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- PDB-7rri: Crystal structure of fast switching S142A/M159T mutant of fluores... -

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基本情報

登録情報
データベース: PDB / ID: 7rri
タイトルCrystal structure of fast switching S142A/M159T mutant of fluorescent protein Dronpa (Dronpa2)
要素Fluorescent protein Dronpa蛍光
キーワードFLUORESCENT PROTEIN (蛍光タンパク質) / Dronpa2
機能・相同性Green fluorescent protein, GFP / Green fluorescent protein-related / 緑色蛍光タンパク質 / 緑色蛍光タンパク質 / 生物発光 / generation of precursor metabolites and energy / identical protein binding / metal ion binding / Fluorescent protein Dronpa
機能・相同性情報
生物種Echinophyllia sp. SC22 (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: 2.643 Å
データ登録者Lin, C.-Y. / Romei, M.G. / Mathews, I.I. / Boxer, S.G.
資金援助 米国, 2件
組織認可番号
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118044 米国
National Science Foundation (NSF, United States)CHE-1740645 米国
引用ジャーナル: J.Am.Chem.Soc. / : 2022
タイトル: Energetic Basis and Design of Enzyme Function Demonstrated Using GFP, an Excited-State Enzyme.
著者: Lin, C.Y. / Romei, M.G. / Mathews, I.I. / Boxer, S.G.
履歴
登録2021年8月9日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年10月13日Provider: repository / タイプ: Initial release
改定 1.12022年3月23日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
改定 1.22023年10月18日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 2.02023年11月15日Group: Atomic model / Data collection / Derived calculations
カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_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: Fluorescent protein Dronpa
B: Fluorescent protein Dronpa
C: Fluorescent protein Dronpa
D: Fluorescent protein Dronpa
E: Fluorescent protein Dronpa
F: Fluorescent protein Dronpa
G: Fluorescent protein Dronpa
H: Fluorescent protein Dronpa


分子量 (理論値)分子数
合計 (水以外)231,5658
ポリマ-231,5658
非ポリマー00
4,630257
1
A: Fluorescent protein Dronpa
C: Fluorescent protein Dronpa
E: Fluorescent protein Dronpa
G: Fluorescent protein Dronpa


分子量 (理論値)分子数
合計 (水以外)115,7824
ポリマ-115,7824
非ポリマー00
724
タイプ名称対称操作
identity operation1_555x,y,z1
2
B: Fluorescent protein Dronpa
D: Fluorescent protein Dronpa
F: Fluorescent protein Dronpa
H: Fluorescent protein Dronpa


分子量 (理論値)分子数
合計 (水以外)115,7824
ポリマ-115,7824
非ポリマー00
724
タイプ名称対称操作
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)79.412, 85.809, 143.167
Angle α, β, γ (deg.)90.00, 95.01, 90.00
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質
Fluorescent protein Dronpa / 蛍光


分子量: 28945.576 Da / 分子数: 8 / 変異: S142A/M159T / 由来タイプ: 組換発現
由来: (組換発現) Echinophyllia sp. SC22 (無脊椎動物)
遺伝子: Dronpa / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q5TLG6
#2: 水 ChemComp-HOH / water /


分子量: 18.015 Da / 分子数: 257 / 由来タイプ: 天然 / : H2O
研究の焦点であるリガンドがあるかY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.1 Å3/Da / 溶媒含有率: 41.39 %
結晶化温度: 292 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.4 / 詳細: 0.1 M Tris-HCl pH 7.4, 0.1 M MgCl2, 18% PEG 3350

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: SSRL / ビームライン: BL12-2 / 波長: 0.9795 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2019年6月24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: 0.9795 Å / 相対比: 1
反射解像度: 2.643→37.29 Å / Num. obs: 54577 / % possible obs: 94.7 % / 冗長度: 13.2 % / Biso Wilson estimate: 34.3 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.277 / Rpim(I) all: 0.079 / Rrim(I) all: 0.289 / Net I/σ(I): 7
反射 シェル解像度: 2.643→2.738 Å / 冗長度: 12.8 % / Rmerge(I) obs: 1.6 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5081 / CC1/2: 0.747 / CC star: 0.925 / Rpim(I) all: 0.46 / Rrim(I) all: 1.67 / % possible all: 90.8

