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- PDB-3v5e: Crystal structure of ClpP from Staphylococcus aureus in the activ... -

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基本情報

登録情報
データベース: PDB / ID: 3v5e
タイトルCrystal structure of ClpP from Staphylococcus aureus in the active, extended conformation
要素ATP-dependent Clp protease proteolytic subunit
キーワードHYDROLASE
機能・相同性
機能・相同性情報


endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / serine-type endopeptidase activity / cytoplasm
類似検索 - 分子機能
ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / 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Staphylococcus aureus subsp. aureus (黄色ブドウ球菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.3 Å
データ登録者Gersch, M. / List, A. / Groll, M. / Sieber, S.
引用ジャーナル: J.Biol.Chem. / 年: 2012
タイトル: Insights into structural network responsible for oligomerization and activity of bacterial virulence regulator caseinolytic protease P (ClpP) protein.
著者: Gersch, M. / List, A. / Groll, M. / Sieber, S.A.
履歴
登録2011年12月16日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02012年2月8日Provider: repository / タイプ: Initial release
改定 1.12012年7月11日Group: Database references
改定 1.22017年11月8日Group: Refinement description / カテゴリ: software / Item: _software.name
改定 1.32023年9月13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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


分子量 (理論値)分子数
合計 (水以外)316,10214
ポリマ－316,10214
非ポリマー00
水1,71195
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area55870 Å2
ΔGint-194 kcal/mol
Surface area91530 Å2
手法PISA
単位格子
Length a, b, c (Å)117.220, 94.860, 139.020
Angle α, β, γ (deg.)90.00, 97.74, 90.00
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCS oper:
IDCodeMatrixベクター
1given(1), (1), (1)
2given(0.896224, 0.428543, -0.114601), (-0.386335, 0.627065, -0.676414), (-0.21801, 0.650492, 0.727551)-3.07743, -35.96543, -9.68188
3given(0.666915, 0.571854, -0.477711), (-0.438751, -0.21681, -0.872061), (-0.602264, 0.791187, 0.106308)-20.05515, -50.74632, -39.37488
4given(0.484054, 0.32442, -0.812677), (-0.122841, -0.894342, -0.430189), (-0.866373, 0.308064, -0.393058)-37.94835, -33.26625, -66.64333
5given(0.477883, -0.119131, -0.870308), (0.32763, -0.895096, 0.302425), (-0.815037, -0.429663, -0.388721)-43.87613, 3.0377, -71.40132
6given(0.666479, -0.435051, -0.605422), (0.572881, -0.220818, 0.789333), (-0.477088, -0.872909, 0.102062)-32.57964, 31.26888, -49.74927
7given(0.898766, -0.382502, -0.214272), (0.422357, 0.62426, 0.657201), (-0.117619, -0.681169, 0.722616)-12.89582, 29.7325, -18.21674
8given(-0.461247, -0.249882, 0.851358), (-0.251245, -0.883467, -0.395425), (0.850957, -0.396288, 0.344715)-8.82465, -35.06339, -4.74587
9given(-0.623415, -0.552991, 0.55277), (-0.551926, -0.18953, -0.812069), (0.553833, -0.811344, -0.187055)-25.41907, -51.33109, -33.78645
10given(-0.860053, -0.481167, 0.169669), (-0.476777, 0.639569, -0.603022), (0.181639, -0.599525, -0.779472)-43.81139, -35.57386, -61.9653
11given(-0.996031, -0.088644, -0.00799), (-0.089002, 0.991532, 0.094564), (-0.00046, 0.0949, -0.995487)-50.15943, 0.98172, -67.81467
12given(-0.931909, 0.32905, 0.152552), (0.327303, 0.581752, 0.744605), (0.156265, 0.743835, -0.649839)-39.78052, 30.00467, -46.50049
13given(-0.716096, 0.460099, 0.524896), (0.457705, -0.258227, 0.850779), (0.526985, 0.849487, -0.025674)-20.81643, 30.24002, -15.58703
14given(-0.506731, 0.197855, 0.839093), (0.200775, -0.919461, 0.338054), (0.838399, 0.339771, 0.426196)-6.73561, 0.9167, 3.77656

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要素

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


