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- PDB-5aao: Crystal structure of fluorogen-activating designed ankyrin repeat... -

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基本情報

登録情報
データベース: PDB / ID: 5aao
タイトルCrystal structure of fluorogen-activating designed ankyrin repeat protein (DARPin) dimer in complex with malachite green
要素FAD3210
キーワードFLUORESCENT PROTEIN / HOMODIMER / DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN) / FLUOROGEN-ACTIVATION / MALACHITE GREEN
機能・相同性Ankyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha / Chem-6FE
機能・相同性情報
生物種SYNTHETIC CONSTRUCT (人工物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.6 Å
データ登録者Batyuk, A. / Schuetz, M. / Kummer, L. / Wu, Y. / Mittl, P. / Plueckthun, A.
引用ジャーナル: J. Mol. Biol. / : 2016
タイトル: Generation of Fluorogen-Activating Designed Ankyrin Repeat Proteins (FADAs) as Versatile Sensor Tools.
著者: Schutz, M. / Batyuk, A. / Klenk, C. / Kummer, L. / de Picciotto, S. / Gulbakan, B. / Wu, Y. / Newby, G.A. / Zosel, F. / Schoppe, J. / Sedlak, E. / Mittl, P.R. / Zenobi, R. / Wittrup, K.D. / Pluckthun, A.
履歴
登録2015年7月27日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02016年2月3日Provider: repository / タイプ: Initial release
改定 1.12017年3月22日Group: Database references
改定 1.22024年1月10日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: FAD3210
B: FAD3210
C: FAD3210
D: FAD3210
E: FAD3210
F: FAD3210
G: FAD3210
H: FAD3210
I: FAD3210
J: FAD3210
K: FAD3210
L: FAD3210
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)224,78418
ポリマ-222,62112
非ポリマー2,1636
6,107339
1
A: FAD3210
I: FAD3210
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)37,4643
ポリマ-37,1042
非ポリマー3601
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-2.5 kcal/mol
Surface area16750 Å2
手法PQS
2
B: FAD3210
C: FAD3210
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)37,4643
ポリマ-37,1042
非ポリマー3601
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-13.5 kcal/mol
Surface area16210 Å2
手法PQS
3
D: FAD3210
E: FAD3210
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)37,4643
ポリマ-37,1042
非ポリマー3601
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-16.5 kcal/mol
Surface area16610 Å2
手法PQS
4
F: FAD3210
G: FAD3210
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)37,4643
ポリマ-37,1042
非ポリマー3601
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-6.5 kcal/mol
Surface area16340 Å2
手法PQS
5
H: FAD3210
J: FAD3210
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)37,4643
ポリマ-37,1042
非ポリマー3601
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-16.1 kcal/mol
Surface area16630 Å2
手法PQS
6
K: FAD3210
L: FAD3210
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)37,4643
ポリマ-37,1042
非ポリマー3601
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-6 kcal/mol
Surface area16640 Å2
手法PQS
単位格子
Length a, b, c (Å)93.512, 109.754, 100.301
Angle α, β, γ (deg.)90.00, 94.35, 90.00
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質
FAD3210


分子量: 18551.766 Da / 分子数: 12 / 由来タイプ: 組換発現 / 由来: (組換発現) SYNTHETIC CONSTRUCT (人工物) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): K-12 / Variant (発現宿主): XL1-BLUE
#2: 化合物
ChemComp-6FE / 4-[[4-(dimethylamino)cyclohexa-2,5-dien-1-ylidene]-(4-methoxyphenyl)methyl]-N,N-dimethyl-aniline / MALACHITE GREEN DERIVATIVE MG-2P


分子量: 360.492 Da / 分子数: 6 / 由来タイプ: 合成 / : C24H28N2O
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 339 / 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: 2.25 Å3/Da / 溶媒含有率: 45.4 % / 解説: NONE
結晶化詳細: 20% (W/V) PEG3350, 0.2 M SODIUM MALONATE, PH 5.0

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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: X06DA / 波長: 1
検出器タイプ: DECTRIS PILATUS 2M-F / 検出器: PIXEL / 日付: 2013年10月25日 / 詳細: TOROIDAL FOCUSING
放射モノクロメーター: BARTELS 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: 2.6→50 Å / Num. obs: 62041 / % possible obs: 100 % / Observed criterion σ(I): 0.86 / 冗長度: 6.9 % / Biso Wilson estimate: 37.64 Å2 / Rmerge(I) obs: 0.2733 / Net I/σ(I): 6.6
