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- PDB-4hnk: Crystal structure of an Enzyme -

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基本情報

登録情報
データベース: PDB / ID: 4hnk
タイトルCrystal structure of an Enzyme
要素ATP-dependent Clp protease proteolytic subunit
キーワードHYDROLASE (加水分解酵素) / Structural Genomics Consortium / SGC / alpha/beta fold / Protease (プロテアーゼ)
機能・相同性
機能・相同性情報


アピコプラスト / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / serine-type endopeptidase activity / タンパク質分解
類似検索 - 分子機能
ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / エンドペプチダーゼClp / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
類似検索 - ドメイン・相同性
ATP-dependent Clp protease proteolytic subunit
類似検索 - 構成要素
生物種Plasmodium falciparum (マラリア病原虫)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.9 Å
データ登録者El Bakkouri, M. / Calmettes, C. / Wernimont, A.K. / Houry, W.A. / Hui, R. / Structural Genomics Consortium (SGC)
引用ジャーナル: J.Biol.Chem. / 年: 2013
タイトル: Structural Insights into the Inactive Subunit of the Apicoplast-localized Caseinolytic Protease Complex of Plasmodium falciparum.
著者: El Bakkouri, M. / Rathore, S. / Calmettes, C. / Wernimont, A.K. / Liu, K. / Sinha, D. / Asad, M. / Jung, P. / Hui, R. / Mohmmed, A. / Houry, W.A.
履歴
登録2012年10月19日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02012年12月5日Provider: repository / タイプ: Initial release
改定 1.12013年1月2日Group: Database references
改定 1.22013年1月30日Group: Database references
改定 1.32024年2月28日Group: Data collection / Database references / Derived calculations
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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: ATP-dependent Clp protease proteolytic subunit
B: ATP-dependent Clp protease proteolytic subunit
C: ATP-dependent Clp protease proteolytic subunit
D: ATP-dependent Clp protease proteolytic subunit
E: ATP-dependent Clp protease proteolytic subunit
F: ATP-dependent Clp protease proteolytic subunit
G: ATP-dependent Clp protease proteolytic subunit
H: ATP-dependent Clp protease proteolytic subunit
I: ATP-dependent Clp protease proteolytic subunit
J: ATP-dependent Clp protease proteolytic subunit
K: ATP-dependent Clp protease proteolytic subunit
L: ATP-dependent Clp protease proteolytic subunit
M: ATP-dependent Clp protease proteolytic subunit
N: ATP-dependent Clp protease proteolytic subunit
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)353,25916
ポリマ－353,07514
非ポリマー1842
水1,26170
1
A: ATP-dependent Clp protease proteolytic subunit
B: ATP-dependent Clp protease proteolytic subunit
C: ATP-dependent Clp protease proteolytic subunit
D: ATP-dependent Clp protease proteolytic subunit
E: ATP-dependent Clp protease proteolytic subunit
F: ATP-dependent Clp protease proteolytic subunit
G: ATP-dependent Clp protease proteolytic subunit
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)176,6308
ポリマ－176,5387
非ポリマー921
水1267
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area12650 Å2
ΔGint-65 kcal/mol
Surface area55410 Å2
手法PISA
2
H: ATP-dependent Clp protease proteolytic subunit
I: ATP-dependent Clp protease proteolytic subunit
J: ATP-dependent Clp protease proteolytic subunit
K: ATP-dependent Clp protease proteolytic subunit
L: ATP-dependent Clp protease proteolytic subunit
M: ATP-dependent Clp protease proteolytic subunit
N: ATP-dependent Clp protease proteolytic subunit
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)176,6308
ポリマ－176,5387
非ポリマー921
水1267
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area13100 Å2
ΔGint-69 kcal/mol
Surface area53910 Å2
手法PISA
単位格子
Length a, b, c (Å)178.785, 105.853, 186.402
Angle α, β, γ (deg.)90.000, 118.100, 90.000
Int Tables number5
Space group name H-MC121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11chain A and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)
21chain B and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)