分子量: 22578.680 Da / 分子数: 14 / 由来タイプ: 組換発現
由来: (組換発現) Staphylococcus aureus subsp. aureus (黄色ブドウ球菌)
株: NCTC 8325 / 遺伝子: clpP, SAOUHSC_00790 / プラスミド: pET301 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 (DE3) / 参照: UniProt: Q2G036, endopeptidase Clp
#2: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 95 / 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: 2.42 Å3/Da / 溶媒含有率: 49.23 %
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: 7
詳細: 200 mM Sodium malonate, 38% MPD, pH 7.0, 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: SLS / ビームライン: X06SA / 波長: 1 Å
検出器タイプ: PSI PILATUS 6M / 検出器: PIXEL / 日付: 2011年2月19日
放射モノクロメーター: double-crystal fixed exit monochromator
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 Å / 相対比: 1
反射解像度: 2.3→50 Å / Num. all: 134296 / Num. obs: 129058 / % possible obs: 96.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 11.21
反射 シェル解像度: 2.3→2.4 Å / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.23 / % possible all: 98.6

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解析

ソフトウェア
名称バージョン分類
RemDAqデータ収集
REFMAC5.6.0119精密化
XDSデータ削減
XSCALEデータスケーリング
REFMAC5.6.0119位相決定
精密化構造決定の手法: 分子置換
開始モデル: PDB entry 3QWD

3qwd


解像度: 2.3→48.2 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 16.709 / SU ML: 0.175 / 交差検証法: THROUGHOUT / ESU R Free: 0.227 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor反射数%反射Selection details
Rfree0.23108 6453 5 %RANDOM
Rwork0.20084 ---
obs0.20235 122589 96.13 %-
all-129058 --
溶媒の処理イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK
原子変位パラメータBiso mean: 48.154 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å2-0.19 Å2
2--0.1 Å20 Å2
3----0.36 Å2
精密化ステップサイクル: LAST / 解像度: 2.3→48.2 Å
タンパク質核酸リガンド溶媒全体
原子数19908 0 0 95 20003
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01920160
X-RAY DIFFRACTIONr_angle_refined_deg0.861.97427202
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.75452548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34625.385910
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.923153710
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.52215112
X-RAY DIFFRACTIONr_chiral_restr0.060.23164
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02114910
X-RAY DIFFRACTIONr_rigid_bond_restr2.059320160
X-RAY DIFFRACTIONr_sphericity_free26.415361
X-RAY DIFFRACTIONr_sphericity_bonded6.22520666
LS精密化 シェル解像度: 2.3→2.358 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.327 462 -
Rwork0.273 8826 -
obs--98.67 %
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)
148.243.11417.34494.85357.278511.0716-1.4231-3.03910.37370.81020.71440.43351.11550.7850.70860.38690.18310.04460.4245-0.01450.1992-62.4343-19.7646-23.1863
20.4643-0.3620.32041.2170.39160.663-0.0482-0.0870.03640.04050.0389-0.0198-0.025-0.08590.00930.2196-0.00760.03380.26910.02910.2488-55.1333-28.379-27.2808
30.09780.0390.19050.28370.17560.40980.0012-0.059-0.04010.02860.0542-0.00970.0114-0.0882-0.05540.239-0.02450.01440.2680.05460.2388-54.2101-35.5003-25.6956
42.8671-0.681.10560.1634-0.24950.52260.0658-0.3025-0.0971-0.00560.08070.00740.1552-0.0998-0.14650.3086-0.054-0.06180.26410.08680.282-54.1991-43.4718-24.6885
50.4614-0.72040.07181.60290.40190.57470.20540.046-0.0215-0.1605-0.0777-0.05860.1606-0.0335-0.12780.2596-0.035-0.00620.220.04650.2676-52.2137-35.0783-38.1369
60.61330.01610.82441.84340.00681.11330.12220.1112-0.03320.0744-0.08090.06010.12910.1315-0.04140.2358-0.0273-0.00130.25340.03820.2595-56.2524-40.4292-38.0435
70.2548-0.2882-0.00930.356-0.00750.0190.0671-0.0329-0.0075-0.0886-0.0350.00080.02740.0326-0.03210.2658-0.01910.0090.23610.01610.2547-31.7933-37.2161-37.4759