反射 シェル解像度: 2.6→2.693 Å / 冗長度: 2.36 % / Mean I/σ(I) obs: 0.86 / % possible all: 100

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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
XSCALE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: PDB ENTRY 1SVX
解像度: 2.6→19.951 Å / SU ML: 0.47 / σ(F): 0.39 / 位相誤差: 30.83 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2622 6090 5 %
Rwork0.2135 --
obs0.2159 61973 99.76 %
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
原子変位パラメータBiso mean: 51.9 Å2
精密化ステップサイクル: LAST / 解像度: 2.6→19.951 Å
タンパク質核酸リガンド溶媒全体
原子数14359 0 162 339 14860
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00114821
X-RAY DIFFRACTIONf_angle_d0.45320144
X-RAY DIFFRACTIONf_dihedral_angle_d9.4268550
X-RAY DIFFRACTIONf_chiral_restr0.0322253
X-RAY DIFFRACTIONf_plane_restr0.0032626
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.62950.3882030.37033809X-RAY DIFFRACTION100
2.6295-2.66040.37432040.38323849X-RAY DIFFRACTION99
2.6604-2.69270.42841930.38683772X-RAY DIFFRACTION98
2.6927-2.72670.40272020.35953888X-RAY DIFFRACTION100
2.7267-2.76250.41452060.34673863X-RAY DIFFRACTION100
2.7625-2.80030.38012010.3323839X-RAY DIFFRACTION100
2.8003-2.84020.36372050.3273896X-RAY DIFFRACTION100
2.8402-2.88240.36912010.30593818X-RAY DIFFRACTION100
2.8824-2.92730.3412090.30383928X-RAY DIFFRACTION100
2.9273-2.97520.34922060.28423861X-RAY DIFFRACTION100
2.9752-3.02630.34232030.28223831X-RAY DIFFRACTION100
3.0263-3.08110.3162020.27823839X-RAY DIFFRACTION100
3.0811-3.14020.32442110.26613938X-RAY DIFFRACTION100
3.1402-3.2040.3472000.26833847X-RAY DIFFRACTION100
3.204-3.27340.30892010.25153849X-RAY DIFFRACTION100
3.2734-3.34920.28922000.23183893X-RAY DIFFRACTION100
3.3492-3.43250.29122030.24033834X-RAY DIFFRACTION100
3.4325-3.52490.28862040.22323798X-RAY DIFFRACTION99
3.5249-3.6280.22922040.19013882X-RAY DIFFRACTION100
3.628-3.74430.23632050.1813837X-RAY DIFFRACTION99
3.7443-3.87720.21112030.17253864X-RAY DIFFRACTION100
3.8772-4.03130.22591970.16833842X-RAY DIFFRACTION99
4.0313-4.21310.20712070.15263858X-RAY DIFFRACTION100
4.2131-4.43290.19531990.13813867X-RAY DIFFRACTION100
4.4329-4.70720.18392010.14623859X-RAY DIFFRACTION100
4.7072-5.06520.23122050.16073883X-RAY DIFFRACTION100
5.0652-5.56480.26462070.17313884X-RAY DIFFRACTION100
5.5648-6.34730.21942050.18273840X-RAY DIFFRACTION100
6.3473-7.91310.17922010.14943867X-RAY DIFFRACTION100
7.9131-19.9520.15952020.13073812X-RAY DIFFRACTION99
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)
19.3396-2.02514.46596.8838-0.97844.19020.1605-1.4002-0.43570.0921-0.05250.24031.7174-0.5071-0.06210.52390.03230.14060.47450.04180.3123-21.69779.4299-18.8491
26.03350.41014.18936.19762.35334.06960.1321-0.4770.10190.85520.40060.4404-0.4155-0.4584-0.42290.49560.06330.06690.45080.0370.1987-24.667118.7385-16.4191
34.93392.17471.56271.6058-0.40642.6409-0.12390.4274-0.7781-0.30210.9085-0.558-0.01750.63630.23520.32820.3001-0.03330.3010.13910.2625-16.114510.2849-24.054
45.78710.10980.52743.15650.57546.20930.3112-0.20020.2378-0.5973-0.0613-0.0948-0.926-0.5973-0.00670.43070.17090.03150.35770.03310.0991-23.918918.4297-27.4418
53.159-0.8151-0.47772.19550.5414.86470.1564-0.1318-0.08220.073-0.07440.16260.6593-0.2131-0.0630.3437-0.01650.01110.29230.06340.2333-18.771814.3162-35.0665
66.71612.56162.31482.3582.05174.155-0.41360.05510.8132-0.74130.4888-0.0465-1.4946-0.7456-0.01390.45580.13630.05980.31980.09930.341-23.294125.2114-35.8407
72.64280.80210.18811.72461.7983.49380.0140.0789-0.04910.05280.2608-0.0680.0499-0.2573-0.29360.27290.01050.00430.25370.06510.1962-18.699714.5144-44.4579
85.83054.49272.5474.32053.29523.30740.0618-0.18361.4247-0.1502-0.14390.8025-0.7171-1.20260.27290.2081-0.0321-0.02380.28570.00190.2875-24.141524.7745-46.5612
