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- PDB-5jd2: SFX structure of corestreptavidin-selenobiotin complex -

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基本情報

登録情報
データベース: PDB / ID: 5jd2
タイトルSFX structure of corestreptavidin-selenobiotin complex
要素Streptavidin
キーワードBiotin binding protein / SAD / SFX / FEL / streptavidin
機能・相同性
機能・相同性情報


biotin binding / extracellular region
類似検索 - 分子機能
Avidin-like / Avidin-like, conserved site / Avidin-like domain signature. / Avidin / : / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin ...Avidin-like / Avidin-like, conserved site / Avidin-like domain signature. / Avidin / : / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin / Beta Barrel / Mainly Beta
類似検索 - ドメイン・相同性
Chem-BYY / Streptavidin
類似検索 - 構成要素
生物種Streptomyces avidinii (バクテリア)
手法X線回折 / 自由電子レーザー / 単波長異常分散 / 分子置換 / 解像度: 1.9 Å
データ登録者DeMirci, H. / Hunter, M.S. / Boutet, S.
資金援助 米国, 1件
組織認可番号国
Department of Energy (DOE, United States) 米国
引用ジャーナル: Nat Commun / 年: 2016
タイトル: Selenium single-wavelength anomalous diffraction de novo phasing using an X-ray-free electron laser.
著者: Hunter, M.S. / Yoon, C.H. / DeMirci, H. / Sierra, R.G. / Dao, E.H. / Ahmadi, R. / Aksit, F. / Aquila, A.L. / Ciftci, H. / Guillet, S. / Hayes, M.J. / Lane, T.J. / Liang, M. / Lundstrom, U. / ...著者: Hunter, M.S. / Yoon, C.H. / DeMirci, H. / Sierra, R.G. / Dao, E.H. / Ahmadi, R. / Aksit, F. / Aquila, A.L. / Ciftci, H. / Guillet, S. / Hayes, M.J. / Lane, T.J. / Liang, M. / Lundstrom, U. / Koglin, J.E. / Mgbam, P. / Rao, Y. / Zhang, L. / Wakatsuki, S. / Holton, J.M. / Boutet, S.
履歴
登録2016年4月15日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02016年11月16日Provider: repository / タイプ: Initial release
改定 1.12017年9月6日Group: Advisory / Author supporting evidence / Derived calculations
カテゴリ: pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
改定 1.22017年11月22日Group: Refinement description / カテゴリ: software
改定 1.32018年2月14日Group: Data collection / カテゴリ: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
改定 1.42019年12月4日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.52024年3月6日Group: Advisory / Data collection / Database references
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _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: Streptavidin
B: Streptavidin
C: Streptavidin
D: Streptavidin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)51,9408
ポリマ－50,7754
非ポリマー1,1654
水4,720262
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 area9090 Å2
ΔGint-57 kcal/mol
Surface area18700 Å2
手法PISA
単位格子
Length a, b, c (Å)50.840, 98.520, 53.430
Angle α, β, γ (deg.)90.000, 112.380, 90.000
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質
Streptavidin


分子量: 12693.756 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Streptomyces avidinii (バクテリア)
発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P22629
#2: 化合物
ChemComp-BYY / 5-[(3aS,4S,6aR)-2-oxohexahydro-1H-selenopheno[3,4-d]imidazol-4-yl]pentanoic acid / selenobiotin / セレノビオチン