85.4543-1.7132-1.7810.80020.23231.13390.2779-0.10270.2469-0.2172-0.02-0.07910.1444-0.1376-0.25790.2873-0.0757-0.05540.30370.09990.3161-26.8684-43.904-32.2131
91.9181.271-0.21451.93371.05161.33440.0168-0.1044-0.11410.1431-0.016-0.07070.1760.0506-0.00080.2944-0.0151-0.05640.1590.03310.301-42.4133-49.4158-37.7412
100.0481-0.1070.09650.80630.05250.35240.07270.0104-0.0551-0.1497-0.02350.09490.07720.0089-0.04930.2878-0.0271-0.05450.18850.00640.2864-49.6581-42.1204-46.5675
1116.30024.8936-8.07554.294920.542613.9867-0.22940.51970.36550.1369-0.40812.26120.1366-0.43430.63750.330.0478-0.02970.35130.13230.3583-56.5187-24.0634-13.9398
120.66190.1329-1.17790.73890.08432.3861-0.12150.0713-0.0652-0.02540.0389-0.0343-0.0232-0.19390.08260.3590.01320.01290.30130.0630.2285-45.7522-28.9998-11.9405
131.59390.0060.11750.76510.05240.1940.0554-0.2153-0.07530.1652-0.0161-0.055-0.06010.0279-0.03930.3073-0.04710.01050.27730.07610.2006-41.7996-32.2546-5.7195
142.4376-0.3899-1.11360.06920.1960.6414-0.0992-0.0788-0.2384-0.0125-0.03630.0143-0.1746-0.09610.13550.47740.0664-0.03270.3420.02980.2477-42.3795-38.613-5.0831
150.2825-0.18170.81440.1182-0.53422.4736-0.03860.02190.03440.01410.0041-0.01570.03450.08330.03450.2845-0.0258-0.02340.2730.0210.2911-33.4083-37.8639-14.3788
160.4316-0.2447-0.73871.18261.47662.65060.03650.1176-0.15910.03050.0726-0.0537-0.1270.0237-0.10920.2629-0.0484-0.00680.2560.0320.3485-41.3311-45.4973-12.3946
172.11140.71910.46150.7180.45720.29220.089-0.11330.12630.1594-0.11840.0550.1158-0.07020.02940.2646-0.0246-0.06350.26640.08720.2762-16.8465-30.108-13.7105
181.35661.0703-1.48333.6275-1.24741.67360.0674-0.14890.04410.18710.01970.0263-0.08540.0803-0.08710.2886-0.0353-0.09660.23840.11130.2527-23.2496-42.6662-7.0985
193.2335-0.96980.21491.15910.01610.03060.05550.1334-0.32590.0756-0.0271-0.19830.05290.0312-0.02840.3046-0.0189-0.01980.21730.06110.292-28.0169-47.2404-18.0258
2011.2964-3.69687.08087.6762-12.081519.22480.0961-0.6366-0.8392-0.25290.31440.270.3025-0.3303-0.41050.3648-0.0987-0.00080.28410.08640.2618-43.4171-49.8365-14.8825
212.7566-0.498-1.10020.09070.1980.44-0.144-0.1104-0.37310.03810.00210.06340.03990.05790.1420.3943-0.09110.03510.3856-0.00040.2106-48.5498-18.4745-0.1176
221.3497-0.2127-0.31040.2168-0.22670.54780.0725-0.10390.00220.0398-0.0959-0.04320.03750.16930.02340.3517-0.0929-0.00690.41080.03690.1844-37.9302-10.3523-0.4719
230.5404-0.34350.17270.43590.01380.469-0.0194-0.1533-0.0550.0596-0.05790.0190.1237-0.08920.07720.35-0.09820.00110.41670.03360.202-34.9967-12.32885.9298
241.3332-1.4619-0.63041.77860.13272.2778-0.103-0.07850.04250.1390.1308-0.0830.2205-0.0641-0.02780.369-0.0951-0.04580.37630.03980.2148-35.8659-17.87879.0427
253.73813.57292.32253.44582.23951.45630.1816-0.0778-0.07810.2972-0.13910.00190.1988-0.0497-0.04250.4115-0.06440.06380.32720.05210.344-24.6288-17.24160.3946
260.3482-0.6318-0.47611.33810.91780.66760.09120.007-0.05480.0594-0.1416-0.0868-0.03-0.05930.05040.4427-0.0948-0.09510.4230.09450.2513-30.1948-21.89119.5021
272.93452.10770.17111.68850.27040.16330.1254-0.25040.06490.2407-0.15930.16960.1379-0.02620.0340.3601-0.0363-0.02490.31720.05640.2868-19.4125-18.7418-2.2018
283.20352.3314-2.78231.8886-1.31645.09310.0164-0.06020.04490.0274-0.02760.07250.00860.2360.01120.2226-0.0162-0.07530.25730.00960.2236-10.86082.9469-6.8379
292.7168-0.23091.54630.07370.16812.618-0.0129-0.369-0.02330.05910.03020.00650.1875-0.1801-0.01730.3849-0.0394-0.0860.32640.05370.1956-16.1304-11.63589.2608
301.6345-0.0740.53620.13890.14890.40210.0885-0.1702-0.19460.2172-0.0158-0.03340.3035-0.0861-0.07280.4242-0.0849-0.07130.350.11170.246-19.4104-24.77925.7663