92.60790.78810.67822.15840.60584.13330.10320.68090.134-0.2455-0.0511-0.2785-0.07680.1386-0.05870.3225-0.02810.04410.3335-0.00420.2225-19.153114.4445-53.9981
106.18095.755-1.7647.93790.05988.58870.50252.32021.0537-0.3369-0.49640.4729-0.7919-0.7633-0.02340.49250.1140.05910.60550.04640.3801-26.779123.5806-57.9825
117.238-2.11394.68455.58871.56585.56510.4415-0.2705-1.56040.5791-0.09950.43431.9065-0.5565-0.18510.76180.03310.09320.59780.01660.3812-20.427132.4221-69.3302
126.13421.59843.22545.29583.71947.22550.274-1.27720.97021.45280.14260.4644-1.287-1.02770.31080.96730.09450.10270.4516-0.08760.3377-22.833541.4607-66.7389
135.0081-0.35420.15233.3101-0.19036.54550.6464-0.58520.13381.0911-1.328-0.311.24440.12580.25690.6439-0.0093-0.06660.46720.06190.4042-14.021133.048-73.9341
145.7249-1.7037-1.20893.2342-0.16145.45430.4812-0.3847-0.4839-0.264-0.64020.5375-0.0841-0.91030.29760.27570.05790.0080.4828-0.04150.3811-22.269337.0919-79.8753
159.0978-3.06521.93348.6943-6.38894.7058-0.2286-0.84740.9770.8311-0.72880.1518-1.3455-0.7996-1.55250.68690.20150.16540.5152-0.22040.3298-20.213246.3175-75.3137
165.09880.8342-0.41792.6575-0.03386.9919-0.1276-0.2374-0.04870.1334-0.05740.31410.0128-0.02810.17930.30830.02950.0070.23160.03610.3533-16.05337.0729-85.111
178.32772.95622.56682.09581.10296.6321-0.1682-0.44171.19150.331-0.05740.3041-1.2533-0.47090.04850.5030.1010.02860.3493-0.02480.3388-20.146348.0845-86.164
181.87060.257-0.95012.49881.50795.438-0.2614-0.25140.0251-0.35530.1778-0.6377-0.1690.4958-0.27070.20440.0052-0.02450.29270.03770.3863-11.654736.9706-92.3217
192.16141.045-0.36064.19260.96515.2904-0.0770.42660.3438-0.09810.0358-0.0164-0.380.09490.05090.2002-0.00040.0080.29740.04360.3092-17.334640.3358-99.0658
204.33560.92920.72422.42850.74015.2718-0.11030.6380.1675-1.0416-0.2477-0.0746-0.911-0.31950.25290.50840.1412-0.02080.5050.0540.3481-23.059240.1122-107.6209
211.9978-4.6058-6.57613.48751.54515.7982-0.2252-1.49031.28420.73280.5303-0.3894-0.09740.68970.00360.5298-0.05280.02650.7687-0.04340.2281-29.762524.4226-70.1595
226.3042.0212-2.94715.02174.30227.6871-0.2344-1.4711-0.91470.5589-0.2879-0.40412.38761.17680.42470.65080.25460.10490.95290.19080.3752-28.178215.3356-67.3301
232.3588-2.15132.61973.87620.60027.60210.161-0.37590.5119-0.76320.31050.5709-0.1454-1.2688-0.29150.3883-0.03090.03830.4941-0.05740.2449-35.120924.2268-75.9253
249.1037-3.2258-1.50723.20490.56866.98770.8954-0.64290.166-0.5922-0.4204-0.57130.12731.5163-0.41760.46050.04380.03110.59550.01530.2087-25.958819.9708-80.2101
255.261-1.8285-0.20064.7469-1.82759.2618-0.2207-0.5479-0.4494-0.12530.19320.62730.69910.2030.04640.4092-0.05070.01380.34730.05640.2989-33.023617.1005-81.5034
264.0413-2.5236-1.76763.51440.79126.19910.0017-0.78380.335-0.13870.2687-0.60270.91351.0807-0.18330.467-0.0379-0.00320.4593-0.00250.2101-24.979819.3256-88.8413
278.07511.8135-8.68783.1874-0.67839.9674-0.6304-1.1423-1.0336-0.9525-0.0468-0.21272.32831.18660.15780.70070.11060.04770.25790.01480.2638-26.91499.3188-87.2727
282.6779-0.3037-0.58090.1939-0.85225.18420.01250.1871-0.1701-0.1023-0.27040.17140.6456-0.45090.0990.4014-0.1639-0.01590.3795-0.03530.3546-34.067520.9186-94.5402
293.97241.7781-1.99266.880.33135.2229-0.2329-0.1008-0.48570.3692-0.0016-0.68610.50160.09940.34760.49080.05620.02220.3006-0.03480.2148-23.697615.4457-97.5907
303.9074-0.4829-1.13384.6812-2.89553.16420.20050.7355-0.2799-0.3331-0.31580.20230.515-0.8075-0.04310.4159-0.07520.01750.4846-0.08830.1842-31.968920.2984-103.7914
316.9279-1.3707-0.36884.533-2.21934.84310.27950.8067-0.7834-0.2567-0.53630.31030.92710.74980.23780.43120.07080.06770.3905-0.04390.2697-20.535916.3672-107.5725
321.99223.39420.88626.55670.06866.2247-0.0060.9263-2.51730.3596-0.78630.15191.0872-0.39560.35480.80780.30810.11080.72-0.14210.5827-60.2401-6.9351-71.5075
335.48163.44094.0077.08853.07572.99960.22371.50810.0396-1.07580.1765-0.82081.11390.5705-0.61141.05540.01040.33671.0066-0.23890.6153-56.8922-2.5073-79.596
