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- PDB-2yme: Crystal structure of a mutant binding protein (5HTBP-AChBP) in co... -

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基本情報

登録情報
データベース: PDB / ID: 2yme
タイトルCrystal structure of a mutant binding protein (5HTBP-AChBP) in complex with granisetron
要素SOLUBLE ACETYLCHOLINE RECEPTOR
キーワードRECEPTOR / PENTAMERIC LIGAND-GATED ION CHANNEL
機能・相同性
機能・相同性情報


acetylcholine receptor activity / acetylcholine-gated monoatomic cation-selective channel activity / response to nicotine / neuron projection / synapse / identical protein binding / membrane / metal ion binding
類似検索 - 分子機能
Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / Distorted Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
Chem-CWB / PHOSPHATE ION / Soluble acetylcholine receptor
類似検索 - 構成要素
生物種APLYSIA CALIFORNICA (無脊椎動物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.4 Å
データ登録者Kesters, D. / Thompson, A.J. / Brams, M. / Elk, R.v. / Spurny, R. / Geitmann, M. / Villalgordo, J.M. / Guskov, A. / Danielson, U.H. / Lummis, S.C.R. ...Kesters, D. / Thompson, A.J. / Brams, M. / Elk, R.v. / Spurny, R. / Geitmann, M. / Villalgordo, J.M. / Guskov, A. / Danielson, U.H. / Lummis, S.C.R. / Smit, A.B. / Ulens, C.
引用ジャーナル: Embo Rep. / : 2013
タイトル: Structural Basis of Ligand Recognition in 5-Ht3 Receptors.
著者: Kesters, D. / Thompson, A.J. / Brams, M. / Van Elk, R. / Spurny, R. / Geitmann, M. / Villalgordo, J.M. / Guskov, A. / Helena Danielson, U. / Lummis, S.C.R. / Smit, A.B. / Ulens, C.
履歴
登録2012年10月9日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02012年12月26日Provider: repository / タイプ: Initial release
改定 1.12013年1月30日Group: Database references
改定 1.22020年7月29日Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
カテゴリ: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 1.32023年12月20日Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: SOLUBLE ACETYLCHOLINE RECEPTOR
B: SOLUBLE ACETYLCHOLINE RECEPTOR
C: SOLUBLE ACETYLCHOLINE RECEPTOR
D: SOLUBLE ACETYLCHOLINE RECEPTOR
E: SOLUBLE ACETYLCHOLINE RECEPTOR
F: SOLUBLE ACETYLCHOLINE RECEPTOR
G: SOLUBLE ACETYLCHOLINE RECEPTOR
H: SOLUBLE ACETYLCHOLINE RECEPTOR
I: SOLUBLE ACETYLCHOLINE RECEPTOR
J: SOLUBLE ACETYLCHOLINE RECEPTOR
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)239,04435
ポリマ-233,43110
非ポリマー5,61325
22,5371251
1
F: SOLUBLE ACETYLCHOLINE RECEPTOR
G: SOLUBLE ACETYLCHOLINE RECEPTOR
H: SOLUBLE ACETYLCHOLINE RECEPTOR
I: SOLUBLE ACETYLCHOLINE RECEPTOR
J: SOLUBLE ACETYLCHOLINE RECEPTOR
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)119,37517
ポリマ-116,7165
非ポリマー2,66012
905
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area14430 Å2
ΔGint-77.2 kcal/mol
Surface area43530 Å2
手法PISA
2
A: SOLUBLE ACETYLCHOLINE RECEPTOR
B: SOLUBLE ACETYLCHOLINE RECEPTOR
C: SOLUBLE ACETYLCHOLINE RECEPTOR
D: SOLUBLE ACETYLCHOLINE RECEPTOR
E: SOLUBLE ACETYLCHOLINE RECEPTOR
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)119,66918
ポリマ-116,7165
非ポリマー2,95313
905
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area14940 Å2
ΔGint-67.8 kcal/mol
Surface area42770 Å2
手法PISA
単位格子
Length a, b, c (Å)83.090, 138.900, 119.890
Angle α, β, γ (deg.)90.00, 91.07, 90.00
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCS oper: (Code: given
Matrix: (-1, -0.029, -0.004), (-0.024, 0.725, 0.689), (-0.017, 0.689, -0.725)
ベクター: 52.963, 0.539, 0.403)

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要素

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タンパク質 / , 2種, 19分子 ABCDEFGHIJ

#1: タンパク質
SOLUBLE ACETYLCHOLINE RECEPTOR / ACHBP


分子量: 23343.137 Da / 分子数: 10 / 断片: ACETYLCHOLINE BINDING DOMAIN, RESIDUES 20-224 / 変異: YES / 由来タイプ: 組換発現
由来: (組換発現) APLYSIA CALIFORNICA (無脊椎動物)
発現宿主: SPODOPTERA FRUGIPERDA (ツマジロクサヨトウ)
株 (発現宿主): SF21 / 参照: UniProt: Q8WSF8
#2: 糖
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-アセチル-β-D-グルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 9 / 由来タイプ: 組換発現 / : C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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非ポリマー , 4種, 1267分子

