - 13
12ASNASNSERSER(chain A and ((resid 7 and (name N or name...AA13 - 2915 - 31
13LYSLYSILEILE(chain A and ((resid 7 and (name N or name...AA31 - 4533 - 47
14GLUGLUPHEPHE(chain A and ((resid 7 and (name N or name...AA47 - 4949 - 51
15LYSLYSASNASN(chain A and ((resid 7 and (name N or name...AA51 - 5953 - 61
16ILEILEILEILE(chain A and ((resid 7 and (name N or name...AA6163
17ILEILEILEILE(chain A and ((resid 7 and (name N or name...AA6466
28ARGARGVALVAL(chain B and ((resid 7 and (name N or name...BB7 - 119 - 13
29ASNASNSERSER(chain B and ((resid 7 and (name N or name...BB13 - 2915 - 31
210LYSLYSILEILE(chain B and ((resid 7 and (name N or name...BB31 - 4533 - 47
211GLUGLUPHEPHE(chain B and ((resid 7 and (name N or name...BB47 - 4949 - 51
212LYSLYSASNASN(chain B and ((resid 7 and (name N or name...BB51 - 5953 - 61
213ILEILEILEILE(chain B and ((resid 7 and (name N or name...BB6163
214ILEILEILEILE(chain B and ((resid 7 and (name N or name...BB6466
315ARGARGVALVAL(chain C and ((resid 7 and (name N or name...CC7 - 119 - 13
316ASNASNSERSER(chain C and ((resid 7 and (name N or name...CC13 - 2915 - 31
317LYSLYSILEILE(chain C and ((resid 7 and (name N or name...CC31 - 4533 - 47
318GLUGLUPHEPHE(chain C and ((resid 7 and (name N or name...CC47 - 4949 - 51
319LYSLYSASNASN(chain C and ((resid 7 and (name N or name...CC51 - 5953 - 61
360ILEILEILEILE(chain C and ((resid 7 and (name N or name...CC6163
320ILEILEILEILE(chain C and ((resid 7 and (name N or name...CC6466
421ARGARGVALVAL(chain D and ((resid 7 and (name N or name...DD7 - 119 - 13
422ASNASNSERSER(chain D and ((resid 7 and (name N or name...DD13 - 2915 - 31
423LYSLYSILEILE(chain D and ((resid 7 and (name N or name...DD31 - 4533 - 47
424GLUGLUPHEPHE(chain D and ((resid 7 and (name N or name...DD47 - 4949 - 51
425LYSLYSASNASN(chain D and ((resid 7 and (name N or name...DD51 - 5953 - 61
426ILEILEILEILE(chain D and ((resid 7 and (name N or name...DD6163
427ILEILEILEILE(chain D and ((resid 7 and (name N or name...DD6466
528ARGARGVALVAL(chain E and ((resid 7 and (name N or name...EE7 - 119 - 13
529ASNASNSERSER(chain E and ((resid 7 and (name N or name...EE13 - 2915 - 31
530LYSLYSILEILE(chain E and ((resid 7 and (name N or name...EE31 - 4533 - 47
531GLUGLUPHEPHE(chain E and ((resid 7 and (name N or name...EE47 - 4949 - 51
532LYSLYSASNASN(chain E and ((resid 7 and (name N or name...EE51 - 5953 - 61
533ILEILEILEILE(chain E and ((resid 7 and (name N or name...EE6163
534ILEILEILEILE(chain E and ((resid 7 and (name N or name...EE6466
635ARGARGVALVAL(chain F and (resseq 7:11 or resseq 13:14 or (resid...FF7 - 119 - 13
636ASNASNSERSER(chain F and (resseq 7:11 or resseq 13:14 or (resid...FF13 - 2915 - 31
637LYSLYSILEILE(chain F and (resseq 7:11 or resseq 13:14 or (resid...FF31 - 4533 - 47
638GLUGLUPHEPHE(chain F and (resseq 7:11 or resseq 13:14 or (resid...FF47 - 4949 - 51
639LYSLYSASNASN(chain F and (resseq 7:11 or resseq 13:14 or (resid...FF51 - 5953 - 61
640ILEILEILEILE(chain F and (resseq 7:11 or resseq 13:14 or (resid...FF6163
641ILEILEILEILE(chain F and (resseq 7:11 or resseq 13:14 or (resid...FF6466
742ARGARGVALVAL(chain G and (resseq 7 or (resid 8 and (name...GG7 - 119 - 13
743ASNASNSERSER(chain G and (resseq 7 or (resid 8 and (name...GG13 - 2915 - 31
744LYSLYSILEILE(chain G and (resseq 7 or (resid 8 and (name...GG31 - 4533 - 47
745GLUGLUPHEPHE(chain G and (resseq 7 or (resid 8 and (name...GG47 - 4949 - 51