345.4367-1.3606-4.02578.42773.99895.83670.16060.6826-0.8576-1.1938-0.2338-0.1953-0.1305-0.20010.28430.43010.06430.03930.5011-0.08940.6388-65.9393-2.4231-68.6558
357.5798-0.95982.41316.10183.41075.69480.58990.50470.9744-0.4827-0.2296-0.97350.17450.2512-0.38360.57770.0720.0930.44680.04890.3043-56.60013.1371-66.9338
361.99464.11113.30589.66334.05684.0032-0.23221.3660.9681-1.36350.0572-0.264-0.30230.2228-0.27610.46990.03210.29880.72620.00930.4202-57.85867.233-76.4875
374.19010.92-3.27336.26521.94095.87870.25070.4974-0.62970.0074-0.1803-0.4402-0.7891-0.7449-0.03810.27020.00760.08870.62440.08780.4742-66.79676.0941-64.6713
381.60331.89021.27235.14440.60018.73760.59091.09140.6317-0.1786-0.1029-1.238-1.57131.1525-0.05560.38370.07440.19410.60540.14180.5066-56.384212.58-65.2405
393.0005-0.2481.84362.32811.39095.85730.00850.4050.6665-0.3052-0.0377-0.1139-0.8454-0.23680.0880.38750.05920.03020.27870.09890.4636-61.14217.5064-55.9203
402.813-1.4739-0.09723.6899-1.58469.1779-0.3026-0.50550.24970.3361-0.4761-0.5668-0.82691.05060.57550.4345-0.0046-0.0720.36820.09080.731-52.664323.8085-48.5443
418.01772.5128-1.36244.67610.76930.6082-0.70392.1152-0.2496-1.15550.2610.64490.5948-1.29380.20670.5658-0.18650.0880.5303-0.43690.5402-54.0983-18.1751-61.9563
423.41681.00180.34313.25922.89194.8084-0.06990.4798-0.3190.0642-0.23760.27170.1265-0.4740.18440.2951-0.06550.03650.3337-0.07850.418-51.25-10.0588-52.6792
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448.08633.3193.57184.1161-2.68028.0298-0.03830.018-1.3619-1.062-0.0766-0.9671.15750.20550.72780.30720.06940.13280.6127-0.27840.635-57.714514.614-120.5244
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476.30672.59846.16537.78514.81096.79-0.45411.8881.0172-1.14110.3606-0.5622-2.29630.6277-0.20930.5487-0.08840.11850.7706-0.15510.4647-55.262728.3394-126.6693
486.03872.20320.53585.4311.34724.24850.12820.4418-0.22130.2756-0.0407-0.3305-0.4625-0.26830.00270.40010.0861-0.03420.3647-0.0940.4414-59.673129.9195-113.459
495.46610.7022-0.7664.31342.51718.04840.50330.29871.2995-0.3796-0.11930.2687-1.3894-0.1784-0.10170.4770.0553-0.12950.3337-0.0110.5237-59.41936.4718-113.3663
504.9920.06621.77694.80330.64597.8038-0.0058-0.07160.68890.1985-0.1103-0.837-0.97930.4060.04880.4731-0.0763-0.05820.2454-0.12310.5012-52.391341.1479-108.7248
512.2147-0.3389-0.00210.08360.19833.2574-0.1205-0.15781.518-0.0576-0.41940.1739-1.569-0.5386-0.39770.65730.2086-0.09620.2946-0.30110.8281-61.824343.1799-102.6138
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536.2685-2.3448-7.06573.76712.21078.07310.47841.888-0.6811-1.303-0.14610.6466-0.9382-1.25310.40850.6191-0.0574-0.1250.5358-0.21030.5527-49.59238.2641-113.2265
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553.31770.2778-0.95696.90622.75334.59860.8530.1138-0.21630.3229-0.6852-1.01330.2756-0.4719-0.35920.382-0.05-0.04240.3844-0.20840.6416-43.891411.2922-108.7053
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575.91530.33660.01986.82710.42996.7450.21620.5246-0.26630.6676-0.20250.2621-0.0131-0.081-0.13640.3431-0.0576-0.01980.34250.00790.3062-43.032115.4733-100.3168
583.29581.5005-1.40543.50233.37087.76-0.5343-0.34470.09340.4428-0.07110.8869-0.1946-1.13250.67660.4551-0.082-0.01530.37510.02160.4103-53.509619.2679-96.9927
599.1707-3.29360.5063.31130.50155.01990.4865-1.6383-0.92551.5202-0.09891.57880.6338-1.0271-0.58240.586-0.30810.08370.64520.02470.5726-53.662111.1244-90.6078
603.2301-0.3921-0.26.73351.97973.66890.3866-0.60.12120.1117-0.4610.02730.23330.02250.060.3507-0.0486-0.06480.3537-0.05860.3041-43.816722.6483-93.5349
612.6192-3.7662.39759.15380.10495.70440.3894-0.8475-0.0688-0.4422-0.6021.2232-0.5897-1.18580.31180.3713-0.06890.07930.6-0.22810.4102-54.047526.5546-91.858
622.95350.802-0.13024.7921-3.89983.28270.0347-1.22010.24791.5780.40861.37180.6581-0.3777-0.42060.6175-0.099-0.03070.7575-0.03480.3119-55.40619.639-84.548