#3: 化合物
ChemComp-CWB / 1-methyl-N-[(1R,5S)-9-methyl-9-azabicyclo[3.3.1]nonan-3-yl]indazole-3-carboxamide / GRANISETRON / グラニセトロン


分子量: 312.409 Da / 分子数: 10 / 由来タイプ: 合成 / : C18H24N4O / コメント: 化学療法薬, アンタゴニスト*YM
#4: 化合物
ChemComp-PO4 / PHOSPHATE ION / ホスファ-ト


分子量: 94.971 Da / 分子数: 5 / 由来タイプ: 合成 / : PO4
#5: 化合物 ChemComp-NA / SODIUM ION / ナトリウムカチオン


分子量: 22.990 Da / 分子数: 1 / 由来タイプ: 合成 / : Na
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1251 / 由来タイプ: 天然 / : 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: 2.75 Å3/Da / 溶媒含有率: 55 % / 解説: NONE
結晶化詳細: 200 MM NA2SO4, BISTRISPROPANE PH 8.5, 18% PEG3350.

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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: ESRF / ビームライン: ID23-1 / 波長: 0.8726
検出器タイプ: ADSC CCD / 検出器: CCD / 日付: 2009年6月12日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.8726 Å / 相対比: 1
反射解像度: 2.4→46.35 Å / Num. obs: 105875 / % possible obs: 99.7 % / Observed criterion σ(I): 1.5 / 冗長度: 3.8 % / Biso Wilson estimate: 35.58 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.6
反射 シェル解像度: 2.4→2.5 Å / 冗長度: 3.7 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.5 / % possible all: 99.9

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解析

ソフトウェア
名称バージョン分類
PHENIX(PHENIX.REFINE)精密化
XDSデータ削減
SCALAデータスケーリング
MOLREP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 2XYS
解像度: 2.4→48.908 Å / SU ML: 0.37 / σ(F): 1.99 / 位相誤差: 24.57 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2263 5292 5 %
Rwork0.1695 --
obs0.1724 105852 99.71 %
溶媒の処理減衰半径: 0.98 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 47.137 Å2 / ksol: 0.338 e/Å3
原子変位パラメータBiso mean: 46 Å2
Baniso -1Baniso -2Baniso -3
1-0.9392 Å20 Å2-7.0484 Å2
2---6.3015 Å20 Å2
3---5.3623 Å2
精密化ステップサイクル: LAST / 解像度: 2.4→48.908 Å
タンパク質核酸リガンド溶媒全体
原子数16400 0 382 1251 18033
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00417262
X-RAY DIFFRACTIONf_angle_d0.80523563
X-RAY DIFFRACTIONf_dihedral_angle_d20.1426430
X-RAY DIFFRACTIONf_chiral_restr0.0512641
X-RAY DIFFRACTIONf_plane_restr0.0052976
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3999-2.42720.34481740.28983308X-RAY DIFFRACTION100
2.4272-2.45570.35441780.27543390X-RAY DIFFRACTION100
2.4557-2.48570.31741770.2633349X-RAY DIFFRACTION100
2.4857-2.51720.33911760.2633354X-RAY DIFFRACTION100
2.5172-2.55030.32481750.25373331X-RAY DIFFRACTION100
2.5503-2.58520.30581770.24663349X-RAY DIFFRACTION100
2.5852-2.62210.3181760.23653339X-RAY DIFFRACTION100
2.6221-2.66130.31111760.23083362X-RAY DIFFRACTION100
2.6613-2.70290.30371750.22083316X-RAY DIFFRACTION100
2.7029-2.74720.28981770.233361X-RAY DIFFRACTION100
2.7472-2.79450.29861770.20643355X-RAY DIFFRACTION100
2.7945-2.84530.27221750.19973335X-RAY DIFFRACTION100
2.8453-2.90010.29111760.19793346X-RAY DIFFRACTION100
2.9001-2.95930.27391790.193389X-RAY DIFFRACTION100
2.9593-3.02360.24031740.19073311X-RAY DIFFRACTION100
3.0236-3.09390.26711760.17163357X-RAY DIFFRACTION100
3.0939-3.17130.24471770.17133364X-RAY DIFFRACTION100
3.1713-3.2570.22161750.17163310X-RAY DIFFRACTION100
3.257-3.35280.23161770.16463372X-RAY DIFFRACTION100
3.3528-3.4610.2221780.16223387X-RAY DIFFRACTION100
3.461-3.58470.22731750.15973314X-RAY DIFFRACTION100
3.5847-3.72820.20251760.15153353X-RAY DIFFRACTION100
3.7282-3.89780.1871770.14123362X-RAY DIFFRACTION100
3.8978-4.10320.1811770.13343362X-RAY DIFFRACTION100
4.1032-4.36010.18071760.1233343X-RAY DIFFRACTION99
4.3601-4.69650.16861760.11493340X-RAY DIFFRACTION99
4.6965-5.16860.15231780.11073373X-RAY DIFFRACTION99
5.1686-5.91550.19951770.14423368X-RAY DIFFRACTION99
5.9155-7.44860.20711770.16313373X-RAY DIFFRACTION99
7.4486-48.91840.19631780.17583387X-RAY DIFFRACTION98
精密化 TLS