3157.8411-26.434738.003113.2469-12.959641.64771.6517-3.0646-4.4764-0.70271.55032.01961.5976-0.8453-3.2020.3985-0.35-0.04730.48620.14840.3743-51.1673-6.6396-3.0212
320.2516-0.40260.20630.7832-0.28370.18680.0596-0.0801-0.0245-0.018-0.02810.01380.054-0.1303-0.03150.294-0.0680.00660.3447-0.00920.1992-43.03392.1782-3.628
331.2250.10040.20140.9562-0.53530.36770.0428-0.23120.06780.1208-0.0995-0.0648-0.00410.01860.05670.276-0.03850.01350.3403-0.08780.1591-42.742110.0752-2.0571
340.77770.5402-0.88440.3772-0.62421.07970.0669-0.05130.01660.03260.00570.0129-0.0142-0.0579-0.07260.2882-0.0479-0.01060.4124-0.03850.161-40.773111.66083.8395
350.1963-0.5307-0.291923.9390.11030.463-0.032-0.09420.0168-0.06470.13510.2542-0.01720.1078-0.10310.27-0.0478-0.04620.34860.0120.2059-28.45288.93-2.8117
363.7235-2.7019-5.62562.04223.98778.7402-0.12090.0218-0.08540.1034-0.2103-0.02180.14950.01320.33120.2934-0.1003-0.03370.47560.00350.2519-34.768412.94086.5058
3720.2482-12.2411-3.44579.0755.02735.8429-0.1579-0.3852-0.39330.06480.24790.11720.05230.2133-0.090.3513-0.0846-0.01980.3630.05820.1867-29.51361.23099.0997
380.83480.399-0.26390.7377-0.04290.1146-0.0781-0.06170.0068-0.07150.0480.00320.0778-0.02360.03010.2617-0.0452-0.04460.2643-0.03320.1908-22.121117.5078-16.5696
391.9979-0.2979-0.23190.92140.92471.2080.1461-0.17840.08660.09-0.072-0.04560.1968-0.075-0.07410.2292-0.0379-0.05020.2618-0.08340.1976-24.991121.8764-1.9044
400.24380.5274-0.43641.2962-1.04170.85350.0289-0.1521-0.03120.1717-0.1402-0.1349-0.07450.12580.11130.3164-0.0339-0.0830.4237-0.03310.1753-21.989410.30495.4237
4119.7388-18.021230.402818.9565-26.722147.26310.8343-0.7725-0.7376-0.0950.56280.29311.6811-1.1922-1.39710.3701-0.1336-0.03630.239-0.01970.1962-55.59061.8771-9.4789
421.2542-0.1460.98360.7179-0.27220.80770.0101-0.1030.0391-0.0365-0.02470.01910.0284-0.06340.01460.2617-0.02820.0280.2247-0.07890.2033-51.612210.4886-16.8464
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460.71350.1904-1.38921.1491-0.60162.80040.0214-0.02860.03150.07880.01180.1183-0.0567-0.0503-0.03320.19590.0049-0.03550.2469-0.04790.2178-35.648922.7224-24.0539
472.8752-1.7852-2.0941.67492.1282.7479-0.27150.07450.11450.3234-0.06580.18120.4353-0.11970.33730.2324-0.0320.00260.11060.00040.2265-36.769419.2941-47.547
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491.62910.3179-0.13120.3836-0.45790.59440.0243-0.24830.16420.1142-0.0893-0.0285-0.1670.0950.0650.2624-0.0167-0.0270.1851-0.07120.2134-35.710430.8505-20.9449
506.9669-6.66424.00279.7229-8.17177.9332-0.11620.0152-0.21390.30650.1750.1598-0.3017-0.2199-0.05880.3459-0.019-0.01080.2133-0.09740.1785-45.500628.9701-8.5206
5133.104132.79050.276232.48020.27310.00420.7062-0.81020.95290.6595-0.75820.9396-0.0120.01020.0520.3533-0.0146-0.01720.3259-0.09980.0912-61.7961.0616-19.4848
520.41870.50090.18090.61480.20480.09280.1346-0.0638-0.02790.1236-0.1074-0.06020.1112-0.0183-0.02720.2323-0.00230.02990.2781-0.01670.2027-59.92173.3606-31.1239
530.81960.1911-0.13930.7231-0.20530.8762-0.116-0.10320.08720.03360.068-0.01680.0401-0.02360.0480.19020.007700.2199-0.05770.1969-64.14673.1436-37.1383
546.2881-0.74830.81274.6081.67840.8028-0.15250.0128-0.04020.24230.1502-0.00230.07420.05530.00230.1429-0.00230.01910.1716-0.04770.1924-69.2863.6353-43.6665
553.6314.60591.17456.05951.48440.3862-0.1306-0.1992-0.0028-0.14590.0528-0.061-0.0695-0.06580.07780.16570.0406-0.01460.3542-0.07120.2386-61.77113.8051-36.2276
567.30416.244710.97826.587110.452517.41270.05240.13960.14320.3274-0.24860.12350.3423-0.0770.19620.22130.02680.0070.24-0.03520.179-53.701410.9226-43.8884
570.82790.8932-0.33420.9764-0.36420.13740.0518-0.0510.01170.068-0.02760.0288-0.04170.0078-0.02420.21450.0613-0.01150.2032-0.07370.2199-63.735716.0113-40.8935