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解析

ソフトウェア
名称バージョン分類
PHENIX1.13rc2_2986精密化
XDSデータ削減
XDSデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 4UTS
解像度: 2.643→37.29 Å / SU ML: 0.34 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 34.19 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2839 2671 5.01 %
Rwork0.2263 --
obs0.2292 53352 94.63 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
精密化ステップサイクル: LAST / 解像度: 2.643→37.29 Å
タンパク質核酸リガンド溶媒全体
原子数13863 0 0 257 14120
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00814399
X-RAY DIFFRACTIONf_angle_d1.41719430
X-RAY DIFFRACTIONf_dihedral_angle_d9.139255
X-RAY DIFFRACTIONf_chiral_restr0.0781985
X-RAY DIFFRACTIONf_plane_restr0.0072529
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.643-2.69090.37871230.29622338X-RAY DIFFRACTION84
2.6909-2.74260.36051460.27552749X-RAY DIFFRACTION98
2.7426-2.79860.32831380.27112639X-RAY DIFFRACTION95
2.7986-2.85940.32741400.27992654X-RAY DIFFRACTION94
2.8594-2.92590.34941450.27972763X-RAY DIFFRACTION99
2.9259-2.99910.33751440.26662727X-RAY DIFFRACTION98
2.9991-3.08010.35791450.26572768X-RAY DIFFRACTION98
3.0801-3.17070.35371440.24552737X-RAY DIFFRACTION97
3.1707-3.2730.2731430.24122710X-RAY DIFFRACTION97
3.273-3.38990.29451410.24272677X-RAY DIFFRACTION96
3.3899-3.52560.30921360.23952604X-RAY DIFFRACTION92
3.5256-3.68590.2981420.21342680X-RAY DIFFRACTION95
3.6859-3.88010.28671430.20972701X-RAY DIFFRACTION96
3.8801-4.12290.23391390.20842656X-RAY DIFFRACTION95
4.1229-4.44080.24091400.19032641X-RAY DIFFRACTION93
4.4408-4.8870.20611370.18612598X-RAY DIFFRACTION92
4.887-5.59230.24951420.18782701X-RAY DIFFRACTION95
5.5923-7.0390.28131390.22652637X-RAY DIFFRACTION92
7.039-37.290.25161440.20932701X-RAY DIFFRACTION93
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)
11.46180.3853-0.21420.7290.06611.77150.34740.4710.0198-0.1214-0.1307-0.0488-0.17750.2279-0.00070.353-0.0069-0.0240.20220.03940.149126.72819.784347.4401
22.1866-0.8818-0.29340.87590.03790.9387-0.20870.15330.1261-0.2407-0.1145-0.0753-0.1350.4917-0.03270.39840.0130.01540.23250.05290.234824.528623.787152.2939
31.77030.12040.56662.3916-0.44983.92010.1442-0.0204-0.3040.0411-0.0454-0.4006-0.48150.8994-0.02540.29380.00250.03030.35910.07750.193840.360812.223758.4504
46.4658-2.2931-3.95652.05032.38533.4884-0.14290.06760.01790.0467-0.01230.32860.3909-0.07690.01290.2925-0.01140.05830.14740.04130.184519.957614.212461.3978
53.0776-0.0876-1.10130.57130.43811.79640.10860.26250.2153-0.1365-0.05830.0183-0.15580.00820.10620.3330.0704-0.02220.21580.01830.101520.312916.626453.2504
61.0983-0.90920.34951.8102-0.26821.7199-0.01420.2531-0.1420.30230.00160.2126-0.17270.0998-0.04040.4472-0.09880.02380.12380.02450.231325.153318.672266.0418
73.4823-4.8517-0.83267.59811.21441.4766-0.1377-0.5055-0.04990.58510.09040.29640.15150.1765-0.0350.33310.00110.0930.24580.01690.24724.267217.305166.9793
80.8328-0.0208-0.17471.19060.72991.85110.3190.12570.00960.1342-0.37340.03340.1894-0.0441-0.01930.2640.00240.03220.22790.02330.199727.548313.228564.2006