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.7072.1198-2.37674.5035-2.0794.8797-0.09680.2408-0.0568-0.35140.0051-0.26610.10270.1410.23380.2074-0.10640.13190.31010.06090.251662.124721.090545.789
23.06810.42-0.11375.4964-0.97261.7591-0.21010.16650.1376-0.4506-0.2013-0.7141-0.080.39350.35970.2885-0.0974-0.03770.23850.22440.549366.44978.000660.8389
30.1398-0.25050.33660.7956-0.56660.8138-0.14730.0136-0.04740.16890.09470.014-0.2421-0.082-0.08210.2559-0.0450.07380.10870.00140.118837.07378.936470.659
46.27250.8673-2.53450.7619-0.6871.81850.0584-0.1676-0.16640.2169-0.1682-0.3499-0.17910.09860.14140.21750.0009-0.12660.08330.04260.213249.862113.515264.9585
50.2447-0.11980.25421.12390.50940.6439-0.16090.15010.2195-0.20520.0573-0.3158-0.29090.2627-0.14020.1391-0.1876-0.03750.20520.1110.379860.223721.937253.5106
62.85463.1812-0.92464.3227-1.41751.3587-0.07350.0638-0.2438-0.10660.1288-0.0794-0.0112-0.01530.03550.2124-0.0245-0.01170.047-0.0030.153344.67891.867566.6766
70.42340.14860.04961.0155-0.16210.6145-0.089-0.0060.08340.1384-0.1291-0.1264-0.04320.08190.00610.188-0.08090.00320.02230.04680.136243.906811.926364.2096
89.35260.2541-3.25722.8180.15055.0711-0.0003-0.67310.12630.89220.00030.3721-0.1105-0.386-0.22610.3808-0.03530.03270.21430.09040.182733.62757.589480.5046
91.2021-0.2232-0.05530.9706-0.07170.6223-0.0601-0.34670.13860.33030.002-0.3316-0.2299-0.0344-0.0290.29850.0078-0.10860.1569-0.0220.197144.889112.490574.2829
102.138-1.6012-1.61634.08082.79762.097-0.2796-0.1989-0.56210.8876-0.01210.3280.49350.09730.19080.6877-0.071-0.24250.25640.0990.616357.4413-3.302477.8426
112.61150.0342-1.85821.64430.44643.21320.0759-0.14520.2330.2908-0.23920.0726-0.2901-0.24060.03480.34750.0113-0.01870.1664-0.04580.110736.524610.570378.5476
122.89363.4701-1.51857.5110.994.8503-0.62180.53020.3701-0.74020.63450.0859-0.5350.7405-0.12740.2351-0.14340.02530.47360.1340.670570.5714-0.326754.9535
137.59437.73340.73558.17551.96655.0025-0.46620.65691.3659-0.86520.3393-0.9925-0.97541.05190.15940.4891-0.07990.06320.5030.09060.827864.26-14.313748.6906
141.7666-0.5953-0.62192.65790.36131.46140.16270.04180.03740.064-0.1022-0.05270.2007-0.0827-0.1010.1924-0.0592-0.0850.05390.06670.240744.4016-16.718864.5566
154.88320.0926-3.09160.0088-0.11522.41250.00110.064-0.35740.28050.088-0.10750.1082-0.1239-0.00940.2180.0039-0.05640.11270.02590.275444.7113-13.079165.6357
162.34170.89730.56481.5010.81441.0883-0.06930.2061-0.2458-0.04530.1257-0.43510.05140.33590.00470.17270.0258-0.04650.180.06390.320758.427-9.523559.1896
175.5377-4.02741.87963.8032-1.27473.54830.394-0.6789-0.44030.0701-0.19280.1870.3013-0.0279-0.24770.2277-0.1051-0.11610.23260.00870.418562.1892-8.910362.9242
180.5428-0.2-0.03551.05110.15730.2510.0381-0.1694-0.17520.2168-0.07110.24080.1844-0.16560.00660.2475-0.22-0.05450.1160.12540.243834.1836-16.699969.3758
191.423-0.4213-1.51071.53670.73934.5441-0.0391-0.104-0.2950.3218-0.09630.02030.22390.32240.11860.2348-0.0189-0.08010.10990.03270.249747.2987-18.950967.1388
201.2016-0.84740.2453.0391-0.92880.61560.051-0.118-0.13330.4663-0.06570.09450.01890.03580.08930.4087-0.0228-0.01820.10990.04030.263141.4804-21.850673.2191
211.1516-1.56620.20043.4426-1.29980.83810.14980.1527-0.0705-0.5193-0.12820.0490.28920.01080.41010.47390.0171-0.2090.13410.07820.366145.752-33.441653.3611
221.7764-0.3323-1.44832.17510.01612.32830.2615-0.10390.07260.18060.0060.1372-0.194-0.0201-0.02550.2779-0.0592-0.0670.08110.0950.266838.1921-20.901671.2435
235.1845-2.03151.11491.8648-1.39166.60140.26940.3352-0.1834-0.0267-0.3464-0.58640.05711.13660.05070.1959-0.01360.05660.4433-0.010.78563.3303-18.874939.6646