580.5292-0.341-0.76121.01210.92031.9539-0.0986-0.1449-0.060.06440.04630.0860.03970.06270.05220.17370.0236-0.01230.1814-0.02740.1827-45.30825.7216-51.6247
591.4461-1.78-0.23562.64920.79021.0484-0.09310.13920.07770.1403-0.0891-0.00370.0262-0.20060.18220.1522-0.012-0.05240.1769-0.0290.1569-55.08718.0224-57.7869
601.4762-0.1935-0.79160.11290.09221.33950.0621-0.03190.2292-0.0350.00510.0064-0.2338-0.057-0.06730.20450.0286-0.03330.1514-0.03910.2107-54.955921.0284-46.9217
610.05870.0406-0.02570.0283-0.01750.01460.1180.0931-0.04110.1423-0.0249-0.0342-0.1176-0.0186-0.09310.94860.1530.01180.3014-0.18510.2375-64.8435-8.5535-25.5066
620.01220.0751-0.01710.697-0.11330.0285-0.03610.0264-0.010.12510.0523-0.03950.0259-0.0019-0.01620.2588-0.01490.03050.3413-0.02680.2187-61.4445-13.9472-35.6859
631.1272-0.32310.00580.78510.15710.4284-0.0221-0.14870.0122-0.0348-0.03980.06130.0140.03980.06190.2069-0.0239-0.00230.2406-0.03970.2078-63.8314-20.9675-40.328
640.391-0.29120.53110.2291-0.38680.7339-0.0238-0.1092-0.00270.05840.0737-0.0421-0.0589-0.1521-0.04990.2262-0.03190.01230.22970.00190.3071-68.5699-16.8117-44.6294
651.40262.54070.69155.49042.23931.44240.09440.01220.04660.03360.0654-0.1099-0.09330.0316-0.15980.2021-0.0038-0.00230.2144-0.01360.215-58.4565-15.9948-50.4886
660.7269-0.40740.14013.5871-2.3891.62720.1388-0.09830.1151-0.0565-0.06080.0465-0.00960.0079-0.0780.16140.00250.010.2809-0.060.1823-68.2656-10.7089-51.5181
670.395-0.0097-0.42991.03220.33580.5718-0.1054-0.0407-0.054-0.00620.0506-0.0420.11460.04360.05480.25070.0124-0.0120.1823-0.04560.1867-42.0744-24.8517-54.2312
681.68550.4726-0.68370.1399-0.26681.05380.078-0.0513-0.0872-0.0008-0.0073-0.01340.1520.0111-0.07070.23610.0008-0.05470.0976-0.05540.2011-57.126-25.0158-59.745
690.004-0.00020.04120.0087-0.03830.90520.0003-0.01350.0223-0.0403-0.01790.00890.0921-0.06390.01760.24110.0382-0.04450.1929-0.06110.2374-57.2259-12.4808-61.458
704.61785.06634.351613.973710.25427.67030.23610.13410.47430.203-0.69290.43330.1785-0.4620.45680.2332-0.00180.02070.1851-0.00860.2535-70.4839-7.9617-53.8697
7147.551-3.40378.402414.4287-5.63521.06340.81312.3413-1.6865-1.27940-1.33241.25851.9968-0.81310.26680.09420.0540.4416-0.12450.47575.13767.2068-58.0951
722.1658-0.01340.16710.61960.04181.67210.04540.10260.05040.04320.0158-0.02940.06610.208-0.06110.2149-0.00280.00570.2260.03110.25160.475314.6002-49.8571
730.7088-0.47170.30180.4425-0.05350.4291-0.13210.0170.07010.01880.0295-0.0653-0.01540.10810.10260.2344-0.0606-0.00460.27040.040.25853.731219.828-46.6792
740.7896-0.19-0.55260.11090.03292.448-0.0757-0.1877-0.1720.1153-0.0342-0.04010.05410.43690.10980.2286-0.0511-0.07120.26330.04750.28444.401525.4003-40.5705
750.7417-0.427-0.57720.26670.33520.46-0.07060.1252-0.04150.0076-0.0177-0.01170.0256-0.08180.08830.2548-0.049-0.04210.24490.03780.3041-6.874325.1855-46.8468
760.4889-0.4235-0.54730.61710.14981.03340.05560.05780.0909-0.0567-0.0883-0.1922-0.0524-0.02680.03270.2682-0.05660.00310.2010.0440.2621-5.527430.6343-52.8356
770.6321-0.34230.04410.28290.3241.6427-0.09620.00950.16420.0397-0.0415-0.04980.18560.08030.13770.2273-0.0253-0.06990.2286-0.0190.2205-15.599820.9958-26.647
781.6788-0.0756-1.45781.12140.07061.48290.0387-0.04190.1824-0.07020.1627-0.0965-0.10350.1572-0.20140.2377-0.0735-0.0720.1579-0.01260.2743-9.178333.8192-33.8099
790.5014-0.18350.05820.8270.71960.7309-0.03350.06030.1914-0.1576-0.05730.0013-0.1895-0.03030.09080.2558-0.0195-0.03360.1840.04820.2517-17.082132.9716-43.6523
8010.188811.03877.250313.63454.998410.0519-0.20060.4291-0.1633-0.27540.4592-0.0916-0.1810.348-0.25860.2699-0.0075-0.04540.21190.06740.2722-7.225133.2871-56.162