91.3246-1.39921.0262.3337-1.64072.92640.17180.02820.40920.05250.0893-0.0362-0.6446-0.04490.16270.3765-0.07760.01680.1982-0.00770.361226.12428.11557.9117
101.7155-1.27711.66591.7331-1.7993.22530.0331-0.04190.15770.1427-0.1868-0.2663-0.54410.41210.05010.2517-0.02860.02230.42710.00830.281433.950524.23762.1968
111.55320.169-0.48161.35080.33331.62590.25670.17420.0644-0.41810.0217-0.2763-0.28160.2390.08470.2856-0.01510.04520.37290.03360.249934.853521.5183-23.6664
121.74220.4708-0.09670.4207-0.27250.7882-0.02950.07910.0443-0.17460.09990.07630.21850.11040.73110.41550.2525-0.06170.44910.15720.123929.326625.3585-24.306
131.7828-0.6218-0.3560.9892-0.03881.34860.03350.34840.306-0.167-0.0329-0.1051-0.36820.1048-0.03970.1615-0.04230.01080.27420.06180.27931.615326.2689-18.6027
141.4889-0.2466-0.68270.3754-0.00910.5442-0.14920.228-0.16550.00910.1082-0.09210.05770.2147-0.42730.1050.0570.00210.312-0.00260.586647.607114.7352-12.6421
156.8884-3.3915-5.56851.87252.57034.6360.15690.0137-0.08930.0140.11960.1634-0.0061-0.14910.09080.2259-0.02210.02390.31520.06160.263526.188717.074-10.0038
165.01860.3162-1.89490.7459-0.15552.0237-0.12260.24360.0583-0.3691-0.01280.0458-0.05890.29890.03760.23720.03550.01970.30320.02470.260731.701116.678-21.2831
170.3012-0.36530.11110.508-0.05690.1395-0.0809-0.03730.14540.04880.02570.1014-0.0927-0.0585-0.03450.16990.1523-0.02140.34080.19070.519813.673128.7986-10.1859
181.6915-0.8053-0.18131.5950.32680.7103-0.03140.139-0.2452-0.0691-0.01510.16060.01660.10910.0275-0.02420.0602-0.01760.24730.06180.412632.224320.0647-4.4929
191.1381-0.1426-0.54121.38591.10722.1598-0.09890.17430.02020.003-0.048-0.0124-0.00180.04510.00050.1114-0.02190.0010.2010.05190.284633.809416.4265-7.1306
201.304-0.73361.02211.8691-0.41852.85580.19550.19990.3109-0.1786-0.1616-0.1496-0.58580.25660.10390.1899-0.05010.02720.3260.0230.317635.502529.56-11.6107
211.69010.54860.4661.8638-0.64470.82830.3008-0.3072-0.25010.0907-0.17270.15610.22870.01830.20840.7157-0.14120.08990.4275-0.02930.3451-1.51992.177498.7931
222.96822.68990.50133.2090.620.94330.1179-0.2041-0.05870.07870.08270.17360.0705-0.23260.31390.4941-0.29640.19070.4232-0.06880.3289-1.63128.892199.2366
231.273-1.06570.25972.1659-0.26390.05550.2735-0.3438-0.23850.1775-0.00030.54120.1694-0.57430.34060.5721-0.14650.02570.5278-0.00450.3373-9.17222.095695.0292
241.00810.28750.18860.7201-0.06780.86430.1559-0.3674-0.0430.2021-0.26670.23390.2082-0.197-0.00210.4827-0.15920.05090.3124-0.05060.27771.41821.920190.1771
251.85340.9029-0.84070.908-1.07642.39690.0312-0.23920.20090.4217-0.0840.27770.448-0.1597-0.00980.4796-0.0759-0.00210.326-0.18340.19194.197311.50292.3679
260.5624-0.6003-0.35151.80150.82771.3761-0.0547-0.03970.28180.08320.0899-0.24260.3248-0.25640.02720.5012-0.09030.01460.2484-0.01260.48550.26275.276680.3964
270.6697-0.96870.33913.0641-1.19381.50180.1617-0.08470.0840.1957-0.01790.1019-0.1341-0.1968-0.05250.4748-0.26020.02570.18740.00150.28732.45427.380.3273
280.47260.48090.14680.67290.56682.17220.1441-0.3504-0.2614-0.0311-0.05370.22640.2631-0.32110.04330.3494-0.13460.01980.3547-0.02240.4076-2.5455-2.870884.7226