633.11071.3452-0.2612.2365-1.53254.23050.1974-0.47870.2007-0.3354-0.2669-0.40020.27370.6109-0.17930.39860.0177-0.04780.398-0.14640.4254-45.302429.3638-86.9643
648.4428-2.90351.327.7516-0.93967.48850.2393-1.62390.81890.5768-0.73510.2833-0.1443-0.9670.65720.4776-0.03640.0190.5996-0.27120.4838-55.558634.8902-87.0172
650.35310.4055-0.51061.424-0.50883.9079-0.3345-1.0492-0.21240.68320.39660.8599-0.3545-0.33340.2484-0.23540.29480.891.1844-0.7610.1896-58.765729.2777-78.6259
662.0054.60651.21242.77690.39946.37870.0844-0.30141.94960.2543-0.39481.0517-1.0212-0.40720.10740.88030.29190.04280.65230.20740.803712.641336.2541-57.93
670.09430.56240.38523.48592.39111.6299-0.98090.4790.8077-1.4471-0.26161.0638-1.0760.324-1.32491.24060.1882-0.07360.78970.79061.502710.92538.0071-67.309
685.0819-1.98951.44872.2422-1.67495.2795-0.1630.80730.7226-0.1999-0.7851-0.8361-0.16330.67140.6990.41090.05590.0290.60350.15770.723918.171830.6665-57.6919
694.22681.5626-0.61057.0160.07894.6882-0.03810.70161.0989-0.3404-0.62930.1389-0.2734-0.3430.39430.49230.1397-0.02670.65950.16650.544513.912824.6581-63.2549
703.18141.2354-2.83952.88741.52668.26370.110.89590.60230.1149-0.64690.45460.1904-0.88420.07060.41370.1599-0.02810.69490.10690.48618.393216.9946-61.0052
714.43192.6454-1.61218.59150.24550.78720.71421.20490.3104-2.04660.22730.5640.3919-0.1384-0.28950.67740.324-0.06080.82920.10390.44339.977517.5002-71.1563
725.01930.7386-0.27854.774-1.11512.03250.22190.66380.09250.1839-0.24160.149-0.2195-0.040.01880.40230.03940.0310.5379-0.04030.398613.149510.272-59.0905
732.61122.0607-0.55799.4963-5.34693.17-0.48171.66840.0158-1.67990.04610.62921.0307-0.705-0.18190.2437-0.0889-0.09130.8949-0.27990.45997.48127.4094-69.2765
743.3441.3661-0.90875.3812-2.10014.4957-0.25260.5782-0.7245-0.82460.2207-0.00860.5382-0.32750.05440.45560.03970.05750.5694-0.13850.53618.73910.0552-59.7499
757.9395-4.9482-5.39885.38141.59585.04730.3058-1.58661.05720.7540.6329-0.88540.0238-0.18390.07931.0261-0.0796-0.2270.76270.10170.4678-32.6840.128-20.3108
760.40280.3367-0.89790.3768-0.48792.65980.0262-0.5816-0.51370.62150.0827-0.25050.6429-0.08140.77341.3067-0.1579-0.4740.95140.91650.2351-30.4443-9.5059-18.418
776.0806-3.34281.6763.48882.37237.06490.5324-1.03860.23551.04450.12611.0839-0.2259-0.6224-0.36280.5686-0.02820.03970.4708-0.00460.3617-37.5327-0.0515-26.3336
782.4712-1.0661-2.25633.5846-0.35442.66370.0262-1.0457-0.57080.57930.1363-0.60860.78640.04330.30560.6227-0.0073-0.16470.46260.29860.5165-29.5425-8.329-29.4673
797.3407-2.58470.90243.62340.22132.21480.4738-0.7978-0.35910.4626-0.60750.14040.24180.9384-0.1250.4208-0.08420.00720.42960.03660.4152-38.0112-2.6335-35.3836
806.9421-1.2674-0.64592.8489-1.16446.89210.19860.2633-0.58840.6281-0.0144-1.0809-0.98430.68010.14210.3232-0.0876-0.01440.2165-0.0610.54-27.328-3.9832-39.5557
812.64370.5654-5.13132.4827-0.28042.0051-0.3674-0.3145-1.2619-0.58010.0614-0.67961.42360.82970.38890.57640.0834-0.15940.2148-0.02010.7583-28.975-14.0946-38.5601
823.94721.0857-0.41782.1394-1.00485.37010.19440.2708-0.2614-0.37440.01740.1090.4554-0.007-0.12410.32110.00540.0040.28-0.0430.3726-32.0248-2.4451-46.5092
835.8843-1.7904-1.74831.5632-0.78315.3876-0.1846-0.0646-0.9576-1.04780.575-1.10320.43250.7631-0.01270.42890.06770.28590.1305-0.19950.7179-26.1381-12.7051-48.7788
841.75262.2826-0.89762.8253-1.44682.9849-0.07080.4159-0.3786-0.25970.0086-0.21750.5091-0.2650.09240.3997-0.01730.00270.3851-0.11160.3767-29.7919-1.6811-55.8062
852.71981.42112.81356.93472.07697.23670.72360.9946-2.3607-0.2611-0.1041-1.43330.6140.8394-0.07980.64310.03870.180.4916-0.16890.7612-21.8898-10.6648-59.3607
864.09970.9786-0.89526.82322.97964.9389-0.59180.93120.1556-0.1152-0.31730.3197-2.27940.51170.53221.0305-0.2983-0.14740.65930.19320.64292.39838.0665-49.1985