746LYSLYSASNASN(chain G and (resseq 7 or (resid 8 and (name...GG51 - 5953 - 61
747ILEILEILEILE(chain G and (resseq 7 or (resid 8 and (name...GG6163
748ILEILEILEILE(chain G and (resseq 7 or (resid 8 and (name...GG6466
849ARGARGVALVAL(chain H and ((resid 7 and (name N or name...HH7 - 119 - 13
850ASNASNSERSER(chain H and ((resid 7 and (name N or name...HH13 - 2915 - 31
851LYSLYSILEILE(chain H and ((resid 7 and (name N or name...HH31 - 4533 - 47
852GLUGLUPHEPHE(chain H and ((resid 7 and (name N or name...HH47 - 4949 - 51
853LYSLYSASNASN(chain H and ((resid 7 and (name N or name...HH51 - 5953 - 61
854ILEILEILEILE(chain H and ((resid 7 and (name N or name...HH6163
855ILEILEILEILE(chain H and ((resid 7 and (name N or name...HH6466

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要素

#1: タンパク質
Peroxin 14


分子量: 7826.022 Da / 分子数: 8 / 由来タイプ: 組換発現
由来: (組換発現) Trypanosoma brucei brucei (トリパノソーマ)
遺伝子: PEX14 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q8IEW2
#2: 化合物
ChemComp-KZ2 / 1-benzothiophene-7-carboxylic acid


分子量: 178.208 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C9H6O2S / タイプ: SUBJECT OF INVESTIGATION
#3: 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: 2 / 由来タイプ: 合成 / 式: C4H10O3
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 151 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.07 Å3/Da / 溶媒含有率: 40.47 %
結晶化温度: 291 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 0.17 M ammonium acetate, 0.085 M sodium citrate pH 5.6, 25.5% PEG4000, 15% glycerol

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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: BESSY / ビームライン: 14.1 / 波長: 0.9184 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2018年6月22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: 0.9184 Å / 相対比: 1
反射解像度: 1.758→39.893 Å / Num. obs: 49925 / % possible obs: 97.6 % / 冗長度: 3.7 % / Biso Wilson estimate: 23.026260966 Å2 / CC1/2: 0.99 / Rsym value: 0.05 / Net I/σ(I): 14.68
反射 シェル解像度: 1.758→1.767 Å / Num. unique obs: 7928

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解析

ソフトウェア
名称バージョン分類
PHENIX1.10.1_2155精密化
PHASER位相決定
Cootモデル構築
XDSデータスケーリング
XDSデータ削減
精密化構造決定の手法: 分子置換 / 解像度: 1.75845964621→39.89 Å / SU ML: 0.241096427044 / 交差検証法: FREE R-VALUE / σ(F): 1.3588830167 / 位相誤差: 28.3646510532
Rfactor反射数%反射
Rfree0.26712042883 2495 5.00531626778 %
Rwork0.230474731299 --
obs0.232337321952 49847 97.4506852261 %
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: 26.3968381408 Å2
精密化ステップサイクル: LAST / 解像度: 1.75845964621→39.89 Å
タンパク質核酸リガンド溶媒全体
原子数3918 0 86 151 4155
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.006688417221394216
X-RAY DIFFRACTIONf_angle_d0.7355721838155709
X-RAY DIFFRACTIONf_chiral_restr0.0426568661816668
X-RAY DIFFRACTIONf_plane_restr0.0048592097099796
X-RAY DIFFRACTIONf_dihedral_angle_d14.35006301182626
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION

解像度 (Å)最高解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7585-1.79230.3409157073391330.283178642673253894.7835344216
1.7923-1.82890.3445959248691390.259210738141261897.1801198449
1.8289-1.86860.2780379000121360.246421570367258797.5985663082
1.8686-1.91210.2975234542341380.242444336803262898.0155917789
1.9121-1.95990.2563672225891380.230052478936260997.5497159091
1.9599-2.01290.320005081571360.224369389741258996.0183227625