242.67312.466-0.83685.9877-0.99766.693-0.01180.4141-0.1375-0.3780.0286-0.3823-0.29590.359-0.0810.2660.1654-0.01570.1442-0.04760.153947.362-18.380327.1973
251.55610.2865-0.23091.53440.41791.21460.207-0.02160.1367-0.115-0.13520.0715-0.0067-0.1617-0.08190.2364-0.0225-0.11810.10720.03090.247927.2403-18.888249.7963
262.4346-0.4383-1.22262.35840.08561.76920.22480.1932-0.381-0.2168-0.1236-0.46680.38320.4294-0.01890.30030.1660.00040.2603-0.02290.37354.151-23.532737.028
272.5466-0.741-1.17814.1252-0.45271.1380.02630.02370.0497-0.21630.12420.2465-0.1575-0.0744-0.0070.2553-0.0388-0.10420.10920.00350.312529.9185-12.805339.765
281.466-0.80780.10641.2975-0.08260.6150.10330.1267-0.1123-0.0062-0.1203-0.19690.09590.1321-0.05080.17820.0638-0.02180.07610.05250.363441.5306-19.199144.7661
290.682-0.705-1.02141.1240.53743.50510.0841-0.2523-0.51220.1673-0.07310.66470.6154-0.50560.14170.2163-0.1319-0.07650.27490.05180.509114.4546-21.97349.4391
300.519-0.201-0.29111.22150.22390.2190.02030.1824-0.2719-0.3304-0.21030.09650.2634-0.16980.14230.2647-0.046-0.06560.0492-0.02390.266832.0091-24.355339.8436
311.55450.4114-0.65821.87340.92252.23850.1765-0.1748-0.26770.2325-0.23520.0269-0.0152-0.0709-0.00660.4817-0.1502-0.04120.2115-0.05020.302323.6624-27.795446.6316
325.37040.95323.68073.460.2463.5427-0.0709-0.80980.6349-0.2706-0.04680.4154-0.1249-0.5360.33320.48360.0355-0.19520.4701-0.19910.442724.9479-17.294324.4603
331.19380.6184-0.48771.23170.09751.43040.1009-0.1313-0.14910.1789-0.08760.04440.0774-0.06290.40140.3262-0.2209-0.05550.1409-0.06920.276621.4969-25.516246.7866
345.9896-0.5932-1.85123.64511.30065.58160.01370.0982-0.471-0.26620.0606-0.56670.3380.74620.06990.23660.13420.17450.4659-0.05270.430350.4745-9.522120.1506
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410.87770.06870.74410.6724-0.86321.9116-0.098-0.1656-0.05950.00630.01660.59160.0169-0.6707-0.01130.1457-0.0027-0.00720.2757-0.09140.411211.48352.225642.7658
421.24361.0611-0.13981.43290.38891.41870.10380.1531-0.122-0.1939-0.0170.3059-0.0962-0.29680.00620.09790.0355-0.08480.1708-0.00110.292820.23582.637630.8033
430.9994-0.65080.63780.4305-0.32621.1995-0.13410.0460.25170.0143-0.0417-0.0008-0.29780.05890.28130.24840.0806-0.17480.1733-0.08270.269619.645114.166628.7679
443.4563-0.1456-1.13220.5167-0.30763.6493-0.0112-0.1478-0.4577-0.0705-0.09510.26990.4423-0.414-0.03440.0982-0.0297-0.08920.1265-0.07560.25611.53271.885635.6711
450.8984-0.6353-0.49784.83683.27372.37930.01820.3586-0.20880.12540.1768-0.74140.42360.9489-0.1650.1568-0.00090.08680.3372-0.00820.345851.485217.464628.3989
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472.6850.0362-3.4350.57580.56535.8354-0.1978-0.0489-0.3897-0.0729-0.350.01410.1629-0.02480.54280.14880.0288-0.03260.1123-0.02090.21723.263814.970453.201
480.8410.2591-1.23390.6581-0.28463.6021-0.07680.15020.2235-0.099-0.1062-0.1611-0.44840.2276-0.10620.3694-0.05570.04190.23540.12470.243244.948526.298230.0439
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501.32820.3215-0.75331.882-0.58212.25830.03260.06080.04240.2536-0.1863-0.1952-0.2396-0.01830.06630.12510.0075-0.00740.07920.01560.183636.37515.742452.1299
511.63050.6999-0.55890.7008-0.31721.79830.04040.05660.12810.01150.0820.1985-0.1906-0.0863-0.10380.11180.02130.03560.1550.03310.129632.926218.388444.6572
524.44610.5151-0.49666.27831.51844.2781-0.0311-0.43640.27270.26640.25020.7261-0.6081-0.8409-0.110.20130.11680.11130.4466-0.08620.472910.185221.815861.6048
531.961-2.7546-1.92944.06713.53845.3523-0.17460.122-0.22360.1954-0.20340.41260.1456-0.40250.22090.2404-0.0282-0.08940.088-0.00030.210128.563823.414957.1514