874.04783.87790.10734.60130.16470.2788-0.2028-0.29541.0280.6448-0.4411-0.1999-0.78920.2214-1.7411.4242-0.8657-0.05650.47480.10110.82625.227741.2545-39.8987
884.27621.97250.94036.759-1.64460.910.06380.19880.51840.3625-0.64410.541-1.32520.6370.34170.7348-0.1258-0.06620.44060.11820.565-3.184732.9803-47.982
896.9221-0.59662.07688.6211.78227.9545-0.20550.19920.58710.84160.1612-1.2883-0.98511.8461-0.24410.5971-0.2228-0.0430.44060.02040.6084.476530.1351-39.32
903.8409-0.21691.36455.8688-1.21574.49030.03830.63621.0765-0.49410.2215-0.9159-0.32030.8732-0.26530.2341-0.07920.04420.41410.06030.3991-0.541122.3011-43.1464
916.812-1.9941-1.30656.34341.2540.39880.3468-1.50291.02241.7830.3063-1.07410.38121.5084-0.12490.5006-0.1026-0.14970.85350.0530.48173.904922.1031-32.1308
922.1441-0.41440.32163.6125-0.48422.06430.0266-0.0685-0.1539-0.11720.0651-0.30390.0820.5796-0.03740.36550.02110.03850.38210.00880.2755-0.469312.9214-42.3887
937.0507-0.108-1.76251.93221.19522.0202-0.4335-1.26760.07011.65470.5383-1.52130.2151.1536-0.22220.44530.0306-0.12760.59880.06860.48244.977411.5608-31.7855
941.9368-1.04850.09144.68742.69229.6398-0.2817-0.083-0.3030.5547-0.35180.44921.1338-0.15450.7150.26070.03140.03790.3442-0.00530.344-4.1695.6315-41.3692
950.249-1.07420.0294.5794-0.99426.0963-1.092-0.97270.20160.27280.0816-0.33930.40410.5130.80820.23180.1435-0.02870.3751-0.01850.53066.10270.4404-42.5714
961.96730.4744-0.05492.4176-0.45619.6618-0.2738-1.2485-0.65920.9370.08-1.14770.82921.65560.02780.69430.1632-0.05580.75010.02730.51717.48390.1816-32.2516
974.58630.2717-0.23858.65130.47485.5971-0.34531.0720.7386-1.09430.3795-0.8379-1.51090.6937-0.19491.2111-0.0983-0.05580.7843-0.32531.1540.20733.9616-91.5524
984.2617-2.0679-0.05444.64450.44542.4977-0.5239-0.632-0.10670.8207-0.11740.279-2.02540.03810.34611.176-0.0657-0.12690.8029-0.39691.55562.04265.5687-82.0532
996.362.4642.091.71250.89944.7343-0.013-0.2751.56090.2192-0.65430.4475-0.2855-1.34050.73620.79160.06270.02750.6963-0.08680.9902-5.4847-1.5283-91.7276
1006.0028-2.7729-2.2526.30171.4985.7948-0.148-0.88221.07811.50970.2754-0.72440.61940.3875-0.02150.7294-0.2445-0.07840.7892-0.20450.76742.4057-5.4407-83.8271
1017.7923-2.08170.7126.77820.06533.33040.1127-0.66991.7873-0.554-0.0612-0.1346-0.38650.276-0.21390.4456-0.15840.00230.65490.05770.5252-1.7732-12.7512-89.3409
1024.1112-1.4783-1.98265.34660.82340.9921-0.1113-1.08880.18790.7722-0.0071-0.06710.04720.4484-0.03990.413-0.0742-0.00870.74960.14470.35880.3449-20.0599-87.329
1033.75150.0101-0.27015.29672.53636.0624-0.3314-0.9374-0.88110.39320.3740.26650.33490.4138-0.03460.4215-0.03980.02840.74450.22780.50790.1565-27.9741-87.0101
1044.1998-1.8152-0.72975.04663.60598.2066-0.3649-0.8242-0.65551.01340.6148-0.62921.66890.29690.2390.5335-0.07110.01320.61310.21840.75748.7619-34.148-89.5047
1051.7575-0.59140.44012.4367-0.68610.6762-0.0942-0.5247-0.18820.50920.15690.8637-0.6574-0.49810.14320.86850.53240.06030.664-0.06630.71439.20615.5147-101.0099
1061.31252.53561.46988.78010.64895.65420.11950.23470.8327-1.1620.07220.7104-2.0783-1.10220.29831.08290.477-0.14370.76720.13981.1347.0318.8885-109.966
1073.19650.07761.42811.7722-1.40164.68710.2711-0.42020.66150.7004-0.7938-0.2373-1.20410.08440.50010.75550.0810.05380.4905-0.05470.785415.53970.6875-101.9252
1086.4339-0.07651.29527.06850.52534.465-0.07240.11450.3945-1.0501-0.36120.7846-0.5016-1.65230.11530.49330.1963-0.0430.6125-0.05230.51637.7768-2.3089-110.5613
1092.63580.02861.77227.33550.44024.11530.241-0.98931.09550.1816-0.16180.65-0.4151-1.0492-0.28550.43040.05630.04830.3972-0.01140.511312.8368-10.0553-106.8335
1103.63212.0286-1.35913.9494-0.81481.43630.60580.7361-0.1569-1.2876-0.56471.5186-0.1655-1.1082-0.30550.43110.1447-0.15490.71320.00570.50478.3815-10.2252-117.8589
1112.01970.36650.14192.94170.05442.534-0.11710.0127-0.0306-0.23580.02020.45020.2943-0.80990.11680.3279-0.092-0.02450.45440.01850.435712.8265-19.4616-107.6165