290.85690.34720.64291.42480.45691.3793-0.0062-0.0420.10650.2125-0.00850.27780.1726-0.72130.26320.4549-0.20920.10510.42370.01720.3641-10.81973.283985.1294
300.441-0.13550.02890.07720.10710.37870.0467-0.0927-0.23680.0687-0.02590.15470.0918-0.2672-0.16740.1124-0.34180.18160.466-0.09270.32615.0027.257427.7052
310.6354-0.0411-0.18331.46490.39510.4360.2063-0.3076-0.2619-0.0495-0.00540.22650.3385-0.3850.30590.2959-0.1208-0.04860.4623-0.07530.24-0.98536.592725.3264
320.66940.2338-0.06722.20570.24121.52280.0885-0.3553-0.1224-0.3324-0.04980.2334-0.1977-0.24690.02410.1981-0.0002-0.00410.2953-0.02250.3165.64613.78820.4357
331.5013-1.2261-0.37471.769-0.05422.4296-0.3554-0.024-0.24230.10840.3146-0.19160.4919-0.247-0.01770.3221-0.1014-0.01610.19980.05630.44874.2186-8.810816.7922
341.07730.5324-0.11322.2735-0.59071.3860.11150.00510.14050.0916-0.00530.23230.0883-0.2223-0.03290.1078-0.12760.04770.2343-0.04770.339311.79896.831420.8632
351.189-0.67160.36260.7466-0.2180.11050.07430.01970.2013-0.0562-0.06990.1362-0.2703-0.31320.26070.13320.19620.05780.2482-0.01210.5459.754126.490613.68
361.1153-0.5763-0.14821.78720.45421.3083-0.0491-0.07060.06950.0516-0.06630.0281-0.037-0.177-0.09630.0520.059-0.09650.3197-0.05920.28717.12734.99628.4031
370.79820.0795-0.07710.49-0.07290.6650.0626-0.1120.17510.0084-0.05930.02650.0391-0.3626-0.0461-0.0304-0.1046-0.09690.231-0.03670.44388.81649.98079.0561
380.96420.46340.24651.10040.02270.52480.0921-0.15-0.01740.16560.0290.0331-0.0104-0.20980.21670.155-0.1595-0.07360.2086-0.02970.39984.0033-0.302713.3837
391.48010.55970.6660.580.76542.3333-0.0229-0.26050.0583-0.0824-0.06080.295-0.0768-0.37810.11870.2208-0.20930.13130.32260.01270.4322-4.25016.388814.2874
401.30140.50350.3581.41540.62261.48360.2078-0.116-0.03830.2229-0.22380.1957-0.14140.1482-0.03130.3996-0.28760.04690.5855-0.05540.300528.287119.086798.8659
412.19131.9212-0.56992.2328-0.58231.46910.1668-0.1533-0.08420.2116-0.1151-0.02290.17120.0781-0.07940.5973-0.221-0.11250.3630.02510.223128.600812.377699.3906
420.79680.3210.00252.2160.12071.59840.1325-0.40350.1160.0511-0.1202-0.14660.03140.0779-0.00520.3755-0.05510.00090.38780.06980.31130.651313.815493.7727
430.84930.4270.48791.0288-0.11981.17920.0791-0.2050.17950.3515-0.17630.1475-0.2835-0.07480.03510.5638-0.26360.01850.4628-0.07830.189429.216333.147787.6256
440.19280.12880.24245.38743.96423.10360.07150.1549-0.1201-0.0821-0.35040.1824-0.19330.2157-0.00410.4814-0.0912-0.01410.3215-0.0970.244819.90713.550284.771
450.89590.4051-0.09351.81640.39281.9850.1396-0.18010.03760.09350.0010.1583-0.1320.20660.15770.557-0.16040.04310.31610.1290.149222.550418.832796.4361
462.9531-0.4541-0.11542.5446-0.01341.76410.332-0.0361-0.21760.3225-0.1749-0.10390.59180.20390.0640.6144-0.0226-0.13530.1909-0.02530.297523.3827-2.698885.1721
471.9812-1.72010.14443.4677-0.53621.8473-0.0020.00670.20910.3179-0.08530.1450.11690.0408-0.04220.4256-0.13140.02790.2215-0.02940.210626.295118.683679.7017