2.0129-2.07210.2499294405871380.215464822365261298.0741797432
2.0721-2.1390.253170793661370.207543773442261597.2781901732
2.139-2.21550.2554307636091390.210509971975263198.2966643009
2.2155-2.30420.2744221835291370.21417772652260897.5479744136
2.3042-2.4090.2434192591271400.214001308885265098.1703026038
2.409-2.5360.286978677571380.221164079447262897.3943661972
2.536-2.69480.2371184588741370.215966881696258896.1877867984
2.6948-2.90290.2107407777261390.237783954064263097.6031018682
2.9029-3.19490.2766131759431410.246467889681268799.1584852735
3.1949-3.65690.2459225828791430.222865876554270598.3425414365
3.6569-4.60620.2580277335561400.212522621242265297.4860335196
4.60620.3119836952891460.268759337559277797.4658219406
精密化 TLS

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0617838950020.0113233628733-0.03722589478950.05011586809240.02980346365310.02594825282390.248267793374-0.0653244389367-0.0224778281488-0.117742247958-0.2045952267870.0819581533225-0.0730216882837-0.402882146570.001859478136430.232986449214-0.00981335994975-0.06329093288970.2584113435920.00139675771640.249784164329108.1028505580.538291138415109.23424164
2-0.00152806571996-0.0180568793250.001198012738150.0132694757332-0.04429984542360.0382560704540.1020693877390.05625354624040.142190502943-0.0683892939728-0.059876444625-0.138701646877-0.183693606535-0.04557431594440.0001525659552490.2023976149440.03212275146750.02243073319580.1903091089060.01865535434120.189331292794110.53294205110.5413038564115.01524476
30.02965085864160.008991682789510.003804337221470.00541615526356-0.004959665436870.00646336115125-0.08993758394210.0111145434940.0426088810050.00598966721956-0.117375709446-0.0527731357265-0.02749805143380.06942248988514.40185371419E-50.2848721393610.0499276069756-0.07345248317970.3760996851590.06150557041760.291782963398109.73744578616.9611211991108.010225463
40.0124076740041-0.00626598371103-0.01027703091060.007479667780680.002294419741090.00419068954167-0.00975455704586-0.0490716160160.0995820382433-0.06876470482160.166946986103-0.0794203275802-0.06599362442750.1465188570614.35404117682E-50.255530972825-0.003557439652390.03713951093810.171454980685-0.01898553959330.220987097497120.99646253113.8157995105111.811204487
50.0717459270225-0.03264788852910.05724216386550.0987945054620.07400239257870.09447607425650.07052446747720.0302118259354-0.01656716520840.0432876885201-0.07766332802640.0415587567356-0.004076399263140.0668161557510.0001897801527030.1427846111030.00297270932709-0.02205987020260.1041739621340.00226587506090.19021229530190.381649681621.9682182454129.644892607
60.0326788627578-0.0485897556796-0.0695181229710.08647861109410.1274785331090.289777619028-0.1383322934720.0161626247392-0.183812260625-0.03005434341540.0668451571872-0.00982083423216-0.0662527412801-0.0849147959881-0.1482378429530.1543573021880.0384630274221-0.01841922374720.0910852197679-0.01715756852670.1395756279483.800811102229.041425971133.676140937
70.05906744051450.0367539593446-0.08257733934290.1058646097680.08539276318010.047365646539-0.165869997836-0.0765265121523-0.04299378022830.05603810911850.122595152556-0.02987587499020.206249629615-0.004967318320160.0003862877175250.1833444708060.0334222339189-0.008157454807980.158219985951-0.006444289161440.195020973028116.39801942310.8600681209134.090253564