31chain C and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)
41chain D and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)
51chain E and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)
61chain F and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)
71chain G and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)
81chain H and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)
91chain I and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)
101chain J and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)
111chain K and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)
121chain L and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)
131chain M and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)
141chain N and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)A62 - 173
121chain A and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)A194 - 242
211chain B and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)B62 - 173
221chain B and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)B194 - 242
311chain C and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)C62 - 173
321chain C and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)C194 - 242
411chain D and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)D62 - 173
421chain D and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)D194 - 242
511chain E and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)E62 - 173
521chain E and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)E194 - 242
611chain F and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)F62 - 173
621chain F and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)F194 - 242
711chain G and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)G62 - 173
721chain G and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)G194 - 242
811chain H and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)H62 - 173
821chain H and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)H194 - 242
911chain I and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)I62 - 173
921chain I and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)I194 - 242
1011chain J and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)J62 - 173
1021chain J and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)J194 - 242
1111chain K and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)K62 - 173
1121chain K and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)K194 - 242
1211chain L and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)L62 - 173
1221chain L and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)L194 - 242
1311chain M and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)M62 - 173
1321chain M and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)M194 - 242
1411chain N and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)N62 - 173
1421chain N and (resseq 62:173 or resseq 194:242 ) and (not element H) and (not element D)N194 - 242

NCS oper:
IDCodeMatrixベクター
1given(-0.853973, 0.451107, -0.259292), (-0.457522, -0.888356, -0.03869), (-0.247797, 0.085591, 0.965024)-102.859001, 10.9776, -15.0034
2given(0.631143, 0.771142, -0.083657), (-0.775332, 0.624024, -0.097232), (-0.022776, 0.126229, 0.99174)-33.724499, -32.539902, -4.38496
3given(-0.204905, -0.965007, -0.163631), (0.968076, -0.22447, 0.11154), (-0.144367, -0.135552, 0.980196)-44.182999, 71.693604, -4.70262
4given(-0.887986, -0.409093, -0.210055), (0.413612, -0.910136, 0.024035), (-0.201011, -0.065539, 0.977394)-87.685402, 54.7673, -9.22837
5given(-0.179347, 0.96437, -0.194488), (-0.970492, -0.205822, -0.12563), (-0.161184, 0.166218, 0.972827)-78.234901, -27.619101, -12.5811
6given(0.624293, -0.773337, -0.110491), (0.781178, 0.617241, 0.093666), (-0.004236, -0.144788, 0.989454)-6.54349, 46.401699, 1.34977