481.2632-1.0798-0.80223.05771.33131.47760.1186-0.3051-0.05130.129-0.0695-0.02170.02070.2079-0.08070.5011-0.1399-0.08970.220.00780.164424.619113.717780.4546
491.1658-0.869-0.86252.01790.10160.8939-0.0376-0.29720.2410.2689-0.0098-0.2623-0.00120.21040.20380.2713-0.2123-0.07010.26630.05180.318429.54223.944484.6688
500.92940.1154-0.72990.6628-0.30331.9078-0.0412-0.1595-0.0950.115-0.0242-0.15730.19340.49210.09060.3276-0.1704-0.08310.4914-0.05410.410637.23416.744286.0482
511.19811.0048-0.35331.41210.61632.17730.2062-0.25850.0865-0.13360.00140.1532-0.34660.18480.06490.2260.0111-0.0910.20680.06420.484434.545122.088327.4256
526.20015.1-1.54385.9587-2.24592.79410.221-0.0924-0.15460.2995-0.0421-0.2934-0.02530.1245-0.01260.11630.0041-0.01370.34150.00660.272134.763115.42227.977
530.70740.8791-0.15073.6929-1.31871.70730.0614-0.40560.12910.07450.0899-0.4541-0.05820.41670.09340.2441-0.10560.02830.3538-0.08570.260740.667220.232925.2121
540.94640.31890.07532.8002-0.28230.81840.1055-0.41380.1717-0.0199-0.21630.05350.07080.214-0.08190.10170.0709-0.09540.26250.07020.35434.064812.980120.4865
552.2157-0.7102-0.05141.91740.43442.7280.0247-0.36210.50030.2543-0.08320.2251-0.56310.4437-0.07830.3574-0.12350.02820.2606-0.04180.375635.561935.587716.764
561.38360.3191-0.1563.34250.96691.75720.12720.0190.02020.1094-0.1312-0.1196-0.09790.1619-0.04440.1337-0.0756-0.02940.24580.01970.281127.526420.156818.8151
570.47520.5262-0.14451.5525-0.37081.56910.1613-0.0736-0.33990.2253-0.15790.0179-0.1426-0.0520.2730.0879-0.0008-0.14150.2318-0.05030.363629.127310.008919.635
580.7734-0.07750.33281.5343-0.29830.84250.0895-0.03430.1238-0.0065-0.090.1187-0.07480.2636-0.09940.0614-0.0164-0.04930.2340.06370.343232.411821.76168.332
590.9242-1.3705-0.96944.6011.82032.09080.1527-0.04030.1905-0.1365-0.0818-0.17550.09830.06750.010.1324-0.0622-0.02350.28680.0370.274930.88616.88689.038
600.56730.5491-0.11750.7659-0.63761.96290.05440.08950.33690.1698-0.0008-0.1717-0.20280.0792-0.0170.2038-0.0821-0.02560.2074-0.03820.321135.69827.15913.3786
611.24810.7299-0.76190.7942-0.65741.9263-0.1141-0.1144-0.08970.0527-0.1612-0.2154-0.08740.5799-0.24870.2193-0.0975-0.10070.37820.0030.284143.511719.97414.7528
620.8337-0.1611-0.15461.2041-0.10962.25060.02810.3960.1582-0.0675-0.02330.25930.3171-0.45110.02530.394-0.0261-0.04920.3036-0.05790.25650.68820.92647.4782
631.052-0.0236-0.00950.7477-0.0991.1179-0.04310.20090.0644-0.0641-0.04060.150.1429-0.21890.02020.36090.0098-0.04660.2393-0.04850.27851.36213.228755.2683
641.1239-1.1133-0.61752.05410.40571.5268-0.17120.13830.06320.46190.02170.12160.3586-0.08210.00910.3962-0.0145-0.04310.2049-0.03820.32032.11762.166666.1027
652.9546-4.1910.91345.9953-1.40981.2976-0.246-0.25020.18530.56860.1286-0.27030.0475-0.16820.03040.35120.0488-0.05310.2715-0.14960.32212.97023.654466.9084
661.4894-0.38560.24511.0854-0.73262.21570.20290.3235-0.0810.1903-0.29740.24270.0723-0.16970.00180.3057-0.0386-0.02290.2572-0.12090.3127-0.25427.63864.0629
671.447-0.9654-0.86521.63381.0022.02530.23880.3298-0.2985-0.2403-0.1160.20750.3155-0.38050.15740.4146-0.1107-0.0220.2857-0.03810.4175-2.3863-5.519759.7271