80.000537185679069-0.0205402266325-0.0241098218260.0144697553688-0.03419918732420.1302391283430.0142223118162-0.04307642977450.0291245185679-0.132075240169-0.0927861327132-0.05328974056050.0237660857722-0.147906508407-0.001462507054030.1272879979870.04063947443240.005068159267850.161619058914-0.005155030020140.162928440827109.6385427816.3569716751129.49252419
90.0576209543523-0.0128704106730.03891705700310.0122367639340.01619060521130.0513956116102-0.0550357618497-0.06610731121770.0460718228775-0.007184661097130.06836980094180.006146115693280.293152547952-0.1014733504350.001173710508080.21056472969-0.0111919429443-0.02096972010880.1472235337560.02221509805480.22514367090376.171432618127.9681329435114.641601292
100.0634944643468-0.04589927067740.07633683108030.0569339967465-0.06383139800090.118607800624-0.1663844037320.0623182528562-0.235082655836-0.03783665648660.0378809117245-0.04681954447170.06857686659570.199804186395-0.03384851323950.2115121523040.06799997005830.02495262752890.166971695614-0.001212620560760.20123703296588.373429963628.4732801457103.469464196
110.2465935112420.06120936588050.03042896388880.0326598534082-0.0189128929310.1258570204250.146082072717-0.1971766017410.03188308859420.062680254685-0.177701096978-0.0914112179988-0.174651432313-0.0464835862514-0.03193468490730.1318069261-0.00424601898783-0.0181981379160.06319089559330.007478824606040.13663858028487.925123808429.6871184018114.945792978
120.00613484059390.00264315395658-0.002321184137180.00287881997997-0.00432743141920.0004278437274760.00121342912908-0.0628721229384-0.213056891080.1825004104820.146265918807-0.146273810528-0.03641986004590.128945227988-0.0002089719407020.1722120667520.0141126621174-0.01846331804020.1866037290640.01784504789720.25297592673591.342161062539.4925665376110.952345951
130.0459924053819-0.0331856247042-0.1764951991230.01235736192640.08046508224010.5745959717050.0302616662537-0.4421304072730.00118920040730.005503798085190.03890901487950.0899145612452-0.04939080883370.617438642525-0.03659967240820.136079416518-0.0197751215894-0.005749995193820.299675784488-0.06619696929020.221486781279110.48009210423.9989329799149.113753955
140.334120904837-0.0372799224664-0.07462187852660.0348844614655-0.001485434405180.01708790399970.0339650788407-0.01197187867040.0704619306880.02479680269330.00651094589798-0.07281286612010.06979706586670.1179452900430.03974621179830.5996860311830.361905294817-0.1181239087850.594192877071-0.07742683468020.211970289675117.1916883329.77282785656161.267900055
150.06049069404910.0606793444809-0.03881571521510.0664186281954-0.01472749959680.147605336243-0.158785515746-0.0493731045728-0.02592034453130.1397188446630.149795954281-0.01743691448530.368200894390.2167413711560.01216628759110.2037744645830.0874983235501-0.01088020698610.296695740053-0.01086730286920.109351861341107.47557840814.7025133481153.325834506
160.02076026326660.01143449279720.001879151363020.0012808833560.00141817524156-0.000121728161548-0.01871905926980.007390624014210.00462767630390.07193701845990.0442434496789-0.05239935702390.09676952491580.0522731072512-1.74222533464E-50.2042446566520.02404609518510.05291257922280.279049313833-0.02315819558170.265982312657111.3750653917.04038607298148.480686536
170.1408889849840.1087695083810.06350252406910.1002297731460.05466620676440.06679498226550.06625796964250.0549915257135-0.2420503442810.06641467473790.077589196369-0.08811575326260.154575830292-0.003062817124940.02438224659180.2275387660380.1005927716920.02446859014890.2405816907050.065247980360.19592544636899.99895903618.473019545152.11640377