7given(-0.99949, 0.030844, 0.008296), (0.030857, 0.999523, 0.001535), (-0.008245, 0.00179, -0.999964)-45.433601, 0.972999, -81.217598
8given(0.8863, 0.374579, 0.272327), (0.393315, -0.919271, -0.015629), (0.244488, 0.120963, -0.962078)-41.0746, 32.306301, -83.223999
9given(-0.582781, 0.807877, 0.08775), (0.811649, 0.583977, 0.014034), (-0.039907, 0.079401, -0.996044)-55.530102, 7.5723, -81.916199
10given(0.176641, -0.981986, 0.067088), (-0.967241, -0.185806, -0.172979), (0.182328, -0.034335, -0.982638)-27.461, 14.3593, -79.590698
11given(0.879935, -0.42806, 0.206106), (-0.420635, -0.903617, -0.080883), (0.220864, -0.015523, -0.975181)-29.8314, 29.474001, -81.055
12given(0.226569, 0.966374, 0.121605), (0.968845, -0.23643, 0.073761), (0.100032, 0.101104, -0.989834)-57.282001, 23.856501, -82.304901
13given(-0.642042, -0.765819, 0.036102), (-0.766345, 0.639687, -0.059294), (0.022315, -0.065736, -0.997587)-30.7542, 5.29507, -81.165703

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要素

#1: タンパク質
ATP-dependent Clp protease proteolytic subunit /


分子量: 25219.664 Da / 分子数: 14 / 由来タイプ: 組換発現
由来: (組換発現) Plasmodium falciparum (マラリア病原虫)
株: 3D7 / 遺伝子: PF14_0348 / プラスミド: pET15-MHL / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 / 参照: UniProt: Q8IL98
#2: 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: 2 / 由来タイプ: 合成 / 式: C3H8O3
#3: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 70 / 由来タイプ: 天然 / 式: H2O

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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: 2.2 Å3/Da / 溶媒含有率: 44.18 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8.6
詳細: 0.25 M CaAcetate, pH 8.6, 7.5% PEG20K and 7.5% PEG MME500, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: CHESS / ビームライン: A1 / 波長: 0.979 Å
検出器タイプ: ADSC QUANTUM 210 / 検出器: CCD / 日付: 2007年4月11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: 0.979 Å / 相対比: 1
反射解像度: 2.9→50 Å / Num. obs: 66514 / % possible obs: 96.7 % / 冗長度: 3.3 % / Rmerge(I) obs: 0.075 / Χ2: 1.956 / Net I/σ(I): 10.5
反射 シェル
解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.9-2.9530.76429870.85187.8
2.95-330.65530660.886190.3
3-3.0630.54431920.959192
3.06-3.1230.47331490.958193.4
3.12-3.1930.35832470.998194.5
3.19-3.2730.28332971.067196
3.27-3.353.10.24333181.17196.7
3.35-3.443.10.1933261.318197.6
3.44-3.543.20.17233521.488198
3.54-3.653.20.14433811.57198.5
3.65-3.783.30.11633982.319199.3
3.78-3.943.50.10234202.051199.3
3.94-4.113.50.09534082.153199.5
4.11-4.333.60.06934392.348199.2
4.33-4.63.60.06433872.809199.1
4.6-4.963.60.05834312.34199.1
4.96-5.463.60.0634172.228199.2
5.46-6.243.60.05934382.208199.3
6.24-7.863.50.04334372.319198.8
7.86-503.30.03234245.264196.2

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位相決定

位相決定手法: 分子置換
Phasing MRPacking: 0

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解析

ソフトウェア
名称バージョン分類NB
SCALEPACKデータスケーリング
PHASER位相決定
PHENIX1.7.1_743精密化
PDB_EXTRACT3.11データ抽出
ADSCQuantumデータ収集
HKL-3000データ削減
精密化構造決定の手法: 分子置換 / 解像度: 2.9→45.542 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 1.03 / σ(F): 1.33 / 位相誤差: 28.39 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2431 3633 3 %
Rwork0.2017 --
obs0.203 66514 88.58 %
溶媒の処理減衰半径: 1.06 Å / VDWプローブ半径: 1.3 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 56.672 Å2 / ksol: 0.302 e/Å3
原子変位パラメータBiso max: 251.97 Å2 / Biso mean: 87.7514 Å2 / Biso min: 12.67 Å2
Baniso -1Baniso -2Baniso -3
1-4.9747 Å20 Å2-4.9814 Å2
2---3.6998 Å20 Å2
3----1.2749 Å2
精密化ステップサイクル: LAST / 解像度: 2.9→45.542 Å
タンパク質核酸リガンド溶媒全体
原子数18850 0 12 70 18932
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00719159
X-RAY DIFFRACTIONf_angle_d1.12625827
X-RAY DIFFRACTIONf_chiral_restr0.0883056
X-RAY DIFFRACTIONf_plane_restr0.0063181
X-RAY DIFFRACTIONf_dihedral_angle_d13.2977230
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11A1288X-RAY DIFFRACTIONPOSITIONAL0.609