分子量: 291.206 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C10H16N2O3Se
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 262 / 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: 2.44 Å3/Da / 溶媒含有率: 49.52 %
結晶化温度: 293 K / 手法: batch mode / 詳細: 24% PEG 1500 and 20% glycerol

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データ収集

回折平均測定温度: 293 K
放射光源由来: 自由電子レーザー / サイト: SLAC LCLS / ビームライン: CXI / 波長: 0.97 Å
検出器タイプ: CS-PAD CXI-1 / 検出器: PIXEL / 日付: 2015年7月17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: 0.97 Å / 相対比: 1
反射解像度: 1.9→32.51 Å / Num. obs: 75562 / % possible obs: 100 % / 冗長度: 1447 % / Net I/σ(I): 14

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類
直接法位相決定
PHENIX精密化
PDB_EXTRACT3.2データ抽出
CrystFELデータ削減
CrystFELデータスケーリング
精密化構造決定の手法: 単波長異常分散 / 解像度: 1.9→32.506 Å / SU ML: 0.19 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 19.92
Rfactor反射数%反射
Rfree0.1995 1393 1.84 %
Rwork0.1651 --
obs0.1658 75562 99.99 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 103.67 Å2 / Biso mean: 34.8312 Å2 / Biso min: 20.06 Å2
精密化ステップサイクル: final / 解像度: 1.9→32.506 Å
タンパク質核酸リガンド溶媒全体
原子数3554 0 63 265 3882
Biso mean--38.82 43.51 -
残基数----474
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0063796
X-RAY DIFFRACTIONf_angle_d1.035210
X-RAY DIFFRACTIONf_chiral_restr0.081586
X-RAY DIFFRACTIONf_plane_restr0.004654
X-RAY DIFFRACTIONf_dihedral_angle_d16.3251318
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9-1.96790.25731430.236574167559
1.9679-2.04670.22091370.207574207557
2.0467-2.13980.23181450.198674357580
2.1398-2.25260.20451360.187473747510
2.2526-2.39370.25941320.190874437575
2.3937-2.57840.23911380.188474187556
2.5784-2.83780.23291460.174974247570
2.8378-3.24810.20851360.158174047540
3.2481-4.0910.15831410.141274357576
4.091-32.51040.17191390.145774007539
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)
16.3148-1.84975.38524.5656-1.91087.4003-0.4276-0.21440.49360.2910.0916-0.146-0.9412-0.13590.37450.45510.0231-0.04260.2324-0.06360.375411.304112.58627.722
28.8213-5.33444.49457.9257-5.86434.35940.18960.31890.45420.1731-0.52940.1889-0.24211.16150.33610.3189-0.0444-0.04860.2498-0.02340.30620.76515.8277.6697
33.42651.97914.2985.45421.95.4759-0.38-0.1517-0.0592-0.0713-0.04370.2737-0.5113-0.31150.23870.3330.0205-0.02530.29590.02190.31925.369511.20121.8033
42.474-1.97671.21921.5996-1.25271.9069-0.1038-0.44410.3233-0.09670.053-0.0927-0.078-0.2502-0.00330.3096-0.0038-0.00530.24970.00540.28458.73258.23-0.5776
58.9833-4.6292-1.22674.48292.76952.3305-0.36820.54030.35830.3497-0.3166-0.06150.00390.47090.55290.32160.00460.01320.26610.06890.39923.90043.4536-0.9288
60.09260.03120.04340.54421.15472.66930.07810.07030.2438-0.53340.2377-0.31380.23990.4457-0.130.3427-0.03530.00810.27660.01580.339920.64178.1941-5.6108
74.1461-1.1706-1.47830.30260.41450.4752-0.05570.18650.0306-0.0346-0.00430.0483-0.2931-0.2449-0.2530.28780.03320.00290.30840.02860.30474.59515.4377-0.7296
84.8360.18536.68540.22810.25192.0048-0.3077-0.63771.01371.0260.1229-0.2381-0.6207-1.3250.22950.46660.10430.11920.3713-0.0130.455-5.04256.176211.8414