180.300203949942-0.224588956558-0.168013497610.1791874516430.1400861746530.118786358768-0.06227127023910.112948597641-0.02404334651380.0852761170538-0.03494089261620.0692807635392-0.102377508902-0.189299104556-0.06787067610170.4350116683880.23835176230.03829149584850.5090893054340.06247995781630.19521584349284.738872019737.139816164790.9949252755
190.000628946026347-0.00136042729704-0.0009777266057140.0008309865674510.001474239539920.0009537870430720.0983568130890.02905222966870.00296591759548-0.06585996499430.0688957108171-0.1259067425880.0582869796681-0.00518492089732-0.0001088589009180.517284069876-0.153957652405-0.07674975496810.708636601366-0.04151551138260.23072921450981.759293286826.129873992881.7148625123
200.0719873158772-0.06632169517880.04016803790640.0739975694352-0.03816239394730.0615854334787-0.107404438942-0.229536623606-0.198536623908-0.0872851515419-0.02398696680850.118177244821-0.00476496333674-0.0622591769125-0.1277633280470.379888209570.1624348173240.03702354194440.4040995951480.224192575054-0.70592595439591.248990145132.177147598489.610205812
210.0428819082316-0.01152147773450.00155962740046-3.89720853219E-50.000148218158401-0.001557313540970.00897070980907-0.0123094803947-0.02148596718880.05202847809620.06576928302060.036054649266-0.00678623875855-0.02757365979610.0001995709808870.3408882399380.02454589566030.02696428209220.3699692754540.003024183479390.18278708938488.709891236724.585186931294.7005893022
220.00106710967862-0.000847268807165-3.01203513551E-50.00475104152477-0.001338083974870.000117063581530.0726715881831-0.0240031285132-0.0172737521090.0631847326103-0.198904257886-0.01482359136130.07658954210630.0564268224774-8.28097680038E-50.2299851052120.0461189046383-0.04897768829390.5632545758390.03955422656260.26076152363199.437472047927.329645246490.456132741
23-0.000554682121197-0.004883707991890.002204155228950.0128301982451-0.004121595044570.003654763820360.229266760211-0.05048425322540.245155175720.09749563272980.03882172531610.0773333707109-0.2593195460090.09257442306910.0006272487934120.4055077655240.04999836063920.006695349809140.332882568621-0.03067337864050.2040706906101.88128287715.14356698491.1839729218
240.07065582229110.0472275909145-0.02020694899720.0481522595992-0.0123210794250.0282168342815-0.141117290506-0.1023935120140.05393967633330.142682329636-0.0791934963887-0.146859990195-0.247695308606-0.0330485294093-0.001691674166840.380463776658-0.00464715251489-0.04123462187230.397098884331-0.006544114820760.180782840861109.6468439812.897790647699.2226540043
250.395340209628-0.399151457734-0.1550619403340.3947632098610.1491369898720.06110669770260.1674830135080.02022202553440.164503260237-0.195130178619-0.0782436497863-0.254703917683-0.07829291145530.006036736790050.02290431831170.4012135081250.0269687466112-0.03081479528110.365304152364-0.01738064235240.122841220387105.866299899.6670347626289.0675343542
260.02762103759290.01810187806850.00531985908850.0931718814257-0.031034242990.0138834759478-0.019659374189-0.00587121859308-0.0784257347103-0.037135648491-0.0284320638298-0.032747740705-0.05254680788710.1168567389710.02516173732290.4342603767460.1273861467450.105501944270.6265025465160.2374285887660.267577472334114.6220997512.566435116287.5852388871