12B1288X-RAY DIFFRACTIONPOSITIONAL0.609
13C1288X-RAY DIFFRACTIONPOSITIONAL0.602
14D1288X-RAY DIFFRACTIONPOSITIONAL0.587
15E1288X-RAY DIFFRACTIONPOSITIONAL0.616
16F1280X-RAY DIFFRACTIONPOSITIONAL0.54
17G1288X-RAY DIFFRACTIONPOSITIONAL0.575
18H1288X-RAY DIFFRACTIONPOSITIONAL0.52
19I1288X-RAY DIFFRACTIONPOSITIONAL0.587
110J1288X-RAY DIFFRACTIONPOSITIONAL0.632
111K1269X-RAY DIFFRACTIONPOSITIONAL0.554
112L1288X-RAY DIFFRACTIONPOSITIONAL0.502
113M1227X-RAY DIFFRACTIONPOSITIONAL0.619
114N1288X-RAY DIFFRACTIONPOSITIONAL0.537
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-2.91470.4719800.39462482256249
2.9147-2.95460.35731200.3454048416879
2.9546-2.99680.42251200.32934124424481
2.9968-3.04150.38881350.31174162429780
3.0415-3.0890.34211250.30244196432183
3.089-3.13970.30741370.28454272440983
3.1397-3.19380.34251360.27144235437184
3.1938-3.25180.31921450.2634443458886
3.2518-3.31440.34211400.25854435457587
3.3144-3.3820.32181420.24654473461588
3.382-3.45550.26611420.23414623476589
3.4555-3.53590.25151410.23014564470590
3.5359-3.62430.27051420.23884677481991
3.6243-3.72220.27191430.24014729487292
3.7222-3.83170.29671490.20814753490293
3.8317-3.95530.24181500.20574831498195
3.9553-4.09660.27941500.19424833498395
4.0966-4.26050.21671530.15844882503596
4.2605-4.45420.18541430.15024884502795
4.4542-4.68880.15791450.13224922506796
4.6888-4.98230.15961450.14194925507096
4.9823-5.36640.20161470.16934909505696
5.3664-5.90540.22381500.20274895504596
5.9054-6.75750.28941520.22474907505996
6.7575-8.50470.17571520.18154831498395
8.5047-45.5420.23951490.1864520466989
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)
12.8411-0.20230.6263.20310.57282.8955-0.0654-0.2991-0.0420.012-0.12140.19680.0858-0.19850.05790.0437-0.0153-0.03860.1715-0.01090.2379-29.825439.8373-21.8515
20.1758-0.66160.74612.5497-2.71033.1431-0.23140.09880.170.4755-0.6371-1.40730.13220.9430.440.49760.204-0.15410.918-0.08190.8911-22.431339.3674-1.4266
35.04321.12832.2768.2315-2.2865.06170.0078-0.79980.37190.8491-0.2955-0.5973-0.28490.27330.22450.1504-0.234-0.01740.6134-0.15720.3826-16.103549.1209-10.835
47.06371.7944-0.29615.34120.98345.1933-0.1053-0.121.02390.2225-0.180.8988-0.8563-0.02780.35250.278-0.0382-0.02260.11850.00960.4349-29.816657.4084-21.5302
52.10840.6138-0.39562.8794-0.86432.65490.129-0.11190.28920.3706-0.2731-0.2555-0.10040.10850.05750.1755-0.123-0.11440.1704-0.01650.6503-67.992511.1198-28.1141
67.7290.8587-2.84267.30821.61349.11760.0789-0.7850.02310.7894-0.06470.5547-0.01050.15180.03690.111-0.0537-0.01160.2375-0.0250.4905-73.61026.1611-22.1055
74.21040.6984-0.69834.20951.01363.4939-0.0305-0.14990.15980.4456-0.13960.37540.5327-0.33290.07160.2476-0.16560.1060.27450.0020.551-79.06533.2986-26.7858
87.74851.5876-2.92953.83432.4141.99970.7254-0.261.5680.5987-0.67840.9747-0.7861-0.6826-0.17620.2819-0.25580.1890.816-0.04920.9033-91.02898.6466-22.302
93.0747-3.307-4.01183.77924.50658.4528-0.3955-0.71070.45760.66060.15620.91760.5232-0.5991-0.23170.487-0.28030.34281.2011-0.30961.2428-94.5309-0.6376-19.1697
109.21760.167-0.00049.6239-4.14152.45160.4053-1.5561-2.28370.8643-0.64650.16790.6317-0.37630.16181.1433-0.51230.15910.78690.07181.1309-84.1463-9.6211-22.3203
118.78832.50960.57078.1794-1.13517.6655-0.22690.7348-0.714-0.3158-0.02250.05221.1489-0.26030.00060.6764-0.40110.07920.3401-0.22940.5573-81.5392-7.4147-30.8466
123.9465-0.97870.65684.01310.05362.45270.2147-0.242-0.12360.2117-0.10810.32580.1061-0.0052-0.03310.1634-0.0086-0.05590.1578-0.02280.3877-53.538146.4867-24.1304
133.84892.33354.58287.18113.31752.00040.0444-0.32980.29631.6273-0.0652-1.26830.33570.7421-0.230.7446-0.1026-0.0490.1781-0.12520.6311-47.611861.5839-15.9797
146.15021.05930.98776.87751.21076.3867-0.0175-0.30180.42950.2592-0.37420.8951-0.6197-0.94470.23760.31140.1526-0.00480.2795-0.07870.5877-63.282861.0698-21.767