681.99670.07140.58590.8535-0.05531.85030.2750.40450.1025-0.2207-0.12720.35980.0515-0.51020.0140.33970.0046-0.07090.39820.01190.37724.79865.2216-23.7547
696.09092.1188-1.84191.9885-0.40490.92440.09330.2148-0.3482-0.2214-0.1116-0.07740.2525-0.3745-0.02020.25750.0218-0.05720.4311-0.12310.243910.33481.2807-24.3067
701.7048-0.355-0.02150.6637-0.57950.59680.09650.2641-0.1766-0.312-0.10860.3150.3613-0.3117-0.03730.2424-0.0256-0.06630.3792-0.10460.35569.9977-0.8972-19.6976
710.1748-0.18740.38630.9790.00811.8461-0.07680.21520.15890.1382-0.08770.3457-0.3905-0.4994-0.04780.27640.0475-0.07530.38770.06690.4435-6.53810.8448-13.1924
726.4779-2.92964.29741.5607-2.20093.4101-0.00080.11590.0074-0.0663-0.2031-0.16470.0342-0.0092-0.0230.2603-0.0551-0.10080.2770.00360.278213.50989.5198-10.0025
732.53950.09420.64411.0743-0.24581.37620.05540.438-0.1316-0.3025-0.1880.18680.1498-0.07190.01350.17060.0783-0.02330.3596-0.06730.333613.98285.9802-17.5816
741.0933-1.256-0.09741.66310.14611.0033-0.02970.0270.2190.1486-0.0155-0.06490.122-0.0921-0.24230.10410.0267-0.0870.2939-0.04340.43977.36556.6483-4.5057
751.4966-0.33960.0861.0093-0.43981.14240.12090.1727-0.06720.03920.03560.1479-0.1963-0.18240.02950.07730.204-0.15890.2956-0.10740.44415.926910.3041-7.2364
760.80350.45530.01560.6588-0.73731.59080.06770.0731-0.1593-0.1807-0.11210.09930.461-0.15730.1242-0.0112-0.1893-0.06720.3233-0.03710.33974.1404-2.8323-11.614
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 32 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 65 )
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 86 )
4X-RAY DIFFRACTION4chain 'A' and (resid 87 through 99 )
5X-RAY DIFFRACTION5chain 'A' and (resid 100 through 133 )
6X-RAY DIFFRACTION6chain 'A' and (resid 134 through 151 )
7X-RAY DIFFRACTION7chain 'A' and (resid 152 through 163 )
8X-RAY DIFFRACTION8chain 'A' and (resid 164 through 188 )
9X-RAY DIFFRACTION9chain 'A' and (resid 189 through 205 )
10X-RAY DIFFRACTION10chain 'A' and (resid 206 through 220 )
11X-RAY DIFFRACTION11chain 'B' and (resid 3 through 20 )
12X-RAY DIFFRACTION12chain 'B' and (resid 21 through 32 )
13X-RAY DIFFRACTION13chain 'B' and (resid 33 through 68 )
14X-RAY DIFFRACTION14chain 'B' and (resid 69 through 86 )
15X-RAY DIFFRACTION15chain 'B' and (resid 87 through 99 )
16X-RAY DIFFRACTION16chain 'B' and (resid 100 through 123 )
17X-RAY DIFFRACTION17chain 'B' and (resid 124 through 135 )
18X-RAY DIFFRACTION18chain 'B' and (resid 136 through 163 )
19X-RAY DIFFRACTION19chain 'B' and (resid 164 through 188 )
20X-RAY DIFFRACTION20chain 'B' and (resid 189 through 220 )
21X-RAY DIFFRACTION21chain 'C' and (resid 3 through 20 )
22X-RAY DIFFRACTION22chain 'C' and (resid 21 through 32 )
23X-RAY DIFFRACTION23chain 'C' and (resid 33 through 44 )
24X-RAY DIFFRACTION24chain 'C' and (resid 45 through 110 )
25X-RAY DIFFRACTION25chain 'C' and (resid 111 through 133 )
26X-RAY DIFFRACTION26chain 'C' and (resid 134 through 151 )
27X-RAY DIFFRACTION27chain 'C' and (resid 152 through 179 )