270.05155977413650.00195162840043-0.01741203136780.00115040941095-0.009827235524550.0428794344476-0.10109114124-0.0395484519442-0.021384872029-0.0213918375329-0.0118132461228-0.08444289436880.1194477401430.0108692281259-0.00797917391780.5512811867850.210798042752-0.002736153731690.3148013365280.0216161137920.104522156654113.2397515481.5916484703691.7193919745
280.2359587096060.312427296321-0.2269304090690.426837885468-0.2801204899840.215867445270.007931323475790.04918567343430.333442502003-0.1568234141050.1847580708140.0596762297618-0.36830467218-0.07192119652880.1470413700480.2393432653970.04037222772010.0346182207430.0834403052969-0.1028358072230.12101228629599.723237390232.0380164374154.187434811
29-0.00278308359397-0.001415130888690.0002290899404510.00110619395536-0.000563184957349-0.002994046117270.006431787680250.00893840645633-0.006063329915720.05616306036680.02904500950140.0963548549659-0.1899786367170.0801819145055-0.0002247493793090.2593493092040.0334565894029-0.04078703075720.174810575036-0.0007614550515980.15965575799384.111818024235.1479139814142.394030981
300.03864188058250.0218364576070.0410902274692-0.003212031173490.03295812423190.0397702001685-0.00594818507311-0.232037690806-0.1024415802890.120230287411-0.0196648454690.07301660749910.0981030963782-0.07258442319593.0629588847E-50.143081560978-0.0289842315147-0.00455959587980.2123162453030.01203522176590.15143969474490.255422626725.332264116151.464616633
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 19 )
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 51 )
3X-RAY DIFFRACTION3chain 'A' and (resid 52 through 57 )
4X-RAY DIFFRACTION4chain 'A' and (resid 58 through 66 )
5X-RAY DIFFRACTION5chain 'B' and (resid -1 through 38 )
6X-RAY DIFFRACTION6chain 'B' and (resid 39 through 66 )
7X-RAY DIFFRACTION7chain 'C' and (resid 0 through 38 )
8X-RAY DIFFRACTION8chain 'C' and (resid 39 through 66 )
9X-RAY DIFFRACTION9chain 'D' and (resid -1 through 19 )
10X-RAY DIFFRACTION10chain 'D' and (resid 20 through 38 )
11X-RAY DIFFRACTION11chain 'D' and (resid 39 through 57 )
12X-RAY DIFFRACTION12chain 'D' and (resid 58 through 66 )
13X-RAY DIFFRACTION13chain 'E' and (resid 0 through 19 )
14X-RAY DIFFRACTION14chain 'E' and (resid 20 through 27 )
15X-RAY DIFFRACTION15chain 'E' and (resid 28 through 51 )
16X-RAY DIFFRACTION16chain 'E' and (resid 52 through 57 )
17X-RAY DIFFRACTION17chain 'E' and (resid 58 through 66 )
18X-RAY DIFFRACTION18chain 'F' and (resid 6 through 19 )
19X-RAY DIFFRACTION19chain 'F' and (resid 20 through 27 )
20X-RAY DIFFRACTION20chain 'F' and (resid 28 through 51 )
21X-RAY DIFFRACTION21chain 'F' and (resid 52 through 57 )
22X-RAY DIFFRACTION22chain 'F' and (resid 58 through 66 )
23X-RAY DIFFRACTION23chain 'G' and (resid 7 through 19 )
24X-RAY DIFFRACTION24chain 'G' and (resid 20 through 37 )
25X-RAY DIFFRACTION25chain 'G' and (resid 38 through 51 )
26X-RAY DIFFRACTION26chain 'G' and (resid 52 through 57 )
27X-RAY DIFFRACTION27chain 'G' and (resid 58 through 66 )
28X-RAY DIFFRACTION28chain 'H' and (resid 1 through 19 )
29X-RAY DIFFRACTION29chain 'H' and (resid 20 through 27 )
30X-RAY DIFFRACTION30chain 'H' and (resid 28 through 66 )

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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://pdbjlc1.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