156.91491.6471-1.33276.4434-2.99933.13-0.536-0.29981.29020.5685-0.29670.1101-0.94910.18440.41640.3346-0.1769-0.13040.51720.14431.1044-32.85733.012-24.2197
164.89030.90213.80943.28320.64662.9756-0.16980.33710.57770.14620.07140.07480.0036-0.80290.0555-0.0218-0.1415-0.02560.3821-0.0450.8219-39.9584-3.0746-26.2397
177.07052.85974.36846.3744-0.72424.0254-0.33242.2137-1.2291-1.1160.4578-0.32680.3632-0.2133-0.19420.2553-0.11560.0540.824-0.16870.7292-30.6905-3.7578-33.0288
188.6519-5.2843-3.96163.70141.28964.48841.0594-3.7809-0.93013.16540.2333-0.31830.04271.22-1.14781.2881-0.4477-0.2282.04810.32951.0106-31.9299-3.1066-7.1642
196.46281.54810.68332.4769-0.50372.4830.3486-0.4269-2.03290.2876-0.0818-1.12410.22620.0434-0.14650.1796-0.0685-0.23440.49320.20551.3831-27.1673-8.2417-23.092
206.43515.1127-5.97414.678-3.53757.8533-0.3668-0.4047-2.47941.84-0.3108-1.54461.0490.06540.45061.1413-0.0514-0.24941.07250.26681.7924-28.0614-17.8955-14.5447
217.72340.09930.24912.04070.03572.01930.4409-1.9428-2.07711.2270.045-0.8541.9425-0.1374-0.51221.33470.07-0.24291.44080.75852.2235-20.2881-21.4459-11.5306
229.0461-2.3203-0.48592.22721.78331.7133-0.4068-1.5156-0.63160.10350.02180.4130.0602-0.1381-0.29690.7891-0.1158-0.61131.03770.49662.1239-13.6617-9.7776-15.3875
230.03490.1927-0.38075.5427-5.83117.44350.5091-0.3905-1.33470.0134-0.6032-1.23970.24840.57080.2080.51890.0331-0.0980.69320.19051.9559-14.9375-7.4065-25.2545
243.7511-0.45090.43643.3165-0.74253.1064-0.1460.48340.37570.0956-0.0039-0.0854-0.50420.2508-0.05630.2465-0.1106-0.00860.13140.02440.4267-54.6906-3.5446-28.8048
256.3099-5.2487-5.6234.36124.67134.9966-0.6547-0.1972-0.02291.27480.3132-0.2981-0.39890.62280.09140.5075-0.03980.01970.3341-0.00780.3537-54.4543-9.5039-9.2495
264.28690.7550.13892.7081-0.1443.92170.10120.087-0.30210.1766-0.02030.01930.22210.2957-0.0360.1201-0.041-0.01730.1059-0.02030.3275-55.1838-15.3267-25.0472
273.62965.39521.00498.68130.28872.4760.6467-0.9757-0.71230.9751-0.62310.16180.6051.7229-0.00810.6775-0.1113-0.05231.1119-0.06360.6147-69.0936-11.8867-4.8994
284.9474-5.9984-1.43522.00165.89075.46540.16780.1921-0.33670.1104-0.56760.8016-0.3637-0.82110.66550.5072-0.17950.00020.28310.03710.3914-69.0316-19.7061-17.3086
298.02850.7311-4.18117.58311.14873.5818-0.5416-0.8548-0.68160.24510.2390.64990.41240.36550.22690.2982-0.00980.11830.30970.12480.7158-61.8849-29.3876-15.6478
302.36570.93850.98792.7912-0.27610.5961-0.3956-0.22910.07750.824-0.14430.29070.6123-0.0781-0.38050.46540.2239-0.0479-0.019-0.34980.4746-48.387-27.1281-19.1898
313.27790.91652.56224.042-1.88153.7879-0.62010.5449-0.1692-0.240.2491-1.5781-0.1531.0489-0.04460.3272-0.04150.06650.3114-0.14120.6421-47.1603-23.8028-28.4353
323.45250.6441-0.37082.1611-0.09022.6904-0.0714-0.5401-0.21560.0949-0.12490.0290.0640.14170.0146-0.12010.0898-0.20540.2563-0.01060.7347-65.430829.6261-27.984
336.9692-0.8426-2.85657.24840.21723.5598-0.0774-1.15170.52760.803-0.07670.8063-0.50960.76650.03340.29470.03210.00420.327-0.07780.7532-73.199230.3112-22.4826
343.00920.34880.16370.9903-0.02630.84370.156-0.19610.40720.0571-0.13570.7381-0.0467-0.29290.1577-0.49180.1577-0.01820.2884-0.10811.0014-77.78733.0279-28.5171
352.98543.20833.31637.19721.66414.6648-0.0649-0.58980.44650.9431-0.79260.2554-0.6304-0.27490.62570.6434-0.25330.1280.96580.01281.1286-81.683339.7054-16.1015
367.3888-1.0676-3.44262.41141.24176.74890.0552-1.23991.19650.45250.50360.5652-0.67460.4964-0.46190.57170.29270.08720.7932-0.19621.3731-86.292144.8451-21.8282
376.17970.80751.15544.0978-2.50852.27730.0805-0.8106-0.07390.372-0.02250.6077-0.3219-1.2556-0.01110.2027-0.07250.04330.9001-0.15180.9768-90.168229.5017-25.947
384.91770.19151.72674.14910.4524.0609-0.19140.1208-0.40350.00430.11880.31630.2654-0.3809-0.11680.1042-0.0335-0.09710.22030.09780.3518-24.709816.1395-25.5622