28X-RAY DIFFRACTION28chain 'C' and (resid 180 through 200 )
29X-RAY DIFFRACTION29chain 'C' and (resid 201 through 228 )
30X-RAY DIFFRACTION30chain 'D' and (resid 3 through 32 )
31X-RAY DIFFRACTION31chain 'D' and (resid 33 through 46 )
32X-RAY DIFFRACTION32chain 'D' and (resid 47 through 66 )
33X-RAY DIFFRACTION33chain 'D' and (resid 67 through 86 )
34X-RAY DIFFRACTION34chain 'D' and (resid 87 through 123 )
35X-RAY DIFFRACTION35chain 'D' and (resid 124 through 135 )
36X-RAY DIFFRACTION36chain 'D' and (resid 136 through 151 )
37X-RAY DIFFRACTION37chain 'D' and (resid 152 through 179 )
38X-RAY DIFFRACTION38chain 'D' and (resid 180 through 200 )
39X-RAY DIFFRACTION39chain 'D' and (resid 201 through 228 )
40X-RAY DIFFRACTION40chain 'E' and (resid 3 through 20 )
41X-RAY DIFFRACTION41chain 'E' and (resid 21 through 32 )
42X-RAY DIFFRACTION42chain 'E' and (resid 33 through 68 )
43X-RAY DIFFRACTION43chain 'E' and (resid 69 through 86 )
44X-RAY DIFFRACTION44chain 'E' and (resid 87 through 99 )
45X-RAY DIFFRACTION45chain 'E' and (resid 100 through 123 )
46X-RAY DIFFRACTION46chain 'E' and (resid 124 through 135 )
47X-RAY DIFFRACTION47chain 'E' and (resid 136 through 151 )
48X-RAY DIFFRACTION48chain 'E' and (resid 152 through 179 )
49X-RAY DIFFRACTION49chain 'E' and (resid 180 through 200 )
50X-RAY DIFFRACTION50chain 'E' and (resid 201 through 228 )
51X-RAY DIFFRACTION51chain 'F' and (resid 3 through 20 )
52X-RAY DIFFRACTION52chain 'F' and (resid 21 through 32 )
53X-RAY DIFFRACTION53chain 'F' and (resid 33 through 46 )
54X-RAY DIFFRACTION54chain 'F' and (resid 47 through 66 )
55X-RAY DIFFRACTION55chain 'F' and (resid 67 through 86 )
56X-RAY DIFFRACTION56chain 'F' and (resid 87 through 112 )
57X-RAY DIFFRACTION57chain 'F' and (resid 113 through 135 )
58X-RAY DIFFRACTION58chain 'F' and (resid 136 through 151 )
59X-RAY DIFFRACTION59chain 'F' and (resid 152 through 179 )
60X-RAY DIFFRACTION60chain 'F' and (resid 180 through 200 )
61X-RAY DIFFRACTION61chain 'F' and (resid 201 through 228 )
62X-RAY DIFFRACTION62chain 'G' and (resid 3 through 32 )
63X-RAY DIFFRACTION63chain 'G' and (resid 33 through 133 )
64X-RAY DIFFRACTION64chain 'G' and (resid 134 through 151 )
65X-RAY DIFFRACTION65chain 'G' and (resid 152 through 163 )
66X-RAY DIFFRACTION66chain 'G' and (resid 164 through 188 )
67X-RAY DIFFRACTION67chain 'G' and (resid 189 through 220 )
68X-RAY DIFFRACTION68chain 'H' and (resid 3 through 20 )
69X-RAY DIFFRACTION69chain 'H' and (resid 21 through 32 )
70X-RAY DIFFRACTION70chain 'H' and (resid 33 through 61 )
71X-RAY DIFFRACTION71chain 'H' and (resid 65 through 86 )
72X-RAY DIFFRACTION72chain 'H' and (resid 87 through 99 )
73X-RAY DIFFRACTION73chain 'H' and (resid 100 through 135 )
74X-RAY DIFFRACTION74chain 'H' and (resid 136 through 163 )
75X-RAY DIFFRACTION75chain 'H' and (resid 164 through 188 )
76X-RAY DIFFRACTION76chain 'H' and (resid 189 through 220 )

+
万見について

-
お知らせ

-
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

-
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