1124.9052-0.80262.06667.6249-2.46891.4726-0.18822.11260.0821-0.9769-0.17550.39870.9676-0.5552-0.0017-0.0374-0.45120.06450.7303-0.08480.58277.3934-20.7375-118.2476
1133.53420.39680.5274.84530.20663.95270.38860.5807-0.4591-0.20220.04210.42380.704-0.6939-0.2290.3266-0.037-0.06070.3394-0.00340.386816.572-26.7347-108.7113
1146.1214-2.6431-5.075.2287-0.12125.5315-0.1140.5768-1.4874-1.3206-0.01310.56290.4791-1.03690.6830.2774-0.26130.00860.68880.13440.75416.295-31.9239-107.5131
1152.40170.1087-2.00127.8305-2.54795.23950.25510.809-1.319-0.9692-0.0736-0.01941.7571-0.3664-0.04210.8375-0.2802-0.31550.8651-0.14960.83444.651-32.1055-117.3792
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 12 THROUGH 24 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 25 THROUGH 35 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 36 THROUGH 49 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 50 THROUGH 68 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 69 THROUGH 92 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 93 THROUGH 101 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 102 THROUGH 125 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 126 THROUGH 134 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 135 THROUGH 158 )
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 159 THROUGH 167 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 13 THROUGH 24 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 25 THROUGH 35 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 36 THROUGH 49 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 50 THROUGH 59 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 60 THROUGH 68 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 69 THROUGH 92 )
17X-RAY DIFFRACTION17CHAIN 'B' AND (RESID 93 THROUGH 101 )
18X-RAY DIFFRACTION18CHAIN 'B' AND (RESID 102 THROUGH 115 )
19X-RAY DIFFRACTION19CHAIN 'B' AND (RESID 116 THROUGH 148 )
20X-RAY DIFFRACTION20CHAIN 'B' AND (RESID 149 THROUGH 166 )
21X-RAY DIFFRACTION21CHAIN 'C' AND (RESID 13 THROUGH 24 )
22X-RAY DIFFRACTION22CHAIN 'C' AND (RESID 25 THROUGH 35 )
23X-RAY DIFFRACTION23CHAIN 'C' AND (RESID 36 THROUGH 49 )
24X-RAY DIFFRACTION24CHAIN 'C' AND (RESID 50 THROUGH 59 )
25X-RAY DIFFRACTION25CHAIN 'C' AND (RESID 60 THROUGH 82 )
26X-RAY DIFFRACTION26CHAIN 'C' AND (RESID 83 THROUGH 92 )
27X-RAY DIFFRACTION27CHAIN 'C' AND (RESID 93 THROUGH 101 )
28X-RAY DIFFRACTION28CHAIN 'C' AND (RESID 102 THROUGH 115 )
29X-RAY DIFFRACTION29CHAIN 'C' AND (RESID 116 THROUGH 134 )
30X-RAY DIFFRACTION30CHAIN 'C' AND (RESID 135 THROUGH 148 )
31X-RAY DIFFRACTION31CHAIN 'C' AND (RESID 149 THROUGH 168 )
32X-RAY DIFFRACTION32CHAIN 'D' AND (RESID 13 THROUGH 24 )
33X-RAY DIFFRACTION33CHAIN 'D' AND (RESID 25 THROUGH 35 )
34X-RAY DIFFRACTION34CHAIN 'D' AND (RESID 36 THROUGH 49 )
35X-RAY DIFFRACTION35CHAIN 'D' AND (RESID 50 THROUGH 59 )
36X-RAY DIFFRACTION36CHAIN 'D' AND (RESID 60 THROUGH 68 )
37X-RAY DIFFRACTION37CHAIN 'D' AND (RESID 69 THROUGH 82 )
38X-RAY DIFFRACTION38CHAIN 'D' AND (RESID 83 THROUGH 101 )
39X-RAY DIFFRACTION39CHAIN 'D' AND (RESID 102 THROUGH 148 )
40X-RAY DIFFRACTION40CHAIN 'D' AND (RESID 149 THROUGH 166 )
41X-RAY DIFFRACTION41CHAIN 'E' AND (RESID 12 THROUGH 35 )
42X-RAY DIFFRACTION42CHAIN 'E' AND (RESID 36 THROUGH 92 )
43X-RAY DIFFRACTION43CHAIN 'E' AND (RESID 93 THROUGH 168 )
44X-RAY DIFFRACTION44CHAIN 'F' AND (RESID 13 THROUGH 24 )
45X-RAY DIFFRACTION45CHAIN 'F' AND (RESID 25 THROUGH 35 )
46X-RAY DIFFRACTION46CHAIN 'F' AND (RESID 36 THROUGH 59 )
47X-RAY DIFFRACTION47CHAIN 'F' AND (RESID 60 THROUGH 68 )
48X-RAY DIFFRACTION48CHAIN 'F' AND (RESID 69 THROUGH 92 )
49X-RAY DIFFRACTION49CHAIN 'F' AND (RESID 93 THROUGH 115 )
50X-RAY DIFFRACTION50CHAIN 'F' AND (RESID 116 THROUGH 134 )
51X-RAY DIFFRACTION51CHAIN 'F' AND (RESID 135 THROUGH 148 )
52X-RAY DIFFRACTION52CHAIN 'F' AND (RESID 149 THROUGH 166 )