397.95834.3132-2.73154.9012-4.68414.9362-0.0249-2.05390.11462.78620.0418-0.3561-0.1362-0.4753-0.10141.31150.1403-0.16170.71660.06910.5457-21.249118.5074-5.4874
404.0334-0.21491.45383.5936-0.62133.9885-0.06250.3119-0.24980.4714-0.1501-0.6229-0.13630.45020.05640.29790.0266-0.24450.32780.04550.4895-13.946618.0693-21.3131
414.0360.3108-2.47661.5189-1.11782.1083-0.5612-0.3985-1.33690.1812-0.42560.28271.62260.48290.45261.66630.0423-0.01740.75690.03750.7488-10.52578.6382-5.4283
423.1314-0.28722.05991.2851-0.70433.43430.0335-0.8291-0.24080.7356-0.234-0.89050.0330.6351-0.74760.61630.3899-0.73271.0432-0.00920.7058-3.130411.7508-11.186
436.473-1.77753.14830.5669-0.17968.0524-0.13850.23540.24320.93-0.1573-1.0889-1.03731.11650.45950.6546-0.1883-0.45960.74670.10690.8476-5.802528.0981-18.9634
443.4248-0.32560.34294.1972-0.43972.81140.17380.6650.325-0.0763-0.1079-0.3048-0.26970.0774-0.03050.21320.12130.04440.34160.08660.2896-14.872539.8836-59.4605
453.78241.0132.24725.3487-3.75286.55271.52330.92130.0578-0.4986-0.11250.8440.51820.2779-0.34130.98130.47390.00881.93580.09440.7012-24.513137.8001-81.4328
464.02091.83310.79813.73681.81422.2219-0.12770.85480.6956-1.2473-0.13750.9192-0.5686-0.58740.37220.68960.399-0.0871.13040.21750.7008-28.821247.7809-70.9601
476.5539-1.33051.56876.6891-0.36817.91110.04030.70121.3945-0.5745-0.504-0.6891-1.66310.40690.43680.66710.0530.13620.41480.20470.8406-14.37557.065-59.5387
485.8779-0.8341-1.97185.16353.23436.70440.2624-0.1410.3292-0.9884-0.12450.7408-0.8907-0.0953-0.25610.37230.0926-0.12380.2606-0.01140.596122.39729.4416-54.3416
497.33370.7167-2.64827.81722.16978.6173-0.06770.71160.1138-1.32550.6312-0.4889-0.95510.4871-0.31710.3228-0.0391-0.04620.4406-0.03720.53427.58464.4257-60.6667
506.75770.41380.28576.8456-0.75253.7606-0.02990.0479-0.0433-0.52630.2844-0.4914-0.0270.8861-0.15970.24860.05570.02160.5784-0.10350.428433.36731.2538-56.8851
517.0533-0.6338-0.81978.2042-0.8054.9656-0.14980.21260.5168-1.12760.3355-2.47630.23111.1185-0.15240.5920.2170.26031.4455-0.1061.080946.5111.1466-62.3786
526.5203-3.37741.2927.85640.35587.880.61751.2358-1.0592-1.1201-0.85040.42580.5660.20560.20560.63480.3346-0.14520.6606-0.15340.76935.1662-11.5917-56.8925
535.69250.9467-0.25496.6309-2.24746.6716-0.0490.511-1.2808-0.12070.30560.3475-0.15260.0455-0.27720.3207-0.1070.00660.3851-0.13330.82935.140238.2134-54.9573
548.3330.05881.85279.3463-1.78862.34650.37981.33770.3021-0.94260.30620.0977-0.61880.24-0.42790.4154-0.0438-0.05890.60070.01080.51799.764843.468-61.502
556.6958-1.072.90734.6237-0.05452.7929-0.01240.78870.147-0.1879-0.0495-0.0896-0.99081.06580.03380.5998-0.28850.08620.60190.02060.598611.276350.0026-57.8127
569.6966-0.74895.66966.36281.51255.28430.03751.63671.6599-0.1241-0.14390.6845-1.37661.54820.0221.5811-0.37040.02740.86140.30261.04187.590561.8734-67.1402
573.44340.6035-1.38152.8358-1.06785.91-0.52541.04810.5821-0.34470.1012-0.4306-0.72070.76220.180.9897-0.77080.05081.0720.09020.750622.71855.3821-57.9855
584.9322-3.56050.87583.90981.53438.4071-0.5718-0.13220.9598-0.137-0.1628-0.0961-1.16690.33330.65640.4130.0044-0.23720.5647-0.17671.1934-9.1456-0.4681-57.9264
594.2589-1.2282-2.6865.9379-0.11365.54240.4980.39230.0818-1.1277-0.53460.82940.13730.4885-0.19760.62470.0866-0.22640.8264-0.05741.0018-14.228-2.9324-65.6089
608.5448-0.60990.56111.38140.75365.173-0.17120.6707-1.3255-0.2568-0.27860.98590.1924-0.61650.17280.45750.0197-0.2070.5894-0.2171.4852-15.842-8.8687-62.4029
615.36712.3443-2.05954.1810.53534.7287-0.20911.493-1.8242-0.9903-0.45560.69120.7725-0.65320.50571.00790.0214-0.45041.031-0.46171.8074-22.1642-15.1025-67.8004
628.88234.80153.1184.50841.32926.95950.2291.7898-0.6183-0.5179-0.14050.43890.5509-1.02190.03120.5652-0.0983-0.40661.2443-0.28591.6776-30.6908-8.7808-65.9755
637.22810.3391-0.88853.71561.4665.242-0.3394-0.53510.1591-0.0349-0.0090.1126-0.3647-0.37530.18470.27380.079-0.13240.2641-0.00190.55058.3578-4.8118-54.3501