540.1414-0.25550.17910.5814-0.45280.5719-0.1630.01370.19310.1837-0.11810.0284-0.35910.01820.01810.22980.1107-0.11260.0477-0.00720.317531.702727.062452.5932
554.5906-1.3252-1.51293.57140.2863.1602-0.06040.2127-0.4501-0.0069-0.01490.64120.0348-0.51580.25620.22210.0874-0.0020.1639-0.09590.349719.294823.499255.6615
568.4562.40844.07816.5114-0.73367.55210.3506-0.441-0.82120.6261-0.15831.2755-0.2873-1.4718-0.24870.3270.04150.14840.6803-0.10080.7471-14.010955.423339.1706
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598.1217-2.72362.33042.9535-1.99841.3943-0.5204-0.60341.32031.22010.2522-0.614-0.30440.06010.0180.58270.0387-0.24070.2257-0.03630.68841.444867.824223.8679
600.7537-0.09720.42091.7943-0.34250.286-0.2989-0.19080.2880.1514-0.01840.3626-0.3954-0.35970.12490.44450.1688-0.17930.2035-0.16430.5013-7.0163.329927.7636
614.5582-2.4607-0.74572.51061.48235.94570.19040.0051.0598-0.4474-0.06190.3353-1.6892-0.2451-0.11350.45820.0494-0.11720.2533-0.0270.41691.105863.217223.3129
620.1067-0.14160.22311.34440.07740.5822-0.07760.02180.3467-0.2093-0.1105-0.0942-0.48990.0189-0.23860.6924-0.0547-0.29640.08180.08350.60554.150671.8329.2956
631.04590.136-0.43341.46820.6450.84470.0644-0.05450.21380.001-0.07860.0288-0.30610.0505-0.12890.5296-0.2659-0.20620.13980.04750.482416.006270.399319.2154
640.9648-1.9432-0.08274.0223-0.16341.07330.1210.2648-0.2553-1.0087-0.19470.5953-0.3047-0.2941-0.07090.86540.0696-0.28020.21290.02220.71560.987178.608310.3525
656.3329-5.87660.06257.8953-0.68992.53010.6191.0332-1.0699-1.9848-0.80021.9702-0.2526-0.6352-0.01960.89770.281-0.24880.4561-0.22560.9928-8.447877.31329.1586
663.3862-0.1674-1.02181.4584-0.10570.50210.1669-0.10610.0862-0.2512-0.0475-0.3462-0.10050.05240.09710.5849-0.1782-0.14820.2430.16110.69918.733572.889710.3165
670.84980.5925-0.04624.05145.37318.0331-0.1396-0.9675-0.0541-0.1832-0.63440.7206-0.2272-1.57430.87770.6760.34320.06180.91220.0350.9078-28.489759.775616.6424
681.89431.2861-4.2530.9769-2.82589.58480.18910.45560.3353-0.05320.35510.8688-0.4094-0.9902-0.47750.66990.1048-0.31530.32210.02860.7125-30.762350.6662-4.325
690.12360.3061-0.16331.0347-0.3380.2337-0.00460.01780.08310.0045-0.0075-0.1207-0.0911-0.00290.00010.5597-0.029-0.23640.21250.1840.4623-2.765159.765-7.2483
703.49620.138-2.33750.3705-0.17071.8714-0.03930.35310.34350.0177-0.00540.2612-0.6094-0.2088-0.08790.6335-0.0012-0.25330.31690.19980.6229-9.782161.267-2.7757
716.9946-3.7515-3.06155.5296-0.082.1826-0.0911-0.62940.79410.12850.15030.9537-0.8471-1.1969-0.19540.5990.3234-0.17530.7333-0.0680.9447-32.789765.915510.3025
721.1581-0.28990.22891.2255-0.36191.1475-0.186-0.12740.3052-0.01070.02230.1879-0.3235-0.2257-0.0280.49020.2063-0.36040.03070.14280.37-12.80759.21412.2978
730.7243-0.3406-0.07560.7702-0.25691.17620.02950.3660.3247-0.2202-0.0909-0.0238-0.40220.1420.05660.5779-0.0689-0.26910.31750.21280.4478-8.985856.6687-13.2471
741.20680.5599-0.03361.6041-0.21450.1556-0.0310.1980.0904-0.4227-0.02060.18670.07090.0546-0.11380.81080.0294-0.04350.27930.22210.5049-8.564470.2346-9.2446
750.3028-0.14850.09430.34470.05360.06380.03180.01720.0587-0.0099-0.0322-0.0892-0.15660.0599-0.06240.6594-0.0936-0.16020.25410.27320.52992.942568.6008-10.2828
760.1304-0.2073-0.06562.2053-0.5990.30110.24390.0211-0.2793-0.0413-0.1236-0.08330.337-0.0131-0.10560.61510.0509-0.34210.45250.17710.4333-18.618649.8682-17.6195
770.8505-0.32060.43840.9983-0.68481.3842-0.04270.03490.0440.14860.0085-0.086-0.25960.063-0.00270.5085-0.0704-0.25720.29360.23290.4236-3.186761.6688-14.5367