93.9158-5.2149-5.33538.28527.01997.32860.2249-0.27420.55840.77650.35950.1723-0.0505-0.5248-0.35590.40680.03520.06530.362-0.03430.34550.11343.494214.5497
105.63693.9387-4.56143.7179-4.76856.60480.00420.22730.1676-0.1389-0.075-0.11310.0427-0.00050.05840.26320.0059-0.01610.20920.00380.263714.08241.857-4.2147
113.34551.4819-3.36443.60141.18386.1366-0.18440.331-0.2729-0.5951-0.6611-0.22550.14880.45780.68550.2979-0.00790.01580.27960.06350.323222.7334.7454-11.6137
129.2994-4.5189-7.43692.8353.71395.947-0.09570.32240.0733-0.14910.0244-0.18470.2306-0.2309-0.10570.2572-0.0310.01870.2204-0.02880.289616.5957-4.0254-5.0953
135.2952-1.1058-1.65330.39360.71124.90810.1142-0.20710.0807-0.1041-0.3261-0.3198-0.7622-0.6953-0.04580.36510.06640.0030.247-0.02990.27927.5462.765110.1445
147.7852-2.2801-3.7142.11781.89782.2374-0.0592-1.74551.02221.70470.1917-0.29380.26810.3820.22980.6580.06880.04550.5387-0.18220.43419.96069.529517.3246
156.7023-3.6531-4.48363.83675.41858.110.1865-0.1782-0.19081.2348-0.44490.42640.7419-0.39320.27850.4018-0.01190.04240.20490.00260.251112.9399-2.33349.4021
160.0872-0.4368-0.46892.122.07432.033-0.03150.33330.45710.1707-0.0683-0.18450.60020.0650.24020.23730.02660.00540.3503-0.00320.272516.4517-7.9949-1.7777
178.6449-0.14122.91811.2631-1.76315.01771.27420.2372-1.4547-1.5981-0.20130.61692.17570.7124-0.46090.59150.1244-0.10360.3295-0.04170.426518.5524-18.3325-8.5782
182.6914-3.3284-3.79686.2867.14718.04810.04050.2237-0.20890.2838-0.27480.15740.56130.25910.15330.28520.05580.00830.2933-0.00760.276419.0227-14.29670.4535
193.6696-2.5401-2.09782.58420.33932.6470.1511-0.43410.23390.9475-0.2043-0.5437-0.3711-0.26740.11930.2967-0.0166-0.0410.27520.01160.264915.83260.780310.7327
206.32863.28940.96892.56910.85399.6497-0.01140.31440.40061.3008-0.1222-0.2425-1.82392.12720.28220.6022-0.1304-0.04930.45360.01930.45917.429812.74212.6924
214.88582.3541-2.6149.9185-4.45148.5606-0.15690.6276-0.0403-0.52610.4865-0.24230.296-0.136-0.40560.2984-0.0599-0.04490.3343-0.00890.24250.0235-10.589-13.2631
222.3981.0559-0.61844.4104-5.376.78510.2091-0.19290.2011-0.09080.29350.99220.2418-0.0375-0.43180.3235-0.0663-0.01180.327-0.02370.3604-3.1878-13.2511-4.9529
232.1651.6758-1.71598.121-0.19022.0658-0.59560.6481.3711-0.62710.24320.0116-1.20420.05560.11950.4681-0.0843-0.11810.40590.07230.33014.0152-0.2169-14.6731
242.54640.7733-4.60935.5117-3.06799.44660.15060.33370.0084-0.0441-0.0457-0.0321-0.4706-0.3957-0.17620.3468-0.0142-0.08990.2610.0020.28290.3557-1.891-8.452
254.17261.1425-3.14284.4365-4.33795.28090.1068-0.45290.10870.45470.42171.2042-0.9166-0.4084-0.54620.4496-0.0489-0.02290.45460.03870.5655-8.0849-10.45632.3868
261.16790.9669-1.9968.9167-1.88713.40930.08371.8271-0.97420.32750.3861.82240.3822-1.555-0.04940.3603-0.06050.05060.7816-0.06640.608-11.9163-5.4408-0.7166
275.7223-1.9927-6.49198.63061.45447.5002-0.15231.15470.409-0.07010.3-0.4598-0.3616-0.6491-0.02270.24030.0331-0.02010.33940.05570.2482-2.9266-0.9555-2.9498