647.48273.2344-3.22128.1212-2.54631.5871-0.73581.7209-0.1883-2.07430.24070.4046-0.5474-1.45190.50340.9556-0.1559-0.08071.0804-0.10880.45548.5206-9.7164-74.1746
656.77680.0615-2.65125.5747-1.04545.546-0.41190.3566-0.9358-0.51960.27360.01810.6807-0.4730.11140.4003-0.0128-0.00160.3088-0.07190.62988.8361-16.3583-58.6871
663.3572-1.73024.6366.4484-0.43777.08540.48970.55850.474-1.7835-0.3346-1.69310.03210.5105-0.05981.28140.39090.49361.07420.04180.877325.9796-11.5256-79.3756
679.34998.0706-2.08839.5232-3.65731.9124-0.58830.9548-0.9899-0.80090.3044-1.2510.35040.07660.40410.72150.08190.07790.5901-0.2650.608822.9011-19.8703-67.1681
688.5971-2.5073-4.20379.6473-0.91732.6793-0.44791.3641-0.528-1.31950.304-1.83271.44380.18510.11551.0489-0.14290.51980.7306-0.40421.45715.6081-29.9428-68.6776
694.3845-0.70691.28616.81381.41968.6058-0.93840.7412-1.0836-1.23030.50941.15090.7944-1.18230.49460.692-0.26270.17590.5787-0.06541.08611.3865-26.3288-60.3397
705.85890.19691.12794.52521.5453.2738-0.02910.6009-1.6532-0.4558-0.10680.70890.22750.0901-0.05050.26-0.095-0.07950.6207-0.24511.058120.538427.5795-53.7109
713.6925-0.36291.4828.653-1.25947.7218-0.2031-1.28290.83321.5535-0.14030.164-0.8396-1.1020.42670.4508-0.1515-0.02430.7333-0.35910.759126.512428.9189-45.0581
723.0981-3.71245.12474.4503-6.14388.47590.3991.63440.0015-3.2735-1.106-0.55760.38820.60250.63941.72370.1074-0.0051.1726-0.09051.12529.251426.6787-70.7162
738.1502-0.36591.47925.8541-1.15742.17420.17860.3770.2992-0.54350.1073-1.06520.07660.2374-0.18780.3539-0.1350.13560.6914-0.15340.747833.016430.5262-54.1747
749.81470.30440.51113.373-3.61283.9438-0.4611.67081.4542-1.21730.1301-2.0273-0.54330.8770.32130.8959-0.37820.44531.3357-0.11471.803441.845638.4603-61.289
754.18084.4492-2.2767.0508-2.61965.33490.16290.9072-1.4472-0.5122-0.6269-1.73340.44121.25860.45470.4865-0.01330.01331.3121-0.08791.617344.65625.0976-54.3878
764.6006-0.83682.92355.497-2.44165.633-0.06250.1778-0.3125-0.1443-0.1395-0.92870.04390.68070.14850.26930.0591-0.0490.4891-0.07640.5456-19.077815.507-58.4195
776.8580.0205-1.03437.19320.41147.19450.13840.8023-0.0536-1.43070.33730.27670.95630.4719-0.26060.55190.195-0.17140.6485-0.02970.4844-24.707218.6024-65.4764
785.5603-0.97642.00754.1038-0.2594.42680.2611-0.0537-0.7135-0.68850.000810.1978-0.4893-0.23820.41440.0709-0.27630.5628-0.00150.7031-31.335218.3445-60.921
795.95482.28521.53535.26411.22064.49660.1071.1414-1.4827-1.75340.34940.73720.7442-0.8646-0.4521.0831-0.1984-0.61641.2416-0.02641.0086-40.862914.7593-72.1557
805.91891.53493.24355.9599-0.8584.7451-0.15990.87130.3228-0.807-0.04211.1882-0.8232-0.71930.24960.61660.3176-0.22171.18330.11110.7076-39.262628.703-62.6029
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 61:168)A61 - 168
2X-RAY DIFFRACTION2chain 'A' and (resseq 169:191)A169 - 191
3X-RAY DIFFRACTION3chain 'A' and (resseq 192:223)A192 - 223
4X-RAY DIFFRACTION4chain 'A' and (resseq 224:243)A224 - 243
5X-RAY DIFFRACTION5chain 'B' and (resseq 61:94)B61 - 94
6X-RAY DIFFRACTION6chain 'B' and (resseq 95:119)B95 - 119
7X-RAY DIFFRACTION7chain 'B' and (resseq 120:194)B120 - 194
8X-RAY DIFFRACTION8chain 'B' and (resseq 195:209)B195 - 209
9X-RAY DIFFRACTION9chain 'B' and (resseq 210:223)B210 - 223
10X-RAY DIFFRACTION10chain 'B' and (resseq 224:233)B224 - 233
11X-RAY DIFFRACTION11chain 'B' and (resseq 234:242)B234 - 242
12X-RAY DIFFRACTION12chain 'C' and (resseq 61:191)C61 - 191
13X-RAY DIFFRACTION13chain 'C' and (resseq 192:209)C192 - 209
14X-RAY DIFFRACTION14chain 'C' and (resseq 210:243)C210 - 243
15X-RAY DIFFRACTION15chain 'D' and (resseq 62:77)D62 - 77
16X-RAY DIFFRACTION16chain 'D' and (resseq 78:94)D78 - 94
17X-RAY DIFFRACTION17chain 'D' and (resseq 95:104)D95 - 104
18X-RAY DIFFRACTION18chain 'D' and (resseq 105:119)D105 - 119
19X-RAY DIFFRACTION19chain 'D' and (resseq 120:168)D120 - 168