8162.9077-28.2832-19.608212.71798.81616.1132-0.11751.08140.24490.2114-0.1458-0.09020.1264-0.34160.26330.32390.0265-0.00440.27080.13020.276311.49555.9589-48.0932
821.1627-0.49190.90790.21-0.38260.73380.09530.04690.0694-0.0367-0.0651-0.02330.1580.0573-0.03020.2686-0.0238-0.00520.3069-0.02950.34349.44496.8398-36.2923
831.37610.6557-0.92230.358-0.30251.3006-0.12670.0291-0.1607-0.00340.0067-0.07140.08380.12180.120.2272-0.0219-0.03450.30430.02490.298313.68236.3627-30.302
841.79592.356-0.53644.1162-3.37727.2174-0.1307-0.1805-0.1409-0.263-0.2032-0.24760.22280.12820.33390.1875-0.0035-0.04880.31770.0420.325818.46015.9075-23.3818
851.336-0.6705-0.7191.39910.24280.4008-0.19890.3915-0.13510.28640.107-0.0240.0815-0.23620.09190.2267-0.0215-0.06590.3354-0.01460.291811.968516.3451-29.6668
860.0315-0.02660.14230.0407-0.16830.7833-0.0020.0315-0.03220.06360.0357-0.0058-0.1729-0.0104-0.03380.2512-0.0163-0.06610.31530.00450.30648.810916.497-24.3897
870.90860.7816-0.54532.4371-1.08060.7258-0.0049-0.1013-0.0411-0.2381-0.0819-0.22440.16770.12080.08680.2252-0.0361-0.06610.24670.02250.2347-5.28635.7184-15.7701
881.81990.67970.9570.26460.38130.5745-0.0409-0.1413-0.1225-0.05830.0126-0.036-0.09620.05590.02830.266-0.0362-0.09620.31550.05180.26264.28197.9319-9.2993
890.0972-0.182-0.30550.34460.57840.99590.0138-0.03910.0402-0.0250.0511-0.0566-0.11640.0838-0.06490.2403-0.0502-0.09050.27330.00270.26370.727420.982-16.0884
9023.52710.30864.77560.0165-0.285811.1568-0.0267-0.24450.65410.01940.05440.013-0.4747-0.2002-0.02770.3072-0.0477-0.02830.1372-0.04150.276811.230825.804-27.0514
9111.5509-13.3471-15.458215.42417.866420.72930.71750.19110.0992-1.0271-0.39-0.1056-1.3251-0.2835-0.32750.6957-0.01970.06320.2220.09150.343815.4979-4.1112-42.8819
920.1488-0.1606-0.07831.47910.32380.08730.0867-0.0982-0.0005-0.1393-0.0567-0.0892-0.03460.0235-0.03010.26330.01170.0060.34620.07320.398912.59-10.7109-33.2776
930.29510.18620.16280.3683-0.24150.59970.0490.0181-0.0712-0.0265-0.0689-0.15360.08250.05020.020.2330.04430.00930.27380.06790.458215.5995-17.8864-29.2788
944.9473-2.5462-0.39753.49791.37461.00160.0152-0.0625-0.0547-0.058-0.02310.0541-0.09950.16320.00790.2152-0.0047-0.00390.31490.10670.324319.934-13.7355-24.5662
950.66662.3742-0.327317.94081.82351.10460.126-0.1163-0.0232-0.2054-0.22410.1028-0.22550.12240.09810.25760.0139-0.02460.29160.05950.36817.141-13.5969-18.4179
960.5428-0.27370.21431.7938-1.140.73180.0729-0.0323-0.03720.2252-0.1604-0.1261-0.11220.08320.08750.2525-0.0279-0.05410.35980.08840.356518.1328-10.7058-17.817
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990.3351-0.268-0.42690.22040.3470.54910.0174-0.0868-0.007-0.03220.0004-0.0016-0.05160.069-0.01770.2259-0.0275-0.11240.35750.08240.3798.2209-12.0283-7.5225
1009.4769-5.305-1.932533.2932-10.50094.8185-0.1081-0.68980.33850.5881-0.1749-1.0942-0.17510.36420.2830.2424-0.0487-0.15320.32930.05790.343921.0226-5.6436-14.5313
10148.75467.204330.77451.0664.547619.4253-2.1210.1281.6487-0.40290.56070.2565-1.66320.08291.56030.5165-0.33840.13110.5090.11120.610314.0433-15.1879-46.2026
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1041.9526-0.29830.46470.92390.2430.2241-0.02210.19760.08020.09540.042-0.08280.04340.0701-0.01990.31470.06830.0550.2940.02020.42515.7943-38.824-46.455
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1091.5182-1.87690.12572.694-0.91364.584-0.01980.0653-0.14670.00340.0078-0.12940.07060.02290.0120.25090.03080.00570.22160.00590.4814-3.2423-47.8081-34.8441