788.71491.8478-1.95444.21091.78255.79760.1209-0.7554-0.76120.4022-0.36790.5439-0.0789-0.85260.36120.3032-0.009-0.06690.74950.20650.8856-32.687141.38495.9708
794.19341.33820.10232.7907-1.45048.9993-0.3538-0.2080.13530.95890.42320.4116-0.15650.11990.03790.522-0.0255-0.11350.33890.20470.436-21.088325.19727.2742
802.3962-0.16860.99561.1214-0.49881.16890.1287-0.0815-0.0778-0.1861-0.13560.12420.05490.0371-0.05470.471-0.0375-0.16040.21430.08920.19-3.70233.6533-7.9178
811.62090.3719-0.23030.1676-0.09940.25290.03060.0937-0.0949-0.05050.15720.1875-0.0664-0.20390.10830.4207-0.0278-0.27290.30450.17060.4258-14.084934.4261-5.2768
823.0926-3.9798-5.57465.98476.95512.0001-0.42360.4009-0.2893-1.16390.07082.5329-0.5176-3.19860.2430.47240.0163-0.17730.91390.24240.8668-39.272939.1722-2.807
830.16240.010.02780.2653-0.04960.3639-0.00960.017-0.0023-0.11940.10490.2202-0.0642-0.26220.09450.3546-0.0536-0.30260.29110.21060.2867-12.332437.3234-1.9184
849.03122.2695-0.03213.0619-3.40294.62660.19230.74870.3929-1.15480.1553-0.12910.36691.1882-0.03940.75580.06140.24070.47040.03890.328912.370433.7664-17.988
850.8306-0.41530.35860.7316-0.75271.3315-0.06920.3807-0.0559-0.54610.13320.16880.0947-0.0891-0.19690.5787-0.1217-0.18580.30370.07780.2759-5.700731.5645-10.9291
865.474.8139-4.11215.4779-3.59226.08630.2514-0.3863-0.25080.2498-0.4546-0.2686-0.00880.68240.23650.7524-0.1356-0.07510.36030.01750.1736-3.104925.9838-15.1847
871.74130.388-1.38274.78331.67941.93880.5478-2.2424-0.05322.1155-0.5136-0.5391-0.22380.59810.04471.6305-0.5388-0.25151.18170.1230.6793-2.962512.0637-0.0725
886.75153.9845-4.87535.0816-4.21596.45680.1388-0.1306-0.0459-0.3055-0.15840.0551-0.24580.60630.06490.6863-0.163-0.13950.26770.06290.27031.664630.065-14.1211
893.18494.5832-0.89976.6059-1.15532.75420.2103-0.37660.78660.232-0.23770.5049-0.1259-0.32120.11090.1506-0.12560.08220.39450.00850.4685-22.000922.844716.3697
905.14953.38163.96865.52382.94875.5383-0.1114-0.25570.0653-0.70940.01731.30510.3076-1.29070.00210.4135-0.2256-0.10340.5534-0.030.4167-10.852825.476628.5372
911.93150.5563-1.12572.1387-0.81413.28510.2482-0.00840.03410.10690.10230.0613-0.04430.1607-0.08570.1691-0.0182-0.0820.15850.06220.190910.623427.030413.696
924.44781.8511-3.64963.2709-2.35714.5119-0.0023-0.1741-0.2518-0.0475-0.1467-0.07590.35960.05090.16320.2326-0.0032-0.06310.12580.0830.19592.789824.003714.1003
934.38744.66320.04626.30412.61244.87680.2351-0.3887-0.76610.7438-0.0780.43270.6585-0.67830.00890.4754-0.16990.0460.39560.18950.4961-19.269612.07919.1875
941.02550.12460.18741.00860.1181.5109-0.04050.0824-0.04560.0472-0.05750.19060.1205-0.24130.08440.1988-0.0028-0.04210.1185-0.02050.2365-2.931727.520814.96
954.53482.9216-1.71516.893-3.45583.97190.1449-0.1673-0.10720.1963-0.2161-0.38650.02310.17090.06550.3361-0.1469-0.09420.24080.03340.2854-7.906920.006414.164
961.90310.2829-0.01392.6293-0.09832.38930.00170.0124-0.1656-0.06280.0626-0.26470.28430.3231-0.03080.19860.031-0.07630.1482-0.02090.234914.081126.722714.8283
972.70032.3169-0.7476.829-3.7145.36870.14590.0317-0.252-0.6206-0.1346-0.03130.52730.86510.05790.3760.136-0.00060.3204-0.08240.251714.739522.0170.6065
982.1987-1.16430.28883.022-0.89962.2843-0.0111-0.07960.280.23970.1233-0.4183-0.1737-0.0814-0.13160.31960.1359-0.05120.18250.01630.344916.425423.017823.5513
992.4649-1.5044-0.09423.11210.40770.0590.15130.18250.0271-0.4653-0.1685-0.2240.21380.13210.04520.21270.1313-0.02010.2140.0530.304119.204124.381510.5235
1003.0440.1789-2.13452.2937-0.37952.02960.01580.15740.00280.06160.08430.4444-0.0008-0.2287-0.27450.1599-0.14540.07030.41020.08120.2555-10.830130.768637.0623