284.86830.7843-6.22472.8576-0.85288.08610.29311.32680.4902-0.1871-0.087-0.35860.2926-0.3801-0.03040.3603-0.0024-0.00580.32240.00480.266612.8825-2.5826-12.8075
297.76544.3689-4.05664.9339-6.64269.83910.56130.89070.1491-1.8525-0.1347-1.04850.7635-0.0717-0.36180.53160.02540.09910.4008-0.01350.352617.715-11.248-14.4977
305.2429-4.8327-5.48064.77575.11475.7891-0.0621-0.38990.252-0.01850.23680.1076-0.22740.296-0.16380.25150.00830.00120.29340.00130.25160.7446-3.1033-0.3447
318.1614.95550.17538.26730.3042.4864-0.08980.32280.6252-0.22840.14161.44510.1562-1.37190.06770.31550.0399-0.01920.56620.01660.4923-12.4482-0.35793.935
329.0195-6.2616-5.38546.17756.21139.22730.1888-0.03770.1797-0.13530.17660.0099-0.16010.0545-0.40760.2140.01460.01120.22030.01960.21562.0244-4.9363.8948
332.52991.70171.00699.6675-3.64412.5534-0.50170.7556-1.0289-0.72830.47550.17490.89750.076-0.05450.4819-0.08330.0860.3963-0.07350.30089.7079-14.594-13.8006
349.45336.57774.69414.71713.51022.8009-0.13160.837-1.3194-0.63930.7277-0.07281.27431.0297-0.56990.56560.0393-0.04860.3391-0.11320.38586.7646-17.4525-11.1903
352.5145-1.8908-2.87892.33931.82983.5459-0.1431-0.23890.17760.60520.2153-0.00580.4724-0.2906-0.05360.23330.02920.00520.30950.02320.2675.3467-9.52644.9276
362.11311.2659-0.86262.98822.34098.9380.1086-0.87340.11911.0970.274-0.1587-0.244-0.433-0.30380.4810.0880.06630.4731-0.00690.35492.5147-1.254219.9237
376.40041.74352.04662.0961.02390.78240.0346-0.5713-0.13540.71590.2970.16320.5965-0.0099-0.06880.39620.06660.07290.3331-0.01120.33085.4112-7.183918.0364
380.9020.47272.64720.99831.2648.21280.0821-0.1024-0.2284-0.03130.22570.14880.28150.3792-0.35490.2384-0.03030.00450.363-0.00560.35025.1754-14.3324.5641
393.26931.50933.24714.54523.66114.43330.07710.5298-0.0643-0.1415-0.09650.0937-0.0121-0.0242-0.10940.330.02270.00220.3065-0.01940.38131.5703-15.7356-9.2768
402.6772.40651.07142.21221.36883.75490.6626-1.483-0.10181.5156-0.84342.0185-0.04840.0715-0.18940.5834-0.0720.05310.5871-0.05690.5548-4.2221-20.2259-11.4976
413.4792-0.68882.13839.3063-4.80189.87480.1709-0.1803-0.662-0.3180.04030.5991.0635-0.2705-0.11850.3658-0.0461-0.02920.224-0.00750.403312.4094-36.13299.1778
427.5569-3.6932.12065.79282.68536.1093-0.1165-0.06620.20030.8424-0.080.02340.37960.56090.40520.3345-0.04170.00460.1957-0.03350.275515.4356-28.1502-0.4995
433.7273.7232-1.78566.2353-4.7164.24490.0729-0.2197-0.0231-0.11320.0730.67570.43280.2211-0.24310.29270.04970.03470.2356-0.03560.315817.7572-33.49898.2961
442.99852.0364-0.51694.29672.16722.32720.3012-1.1128-0.48181.6336-0.2825-0.54550.7954-0.3836-0.06420.46950.00770.06430.41160.06110.366613.8002-33.763421.9597
452.454-0.3857-0.26315.0014-1.8235.82340.10910.013-0.06360.15640.11140.395-0.2278-0.0694-0.22860.30670.0479-0.01030.17350.00380.307921.3023-32.482411.4543
465.93813.245-1.16646.2916-1.65170.4185-0.01630.52660.34980.07940.04490.11610.26290.3412-0.2450.32040.00250.03280.28050.00130.311527.2583-26.36181.5266
472.81810.6353-0.93360.2821-0.04361.9697-0.07650.0503-0.4048-0.26890.06210.10150.30730.47050.10220.28880.05650.00760.19730.00220.318725.9481-31.514910.228