20X-RAY DIFFRACTION20chain 'D' and (resseq 169:209)D169 - 209
21X-RAY DIFFRACTION21chain 'D' and (resseq 210:223)D210 - 223
22X-RAY DIFFRACTION22chain 'D' and (resseq 224:233)D224 - 233
23X-RAY DIFFRACTION23chain 'D' and (resseq 234:243)D234 - 243
24X-RAY DIFFRACTION24chain 'E' and (resseq 61:104)E61 - 104
25X-RAY DIFFRACTION25chain 'E' and (resseq 105:119)E105 - 119
26X-RAY DIFFRACTION26chain 'E' and (resseq 120:172)E120 - 172
27X-RAY DIFFRACTION27chain 'E' and (resseq 173:190)E173 - 190
28X-RAY DIFFRACTION28chain 'E' and (resseq 191:209)E191 - 209
29X-RAY DIFFRACTION29chain 'E' and (resseq 210:223)E210 - 223
30X-RAY DIFFRACTION30chain 'E' and (resseq 224:233)E224 - 233
31X-RAY DIFFRACTION31chain 'E' and (resseq 234:243)E234 - 243
32X-RAY DIFFRACTION32chain 'F' and (resseq 61:94)F61 - 94
33X-RAY DIFFRACTION33chain 'F' and (resseq 95:119)F95 - 119
34X-RAY DIFFRACTION34chain 'F' and (resseq 120:168)F120 - 168
35X-RAY DIFFRACTION35chain 'F' and (resseq 169:193)F169 - 193
36X-RAY DIFFRACTION36chain 'F' and (resseq 194:219)F194 - 219
37X-RAY DIFFRACTION37chain 'F' and (resseq 220:243)F220 - 243
38X-RAY DIFFRACTION38chain 'G' and (resseq 61:104)G61 - 104
39X-RAY DIFFRACTION39chain 'G' and (resseq 105:119)G105 - 119
40X-RAY DIFFRACTION40chain 'G' and (resseq 120:168)G120 - 168
41X-RAY DIFFRACTION41chain 'G' and (resseq 169:193)G169 - 193
42X-RAY DIFFRACTION42chain 'G' and (resseq 194:223)G194 - 223
43X-RAY DIFFRACTION43chain 'G' and (resseq 224:243)G224 - 243
44X-RAY DIFFRACTION44chain 'H' and (resseq 61:172)H61 - 172
45X-RAY DIFFRACTION45chain 'H' and (resseq 173:188)H173 - 188
46X-RAY DIFFRACTION46chain 'H' and (resseq 189:223)H189 - 223
47X-RAY DIFFRACTION47chain 'H' and (resseq 224:243)H224 - 243
48X-RAY DIFFRACTION48chain 'I' and (resseq 61:94)I61 - 94
49X-RAY DIFFRACTION49chain 'I' and (resseq 95:119)I95 - 119
50X-RAY DIFFRACTION50chain 'I' and (resseq 120:194)I120 - 194
51X-RAY DIFFRACTION51chain 'I' and (resseq 195:223)I195 - 223
52X-RAY DIFFRACTION52chain 'I' and (resseq 224:243)I224 - 243
53X-RAY DIFFRACTION53chain 'J' and (resseq 61:94)J61 - 94
54X-RAY DIFFRACTION54chain 'J' and (resseq 95:119)J95 - 119
55X-RAY DIFFRACTION55chain 'J' and (resseq 120:190)J120 - 190
56X-RAY DIFFRACTION56chain 'J' and (resseq 191:223)J191 - 223
57X-RAY DIFFRACTION57chain 'J' and (resseq 224:242)J224 - 242
58X-RAY DIFFRACTION58chain 'K' and (resseq 61:94)K61 - 94
59X-RAY DIFFRACTION59chain 'K' and (resseq 95:119)K95 - 119
60X-RAY DIFFRACTION60chain 'K' and (resseq 120:156)K120 - 156
61X-RAY DIFFRACTION61chain 'K' and (resseq 157:219)K157 - 219
62X-RAY DIFFRACTION62chain 'K' and (resseq 220:243)K220 - 243
63X-RAY DIFFRACTION63chain 'L' and (resseq 61:104)L61 - 104
64X-RAY DIFFRACTION64chain 'L' and (resseq 105:119)L105 - 119
65X-RAY DIFFRACTION65chain 'L' and (resseq 120:172)L120 - 172
66X-RAY DIFFRACTION66chain 'L' and (resseq 173:189)L173 - 189
67X-RAY DIFFRACTION67chain 'L' and (resseq 190:209)L190 - 209
68X-RAY DIFFRACTION68chain 'L' and (resseq 210:223)L210 - 223
69X-RAY DIFFRACTION69chain 'L' and (resseq 224:243)L224 - 243
70X-RAY DIFFRACTION70chain 'M' and (resseq 61:94)M61 - 94
71X-RAY DIFFRACTION71chain 'M' and (resseq 95:104)M95 - 104
72X-RAY DIFFRACTION72chain 'M' and (resseq 105:119)M105 - 119
73X-RAY DIFFRACTION73chain 'M' and (resseq 120:168)M120 - 168
74X-RAY DIFFRACTION74chain 'M' and (resseq 169:219)M169 - 219
75X-RAY DIFFRACTION75chain 'M' and (resseq 220:243)M220 - 243
76X-RAY DIFFRACTION76chain 'N' and (resseq 61:94)N61 - 94
77X-RAY DIFFRACTION77chain 'N' and (resseq 95:119)N95 - 119
78X-RAY DIFFRACTION78chain 'N' and (resseq 120:168)N120 - 168
79X-RAY DIFFRACTION79chain 'N' and (resseq 169:223)N169 - 223
80X-RAY DIFFRACTION80chain 'N' and (resseq 224:243)N224 - 243

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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