1013.4943-0.17520.25725.2785-1.53265.77930.0786-0.52980.13730.668-0.07191.21710.1602-0.9559-0.04210.408-0.07420.01860.3285-0.1590.5706-3.017949.47641.0022
1021.81740.2713-0.19742.01380.26311.84790.06510.0780.2406-0.23020.11030.0053-0.1486-0.0095-0.10290.1521-0.0736-0.02290.14620.03190.231718.938846.93219.5592
1033.32841.9967-1.04133.033-0.83762.63090.0971-0.42770.18810.2608-0.22620.0398-0.0845-0.04260.12150.1478-0.0183-0.05410.1685-0.00540.23111.916140.704534.4552
1042.9991.6922-2.03682.4312-1.6543.29980.012-0.42330.0632-0.1177-0.19610.13960.00620.43660.16770.092-0.0168-0.040.14790.03950.14889.331642.546627.4125
1054.65850.4518-2.43432.97651.1865.0921-0.01190.35020.06050.12330.022-1.2334-0.18521.2904-0.00180.2262-0.173-0.0130.55960.01980.723133.587752.165118.858
1063.1747-1.5393-2.87783.40861.39523.57570.4553-0.55880.5722-0.1015-0.0502-0.2116-0.57730.2259-0.32390.2856-0.0411-0.10520.2556-0.1190.41357.925556.665633.6902
1075.521-5.1607-4.79366.3544.76234.215-0.2034-0.52820.29190.51950.1937-0.60730.10420.3642-0.15420.28340.0131-0.13750.3362-0.00560.21719.044444.422936.008
1083.14760.0192-0.82890.22311.02064.92760.1124-0.15770.2541-0.09250.0934-0.1876-0.46850.2602-0.01280.1258-0.0092-0.14550.156-0.00970.343124.58545.71226.2839
1091.74830.7851-1.05045.03423.48585.86110.0134-0.4160.67530.0149-0.29670.6956-0.7511-0.29720.18650.3514-0.0753-0.24040.253-0.27760.468913.624461.246236.4899
1107.7371-1.2877-0.23448.70391.45352.8585-0.10110.1453-0.4964-0.34270.3364-1.22270.00941.2918-0.38590.2433-0.1027-0.00460.4659-0.06660.546232.923845.999318.8806
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:13)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 14:27)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 28:46)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 47:64)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 65:85)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 86:97)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 98:130)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 131:142)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 143:183)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 184:193)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 194:205)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 1:13)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 14:22)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 23:45)
15X-RAY DIFFRACTION15(CHAIN B AND RESID 46:58)
16X-RAY DIFFRACTION16(CHAIN B AND RESID 59:102)
17X-RAY DIFFRACTION17(CHAIN B AND RESID 103:114)
18X-RAY DIFFRACTION18(CHAIN B AND RESID 115:140)
19X-RAY DIFFRACTION19(CHAIN B AND RESID 141:171)
20X-RAY DIFFRACTION20(CHAIN B AND RESID 172:183)
21X-RAY DIFFRACTION21(CHAIN B AND RESID 184:192)
22X-RAY DIFFRACTION22(CHAIN B AND RESID 193:205)
23X-RAY DIFFRACTION23(CHAIN C AND RESID 1:12)
24X-RAY DIFFRACTION24(CHAIN C AND RESID 13:30)
25X-RAY DIFFRACTION25(CHAIN C AND RESID 31:55)
26X-RAY DIFFRACTION26(CHAIN C AND RESID 56:85)
27X-RAY DIFFRACTION27(CHAIN C AND RESID 86:96)
28X-RAY DIFFRACTION28(CHAIN C AND RESID 97:123)
29X-RAY DIFFRACTION29(CHAIN C AND RESID 124:140)
30X-RAY DIFFRACTION30(CHAIN C AND RESID 141:170)
31X-RAY DIFFRACTION31(CHAIN C AND RESID 171:182)
32X-RAY DIFFRACTION32(CHAIN C AND RESID 183:193)
33X-RAY DIFFRACTION33(CHAIN C AND RESID 194:205)
34X-RAY DIFFRACTION34(CHAIN D AND RESID 1:11)
35X-RAY DIFFRACTION35(CHAIN D AND RESID 12:22)
36X-RAY DIFFRACTION36(CHAIN D AND RESID 23:54)
37X-RAY DIFFRACTION37(CHAIN D AND RESID 55:67)
38X-RAY DIFFRACTION38(CHAIN D AND RESID 68:75)