484.3906-0.4443-4.88030.14160.49585.35130.1880.02610.25070.2595-0.0010.53490.0699-0.0693-0.16330.33340.01330.10710.28610.04830.40858.7647-29.095621.6038
492.41663.17260.33964.843-1.00563.4404-0.2112-1.166-0.40470.26610.63540.73040.3383-0.7842-0.14240.3138-0.03440.10610.45470.11930.6625-1.4225-28.088917.1237
508.0617-1.0508-4.67682.76880.08713.6894-0.2815-0.37840.26470.04170.17090.1980.35460.12540.17790.2750.0039-0.02150.1940.0040.230119.808-24.96312.7296
513.6264-4.0053-1.65784.41882.12892.28980.12170.3631-0.20190.16230.2856-0.80990.38330.6628-0.46260.30980.0713-0.01070.3554-0.03740.361133.9805-28.87218.6176
525.55330.7029-1.63472.00460.37272.3178-0.1333-0.7512-0.2305-0.08060.0701-0.08820.11760.11220.00550.2454-0.00750.01950.19270.00130.225322.9247-20.925710.4327
533.6350.1242-3.00450.90980.14763.8262-0.03471.0229-1.1917-0.1609-0.65961.44090.7924-2.03771.22180.4512-0.1926-0.05860.4887-0.11460.58792.5373-31.32110.3271
542.62922.034-2.18085.62891.62746.2235-0.49520.43960.1059-0.38720.08950.84350.8518-1.32790.81110.3196-0.1360.0180.3339-0.06770.5155.3026-30.76965.8102
558.77046.31861.25444.62271.6216.0528-0.09-0.53261.0134-0.2951-0.16581.1942-0.2683-0.36180.39660.22050.0172-0.03230.1559-0.03060.314313.9079-19.24947.5823
563.02633.5341-0.00915.70560.13890.0223-0.3910.2989-0.1889-0.23690.4074-0.6119-0.1007-0.10810.1020.2275-0.03380.01480.34180.03790.249226.4194-13.02199.0241
575.286-2.43065.68752.4595-2.28946.2279-0.9749-0.43341.21510.52480.25580.3099-0.5282-0.25120.32840.35020.00970.0080.3075-0.00630.387427.6351-3.87628.3704
582.59181.8631.78672.396-0.21853.03280.34140.1148-0.10930.1883-0.2248-0.2047-0.03230.0852-0.04660.26240.0350.01580.2628-0.00820.233918.793-13.47164.8903
595.00592.47821.72.6062-1.68395.292-0.12760.6433-0.3471-0.5571-0.11590.56510.3053-0.18230.32790.2658-0.0345-0.00630.2977-0.01070.309810.8312-28.28583.8605
605.2799-5.91440.47287.76780.61653.8087-0.33820.6554-0.8762-0.012-0.29230.77210.06971.93090.35080.5073-0.0993-0.06720.5047-0.03980.497812.405-38.06180.5495
612.5371-3.57992.60468.33981.04639.4285-0.1674-0.31020.23310.16470.4583-0.53840.06550.0304-0.29060.24780.0117-0.02260.3587-0.07230.24927.2167-14.176128.12
628.5051-0.139-0.33542.4264.75019.7238-0.15150.61460.1050.2869-0.40340.532-1.2332-0.20520.50070.44380.0266-0.06890.3257-0.0210.370616.3638-7.211728.0105
635.7312-1.5084-5.41735.22695.0117.7578-0.1148-0.03040.43610.57360.5228-0.40350.5148-0.2637-0.39580.35040.0147-0.01850.40390.03060.281223.2409-17.52529.0404
644.55053.85232.70077.003-0.56813.79340.07211.0494-2.6235-0.0262-0.08270.3211.40230.9885-0.16010.50030.1034-0.08050.3267-0.0570.455229.383-25.266822.3277
654.0998-4.7698-2.3637.12211.11263.7665-0.607-0.67390.34280.87620.45650.00070.404-0.11550.17420.44010.0449-0.05180.3186-0.06060.300617.8609-18.72729.8496
664.63243.4203-2.96484.4725-0.30083.6837-0.80511.4016-1.14791.63880.4436-0.1615-1.8286-1.9790.20160.66280.11610.0970.6642-0.0350.47139.2705-14.275931.9544