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1240.72521.5709-0.57387.2152-3.53861.83830.07510.0899-0.19070.0435-0.0914-0.18140.02380.08090.01630.28980.06750.12160.3039-0.01830.2196-12.801-12.4757-78.3322
1250.6152-0.3616-0.16250.98471.10261.36020.01360.1065-0.1599-0.1188-0.03540.0638-0.13090.03040.02180.2620.06290.08930.2841-0.02980.2344-20.1589-15.8137-75.9326
1262.6771-0.83180.98960.3409-0.4580.66670.0110.1725-0.0869-0.1041-0.1178-0.07370.13110.15120.10680.28970.02590.09940.2086-0.02050.2575-29.0946-15.9666-67.3678
1272.61740.7022-2.97560.93470.63726.23070.11580.0160.01970.11510.1008-0.15450.14210.0218-0.21670.189-0.0316-0.02150.1706-0.040.1732-39.59514.2723-60.6494
1282.2254-0.9052-0.6964.22911.69931.83190.07740.34850.2401-0.1791-0.1134-0.15960.21420.00920.0360.28870.03670.02340.2304-0.00610.1197-32.9327-7.8423-78.1177
1292.0286-1.3946-0.11721.592-0.04690.11220.08390.1287-0.3671-0.3787-0.13830.18320.1720.04490.05440.34130.03480.05650.2405-0.10080.2218-31.8024-19.9475-74.6167
1303.8398-3.62680.135214.1631-13.341516.26690.32870.5634-0.3808-0.8231-0.5650.17250.6530.0840.23640.37580.04390.01850.253-0.09560.2446-17.7608-24.1558-80.8534
1318.33697.4033-15.986.5857-14.211630.67120.0783-0.6003-0.67080.4068-0.8546-0.5107-0.8741.07030.77630.15050.03980.13160.32220.26840.69151.446-1.1885-65.2324
1320.3488-0.28230.2261.6087-0.42860.19090.0374-0.029-0.10170.0434-0.0161-0.18560.00710.0006-0.02130.1654-0.00530.02670.26070.02860.2697-7.40576.795-63.7505
1331.057-0.2807-0.42640.49440.39490.4177-0.0869-0.05290.0604-0.10480.0088-0.00410.0163-0.00620.07820.2088-0.01790.03920.22640.06050.2144-7.960614.0678-64.6832
1343.23340.68341.1495.62590.34931.87860.23950.17840.14640.1077-0.2152-0.2692-0.0480.309-0.02440.1185-0.01050.01850.20650.04980.2121-8.721722.3818-65.7892
1350.1145-0.0180.09140.0046-0.01170.07690.09930.0362-0.0963-0.0037-0.02920.02410.10520.0059-0.07010.27190.01680.07240.28380.01410.2472-13.846211.4817-72.5354
1361.88843.3802-0.606519.39552.01390.9156-0.1102-0.11840.05050.40250.1695-0.02920.15290.1361-0.05940.20650.00470.00290.27410.04080.156-22.50912.3361-63.9453
1374.87311.17972.4660.74030.21892.8121-0.02340.10090.0048-0.0671-0.0643-0.2231-0.1020.02010.08780.20110.00930.0540.21190.07370.1733-17.425914.6121-74.1681
1381.0304-0.03010.01191.41740.50630.206-0.1493-0.02050.0803-0.04650.11550.0205-0.00930.11260.03380.1970.012-0.02340.21910.05780.1625-29.202318.144-51.227
1393.2158-0.86140.89612.478-1.04430.55720.07250.14470.1513-0.0276-0.1391-0.17690.04250.12230.06650.1668-0.0067-0.03670.17640.03040.1639-26.814225.1341-64.6156
1402.4446-0.7922-1.46441.52220.90941.0575-0.06150.22430.001-0.10780.0319-0.00740.0541-0.0380.02960.22710.0375-0.01990.22950.05030.1356-29.086214.0229-72.0313
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 20
2X-RAY DIFFRACTION2A21 - 41
3X-RAY DIFFRACTION3A42 - 77
4X-RAY DIFFRACTION4A78 - 88
5X-RAY DIFFRACTION5A89 - 101
6X-RAY DIFFRACTION6A102 - 117
7X-RAY DIFFRACTION7A118 - 136
8X-RAY DIFFRACTION8A137 - 144
9X-RAY DIFFRACTION9A145 - 164
10X-RAY DIFFRACTION10A165 - 191
11X-RAY DIFFRACTION11B17 - 20
12X-RAY DIFFRACTION12B21 - 41
13X-RAY DIFFRACTION13B42 - 80
14X-RAY DIFFRACTION14B81 - 94
15X-RAY DIFFRACTION15B95 - 104
16X-RAY DIFFRACTION16B105 - 118
17X-RAY DIFFRACTION17B119 - 142
18X-RAY DIFFRACTION18B143 - 164
19X-RAY DIFFRACTION19B165 - 185
20X-RAY DIFFRACTION20B186 - 191
21X-RAY DIFFRACTION21C17 - 29
22X-RAY DIFFRACTION22C30 - 52
23X-RAY DIFFRACTION23C53 - 83
24X-RAY DIFFRACTION24C84 - 94
25X-RAY DIFFRACTION25C95 - 102
26X-RAY DIFFRACTION26C103 - 116
27X-RAY DIFFRACTION27C117 - 128
28X-RAY DIFFRACTION28C129 - 143
29X-RAY DIFFRACTION29C144 - 165
30X-RAY DIFFRACTION30C166 - 191
31X-RAY DIFFRACTION31D17 - 20
32X-RAY DIFFRACTION32D21 - 41