53X-RAY DIFFRACTION53CHAIN 'G' AND (RESID 13 THROUGH 24 )
54X-RAY DIFFRACTION54CHAIN 'G' AND (RESID 25 THROUGH 35 )
55X-RAY DIFFRACTION55CHAIN 'G' AND (RESID 36 THROUGH 49 )
56X-RAY DIFFRACTION56CHAIN 'G' AND (RESID 50 THROUGH 68 )
57X-RAY DIFFRACTION57CHAIN 'G' AND (RESID 69 THROUGH 82 )
58X-RAY DIFFRACTION58CHAIN 'G' AND (RESID 83 THROUGH 92 )
59X-RAY DIFFRACTION59CHAIN 'G' AND (RESID 93 THROUGH 101 )
60X-RAY DIFFRACTION60CHAIN 'G' AND (RESID 102 THROUGH 115 )
61X-RAY DIFFRACTION61CHAIN 'G' AND (RESID 116 THROUGH 125 )
62X-RAY DIFFRACTION62CHAIN 'G' AND (RESID 126 THROUGH 134 )
63X-RAY DIFFRACTION63CHAIN 'G' AND (RESID 135 THROUGH 148 )
64X-RAY DIFFRACTION64CHAIN 'G' AND (RESID 149 THROUGH 158 )
65X-RAY DIFFRACTION65CHAIN 'G' AND (RESID 159 THROUGH 168 )
66X-RAY DIFFRACTION66CHAIN 'H' AND (RESID 13 THROUGH 24 )
67X-RAY DIFFRACTION67CHAIN 'H' AND (RESID 25 THROUGH 35 )
68X-RAY DIFFRACTION68CHAIN 'H' AND (RESID 36 THROUGH 49 )
69X-RAY DIFFRACTION69CHAIN 'H' AND (RESID 50 THROUGH 82 )
70X-RAY DIFFRACTION70CHAIN 'H' AND (RESID 83 THROUGH 92 )
71X-RAY DIFFRACTION71CHAIN 'H' AND (RESID 93 THROUGH 101 )
72X-RAY DIFFRACTION72CHAIN 'H' AND (RESID 102 THROUGH 125 )
73X-RAY DIFFRACTION73CHAIN 'H' AND (RESID 126 THROUGH 134 )
74X-RAY DIFFRACTION74CHAIN 'H' AND (RESID 135 THROUGH 166 )
75X-RAY DIFFRACTION75CHAIN 'I' AND (RESID 12 THROUGH 24 )
76X-RAY DIFFRACTION76CHAIN 'I' AND (RESID 25 THROUGH 35 )
77X-RAY DIFFRACTION77CHAIN 'I' AND (RESID 36 THROUGH 49 )
78X-RAY DIFFRACTION78CHAIN 'I' AND (RESID 50 THROUGH 68 )
79X-RAY DIFFRACTION79CHAIN 'I' AND (RESID 69 THROUGH 82 )
80X-RAY DIFFRACTION80CHAIN 'I' AND (RESID 83 THROUGH 92 )
81X-RAY DIFFRACTION81CHAIN 'I' AND (RESID 93 THROUGH 101 )
82X-RAY DIFFRACTION82CHAIN 'I' AND (RESID 102 THROUGH 125 )
83X-RAY DIFFRACTION83CHAIN 'I' AND (RESID 126 THROUGH 134 )
84X-RAY DIFFRACTION84CHAIN 'I' AND (RESID 135 THROUGH 158 )
85X-RAY DIFFRACTION85CHAIN 'I' AND (RESID 159 THROUGH 168 )
86X-RAY DIFFRACTION86CHAIN 'J' AND (RESID 12 THROUGH 24 )
87X-RAY DIFFRACTION87CHAIN 'J' AND (RESID 25 THROUGH 35 )
88X-RAY DIFFRACTION88CHAIN 'J' AND (RESID 36 THROUGH 49 )
89X-RAY DIFFRACTION89CHAIN 'J' AND (RESID 50 THROUGH 68 )
90X-RAY DIFFRACTION90CHAIN 'J' AND (RESID 69 THROUGH 92 )
91X-RAY DIFFRACTION91CHAIN 'J' AND (RESID 93 THROUGH 101 )
92X-RAY DIFFRACTION92CHAIN 'J' AND (RESID 102 THROUGH 125 )
93X-RAY DIFFRACTION93CHAIN 'J' AND (RESID 126 THROUGH 134 )
94X-RAY DIFFRACTION94CHAIN 'J' AND (RESID 135 THROUGH 148 )
95X-RAY DIFFRACTION95CHAIN 'J' AND (RESID 149 THROUGH 158 )
96X-RAY DIFFRACTION96CHAIN 'J' AND (RESID 159 THROUGH 168 )
97X-RAY DIFFRACTION97CHAIN 'K' AND (RESID 13 THROUGH 24 )
98X-RAY DIFFRACTION98CHAIN 'K' AND (RESID 25 THROUGH 35 )
99X-RAY DIFFRACTION99CHAIN 'K' AND (RESID 36 THROUGH 49 )
100X-RAY DIFFRACTION100CHAIN 'K' AND (RESID 50 THROUGH 68 )
101X-RAY DIFFRACTION101CHAIN 'K' AND (RESID 69 THROUGH 92 )
102X-RAY DIFFRACTION102CHAIN 'K' AND (RESID 93 THROUGH 125 )
103X-RAY DIFFRACTION103CHAIN 'K' AND (RESID 126 THROUGH 148 )
104X-RAY DIFFRACTION104CHAIN 'K' AND (RESID 149 THROUGH 166 )
105X-RAY DIFFRACTION105CHAIN 'L' AND (RESID 13 THROUGH 24 )
106X-RAY DIFFRACTION106CHAIN 'L' AND (RESID 25 THROUGH 35 )
107X-RAY DIFFRACTION107CHAIN 'L' AND (RESID 36 THROUGH 49 )
108X-RAY DIFFRACTION108CHAIN 'L' AND (RESID 50 THROUGH 68 )
109X-RAY DIFFRACTION109CHAIN 'L' AND (RESID 69 THROUGH 92 )
110X-RAY DIFFRACTION110CHAIN 'L' AND (RESID 93 THROUGH 101 )
111X-RAY DIFFRACTION111CHAIN 'L' AND (RESID 102 THROUGH 125 )
112X-RAY DIFFRACTION112CHAIN 'L' AND (RESID 126 THROUGH 134 )
113X-RAY DIFFRACTION113CHAIN 'L' AND (RESID 135 THROUGH 148 )
114X-RAY DIFFRACTION114CHAIN 'L' AND (RESID 149 THROUGH 158 )
115X-RAY DIFFRACTION115CHAIN 'L' AND (RESID 159 THROUGH 167 )

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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