675.027-4.4058-2.90186.72154.20872.66110.2991-1.6366-0.1807-0.19510.3945-0.2814-0.60241.5234-0.59710.37720.01560.04240.41020.05810.238215.0208-21.75728.8754
689.40664.9024-7.42247.6676-5.75698.4887-0.0889-0.4314-0.2780.0429-0.2061-0.2298-0.03120.62010.30190.24890.0338-0.04050.2495-0.00530.284330.7092-21.497417.4009
697.3328-1.4777-2.89572.12244.27899.9006-0.5330.39360.1221-0.06370.3849-0.7619-0.49580.74540.1070.3003-0.0208-0.05020.37710.02550.474335.9633-11.882713.3371
707.045-2.9394-5.64675.46512.42754.4104-0.2412-0.16270.1680.29170.1046-0.1120.014-0.12350.08690.2733-0.0172-0.0160.2734-0.00660.225820.1234-18.904219.5171
717.43824.6836-4.72129.8933-5.51013.9588-0.2794-0.4155-0.3731.07070.37070.0944-0.1328-0.3858-0.13550.44160.07660.07450.34750.01890.29488.0873-23.583528.315
726.1057-7.78125.81439.8619-7.3665.5469-0.284-0.77130.34270.7582-0.01860.0781-1.4457-0.50160.18070.35-0.0170.10390.50510.0210.36943.5289-22.644228.9021
733.8077-1.5584-0.1873.01340.58163.6552-0.2708-0.5671-0.03470.35790.10930.2047-0.05820.48590.19370.2896-0.02520.02180.28430.01980.211614.4947-17.404518.2121
746.3096-1.2162-1.74322.1949-1.53314.9544-0.0292-0.32741.18290.54190.0667-0.582-0.91330.35630.00580.38330.0049-0.08750.3698-0.090.536530.7414-7.550521.0874
754.67874.70784.35915.04764.89764.9403-0.85980.82890.3544-0.07730.7223-0.0589-0.61430.97890.17460.3376-0.0255-0.02540.2647-0.0050.329823.3454-8.549518.7842
767.06597.89164.97138.9195.6446.77870.0073-0.34560.27760.1059-0.00060.4783-0.01810.00990.06350.24130.02780.06070.23530.02640.28548.2529-16.560116.1864
775.0347-4.81525.68694.9876-5.4786.39360.00220.3436-1.283-1.08680.72611.14510.5137-0.8416-0.68210.3721-0.0397-0.02180.41240.07010.5484-3.5703-22.94229.9798
787.6488-2.2367.88932.8168-1.77218.23430.18550.085-0.42820.18990.51440.7667-0.173-0.118-0.68470.2735-0.02880.03630.28260.09050.41640.4784-16.6119.7203
796.40923.98835.32234.48653.55444.4213-0.0113-0.540.58120.079-0.38870.2319-0.4468-0.58570.34450.28760.0120.0440.3248-0.01580.22414.9776-8.913918.3784
804.69612.52714.02612.59471.50373.82130.2669-1.12071.34290.3055-0.5108-0.18210.6737-0.15140.13980.3328-0.03040.02030.4251-0.07650.359324.2292-5.422430.0633
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 16:22)A16 - 22
2X-RAY DIFFRACTION2(chain A and resid 23:28)A23 - 28
3X-RAY DIFFRACTION3(chain A and resid 29:36)A29 - 36
4X-RAY DIFFRACTION4(chain A and resid 37:43)A37 - 43
5X-RAY DIFFRACTION5(chain A and resid 44:50)A44 - 50
6X-RAY DIFFRACTION6(chain A and resid 51:54)A51 - 54
7X-RAY DIFFRACTION7(chain A and resid 55:60)A55 - 60
8X-RAY DIFFRACTION8(chain A and resid 61:66)A61 - 66
9X-RAY DIFFRACTION9(chain A and resid 67:73)A67 - 73
10X-RAY DIFFRACTION10(chain A and resid 74:81)A74 - 81
11X-RAY DIFFRACTION11(chain A and resid 82:85)A82 - 85
12X-RAY DIFFRACTION12(chain A and resid 86:91)A86 - 91
13X-RAY DIFFRACTION13(chain A and resid 92:97)A92 - 97
14X-RAY DIFFRACTION14(chain A and resid 98:104)A98 - 104
15X-RAY DIFFRACTION15(chain A and resid 105:108)A105 - 108
16X-RAY DIFFRACTION16(chain A and resid 109:113)A109 - 113