33X-RAY DIFFRACTION33D42 - 80
34X-RAY DIFFRACTION34D81 - 94
35X-RAY DIFFRACTION35D95 - 102
36X-RAY DIFFRACTION36D103 - 112
37X-RAY DIFFRACTION37D113 - 118
38X-RAY DIFFRACTION38D119 - 142
39X-RAY DIFFRACTION39D143 - 164
40X-RAY DIFFRACTION40D165 - 191
41X-RAY DIFFRACTION41E17 - 20
42X-RAY DIFFRACTION42E21 - 41
43X-RAY DIFFRACTION43E42 - 79
44X-RAY DIFFRACTION44E80 - 94
45X-RAY DIFFRACTION45E95 - 116
46X-RAY DIFFRACTION46E117 - 128
47X-RAY DIFFRACTION47E129 - 143
48X-RAY DIFFRACTION48E144 - 164
49X-RAY DIFFRACTION49E165 - 185
50X-RAY DIFFRACTION50E186 - 191
51X-RAY DIFFRACTION51F17 - 20
52X-RAY DIFFRACTION52F21 - 41
53X-RAY DIFFRACTION53F42 - 77
54X-RAY DIFFRACTION54F78 - 87
55X-RAY DIFFRACTION55F88 - 94
56X-RAY DIFFRACTION56F95 - 102
57X-RAY DIFFRACTION57F103 - 116
58X-RAY DIFFRACTION58F117 - 135
59X-RAY DIFFRACTION59F136 - 165
60X-RAY DIFFRACTION60F166 - 191
61X-RAY DIFFRACTION61G17 - 20
62X-RAY DIFFRACTION62G21 - 41
63X-RAY DIFFRACTION63G42 - 83
64X-RAY DIFFRACTION64G84 - 94
65X-RAY DIFFRACTION65G95 - 107
66X-RAY DIFFRACTION66G108 - 118
67X-RAY DIFFRACTION67G119 - 143
68X-RAY DIFFRACTION68G144 - 164
69X-RAY DIFFRACTION69G165 - 185
70X-RAY DIFFRACTION70G186 - 191
71X-RAY DIFFRACTION71H17 - 20
72X-RAY DIFFRACTION72H21 - 41
73X-RAY DIFFRACTION73H42 - 73
74X-RAY DIFFRACTION74H74 - 87
75X-RAY DIFFRACTION75H88 - 106
76X-RAY DIFFRACTION76H107 - 118
77X-RAY DIFFRACTION77H119 - 143
78X-RAY DIFFRACTION78H144 - 164
79X-RAY DIFFRACTION79H165 - 185
80X-RAY DIFFRACTION80H186 - 191
81X-RAY DIFFRACTION81I17 - 20
82X-RAY DIFFRACTION82I21 - 41
83X-RAY DIFFRACTION83I42 - 77
84X-RAY DIFFRACTION84I78 - 86
85X-RAY DIFFRACTION85I87 - 94
86X-RAY DIFFRACTION86I95 - 116
87X-RAY DIFFRACTION87I117 - 135
88X-RAY DIFFRACTION88I136 - 164
89X-RAY DIFFRACTION89I165 - 185
90X-RAY DIFFRACTION90I186 - 191
91X-RAY DIFFRACTION91J17 - 20
92X-RAY DIFFRACTION92J21 - 41
93X-RAY DIFFRACTION93J42 - 83
94X-RAY DIFFRACTION94J84 - 94
95X-RAY DIFFRACTION95J95 - 102
96X-RAY DIFFRACTION96J103 - 117
97X-RAY DIFFRACTION97J118 - 143
98X-RAY DIFFRACTION98J144 - 164
99X-RAY DIFFRACTION99J165 - 185
100X-RAY DIFFRACTION100J186 - 191
101X-RAY DIFFRACTION101K17 - 20
102X-RAY DIFFRACTION102K21 - 41
103X-RAY DIFFRACTION103K42 - 73
104X-RAY DIFFRACTION104K74 - 88
105X-RAY DIFFRACTION105K89 - 100
106X-RAY DIFFRACTION106K101 - 116
107X-RAY DIFFRACTION107K117 - 128
108X-RAY DIFFRACTION108K129 - 144
109X-RAY DIFFRACTION109K145 - 164
110X-RAY DIFFRACTION110K165 - 191
111X-RAY DIFFRACTION111L17 - 20
112X-RAY DIFFRACTION112L21 - 41
113X-RAY DIFFRACTION113L42 - 79
114X-RAY DIFFRACTION114L80 - 94
115X-RAY DIFFRACTION115L95 - 102
116X-RAY DIFFRACTION116L103 - 116
117X-RAY DIFFRACTION117L117 - 135
118X-RAY DIFFRACTION118L136 - 165
119X-RAY DIFFRACTION119L166 - 185
120X-RAY DIFFRACTION120L186 - 191
121X-RAY DIFFRACTION121M17 - 29
122X-RAY DIFFRACTION122M30 - 41
123X-RAY DIFFRACTION123M42 - 83
124X-RAY DIFFRACTION124M84 - 94
125X-RAY DIFFRACTION125M95 - 116
126X-RAY DIFFRACTION126M117 - 128
127X-RAY DIFFRACTION127M129 - 143
128X-RAY DIFFRACTION128M144 - 164
129X-RAY DIFFRACTION129M165 - 185
130X-RAY DIFFRACTION130M186 - 191
131X-RAY DIFFRACTION131N17 - 20
132X-RAY DIFFRACTION132N21 - 41
133X-RAY DIFFRACTION133N42 - 77
134X-RAY DIFFRACTION134N78 - 86
135X-RAY DIFFRACTION135N87 - 94
136X-RAY DIFFRACTION136N95 - 102
137X-RAY DIFFRACTION137N103 - 116
138X-RAY DIFFRACTION138N117 - 144
139X-RAY DIFFRACTION139N145 - 164
140X-RAY DIFFRACTION140N165 - 191

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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://pdbjlvh1.pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る