39X-RAY DIFFRACTION39(CHAIN D AND RESID 76:99)
40X-RAY DIFFRACTION40(CHAIN D AND RESID 100:117)
41X-RAY DIFFRACTION41(CHAIN D AND RESID 118:137)
42X-RAY DIFFRACTION42(CHAIN D AND RESID 138:173)
43X-RAY DIFFRACTION43(CHAIN D AND RESID 174:193)
44X-RAY DIFFRACTION44(CHAIN D AND RESID 194:205)
45X-RAY DIFFRACTION45(CHAIN E AND RESID 1:18)
46X-RAY DIFFRACTION46(CHAIN E AND RESID 19:32)
47X-RAY DIFFRACTION47(CHAIN E AND RESID 33:54)
48X-RAY DIFFRACTION48(CHAIN E AND RESID 55:73)
49X-RAY DIFFRACTION49(CHAIN E AND RESID 74:83)
50X-RAY DIFFRACTION50(CHAIN E AND RESID 84:100)
51X-RAY DIFFRACTION51(CHAIN E AND RESID 101:128)
52X-RAY DIFFRACTION52(CHAIN E AND RESID 129:136)
53X-RAY DIFFRACTION53(CHAIN E AND RESID 137:143)
54X-RAY DIFFRACTION54(CHAIN E AND RESID 144:194)
55X-RAY DIFFRACTION55(CHAIN E AND RESID 195:205)
56X-RAY DIFFRACTION56(CHAIN F AND RESID 1:12)
57X-RAY DIFFRACTION57(CHAIN F AND RESID 13:17)
58X-RAY DIFFRACTION58(CHAIN F AND RESID 18:52)
59X-RAY DIFFRACTION59(CHAIN F AND RESID 53:57)
60X-RAY DIFFRACTION60(CHAIN F AND RESID 58:113)
61X-RAY DIFFRACTION61(CHAIN F AND RESID 114:119)
62X-RAY DIFFRACTION62(CHAIN F AND RESID 120:156)
63X-RAY DIFFRACTION63(CHAIN F AND RESID 157:173)
64X-RAY DIFFRACTION64(CHAIN F AND RESID 174:188)
65X-RAY DIFFRACTION65(CHAIN F AND RESID 189:197)
66X-RAY DIFFRACTION66(CHAIN F AND RESID 198:205)
67X-RAY DIFFRACTION67(CHAIN G AND RESID 1:18)
68X-RAY DIFFRACTION68(CHAIN G AND RESID 19:26)
69X-RAY DIFFRACTION69(CHAIN G AND RESID 27:46)
70X-RAY DIFFRACTION70(CHAIN G AND RESID 47:59)
71X-RAY DIFFRACTION71(CHAIN G AND RESID 60:70)
72X-RAY DIFFRACTION72(CHAIN G AND RESID 71:127)
73X-RAY DIFFRACTION73(CHAIN G AND RESID 128:155)
74X-RAY DIFFRACTION74(CHAIN G AND RESID 156:166)
75X-RAY DIFFRACTION75(CHAIN G AND RESID 167:179)
76X-RAY DIFFRACTION76(CHAIN G AND RESID 180:192)
77X-RAY DIFFRACTION77(CHAIN G AND RESID 193:205)
78X-RAY DIFFRACTION78(CHAIN H AND RESID 1:14)
79X-RAY DIFFRACTION79(CHAIN H AND RESID 15:23)
80X-RAY DIFFRACTION80(CHAIN H AND RESID 24:45)
81X-RAY DIFFRACTION81(CHAIN H AND RESID 46:66)
82X-RAY DIFFRACTION82(CHAIN H AND RESID 67:72)
83X-RAY DIFFRACTION83(CHAIN H AND RESID 73:124)
84X-RAY DIFFRACTION84(CHAIN H AND RESID 125:139)
85X-RAY DIFFRACTION85(CHAIN H AND RESID 140:173)
86X-RAY DIFFRACTION86(CHAIN H AND RESID 174:184)
87X-RAY DIFFRACTION87(CHAIN H AND RESID 185:191)
88X-RAY DIFFRACTION88(CHAIN H AND RESID 192:205)
89X-RAY DIFFRACTION89(CHAIN I AND RESID 1:13)
90X-RAY DIFFRACTION90(CHAIN I AND RESID 14:22)
91X-RAY DIFFRACTION91(CHAIN I AND RESID 23:46)
92X-RAY DIFFRACTION92(CHAIN I AND RESID 47:63)
93X-RAY DIFFRACTION93(CHAIN I AND RESID 64:69)
94X-RAY DIFFRACTION94(CHAIN I AND RESID 70:101)
95X-RAY DIFFRACTION95(CHAIN I AND RESID 102:114)
96X-RAY DIFFRACTION96(CHAIN I AND RESID 115:158)
97X-RAY DIFFRACTION97(CHAIN I AND RESID 159:173)
98X-RAY DIFFRACTION98(CHAIN I AND RESID 174:192)
99X-RAY DIFFRACTION99(CHAIN I AND RESID 193:205)
100X-RAY DIFFRACTION100(CHAIN J AND RESID 1:13)
101X-RAY DIFFRACTION101(CHAIN J AND RESID 14:30)
102X-RAY DIFFRACTION102(CHAIN J AND RESID 31:54)
103X-RAY DIFFRACTION103(CHAIN J AND RESID 55:99)
104X-RAY DIFFRACTION104(CHAIN J AND RESID 100:127)
105X-RAY DIFFRACTION105(CHAIN J AND RESID 128:138)
106X-RAY DIFFRACTION106(CHAIN J AND RESID 139:152)
107X-RAY DIFFRACTION107(CHAIN J AND RESID 153:164)
108X-RAY DIFFRACTION108(CHAIN J AND RESID 165:184)
109X-RAY DIFFRACTION109(CHAIN J AND RESID 185:200)
110X-RAY DIFFRACTION110(CHAIN J AND RESID 201:205)

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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