17X-RAY DIFFRACTION17(chain A and resid 114:119)A114 - 119
18X-RAY DIFFRACTION18(chain A and resid 120:125)A120 - 125
19X-RAY DIFFRACTION19(chain A and resid 126:130)A126 - 130
20X-RAY DIFFRACTION20(chain A and resid 131:134)A131 - 134
21X-RAY DIFFRACTION21(chain B and resid 16:22)B16 - 22
22X-RAY DIFFRACTION22(chain B and resid 23:30)B23 - 30
23X-RAY DIFFRACTION23(chain B and resid 31:36)B31 - 36
24X-RAY DIFFRACTION24(chain B and resid 37:43)B37 - 43
25X-RAY DIFFRACTION25(chain B and resid 44:49)B44 - 49
26X-RAY DIFFRACTION26(chain B and resid 50:53)B50 - 53
27X-RAY DIFFRACTION27(chain B and resid 54:57)B54 - 57
28X-RAY DIFFRACTION28(chain B and resid 58:65)B58 - 65
29X-RAY DIFFRACTION29(chain B and resid 66:72)B66 - 72
30X-RAY DIFFRACTION30(chain B and resid 73:80)B73 - 80
31X-RAY DIFFRACTION31(chain B and resid 81:85)B81 - 85
32X-RAY DIFFRACTION32(chain B and resid 86:94)B86 - 94
33X-RAY DIFFRACTION33(chain B and resid 95:100)B95 - 100
34X-RAY DIFFRACTION34(chain B and resid 101:105)B101 - 105
35X-RAY DIFFRACTION35(chain B and resid 106:111)B106 - 111
36X-RAY DIFFRACTION36(chain B and resid 112:118)B112 - 118
37X-RAY DIFFRACTION37(chain B and resid 119:123)B119 - 123
38X-RAY DIFFRACTION38(chain B and resid 124:128)B124 - 128
39X-RAY DIFFRACTION39(chain B and resid 129:132)B129 - 132
40X-RAY DIFFRACTION40(chain B and resid 133:134)B133 - 134
41X-RAY DIFFRACTION41(chain C and resid 16:22)C16 - 22
42X-RAY DIFFRACTION42(chain C and resid 23:26)C23 - 26
43X-RAY DIFFRACTION43(chain C and resid 27:31)C27 - 31
44X-RAY DIFFRACTION44(chain C and resid 32:39)C32 - 39
45X-RAY DIFFRACTION45(chain C and resid 40:44)C40 - 44
46X-RAY DIFFRACTION46(chain C and resid 45:51)C45 - 51
47X-RAY DIFFRACTION47(chain C and resid 52:56)C52 - 56
48X-RAY DIFFRACTION48(chain C and resid 57:65)C57 - 65
49X-RAY DIFFRACTION49(chain C and resid 66:72)C66 - 72
50X-RAY DIFFRACTION50(chain C and resid 73:79)C73 - 79
51X-RAY DIFFRACTION51(chain C and resid 80:84)C80 - 84
52X-RAY DIFFRACTION52(chain C and resid 85:94)C85 - 94
53X-RAY DIFFRACTION53(chain C and resid 95:100)C95 - 100
54X-RAY DIFFRACTION54(chain C and resid 101:105)C101 - 105
55X-RAY DIFFRACTION55(chain C and resid 106:109)C106 - 109
56X-RAY DIFFRACTION56(chain C and resid 110:115)C110 - 115
57X-RAY DIFFRACTION57(chain C and resid 116:120)C116 - 120
58X-RAY DIFFRACTION58(chain C and resid 121:127)C121 - 127
59X-RAY DIFFRACTION59(chain C and resid 128:131)C128 - 131
60X-RAY DIFFRACTION60(chain C and resid 132:135)C132 - 135
61X-RAY DIFFRACTION61(chain D and resid 16:21)D16 - 21
62X-RAY DIFFRACTION62(chain D and resid 22:27)D22 - 27
63X-RAY DIFFRACTION63(chain D and resid 28:33)D28 - 33
64X-RAY DIFFRACTION64(chain D and resid 34:39)D34 - 39
65X-RAY DIFFRACTION65(chain D and resid 40:44)D40 - 44
66X-RAY DIFFRACTION66(chain D and resid 45:52)D45 - 52
67X-RAY DIFFRACTION67(chain D and resid 53:57)D53 - 57
68X-RAY DIFFRACTION68(chain D and resid 58:64)D58 - 64
69X-RAY DIFFRACTION69(chain D and resid 65:71)D65 - 71
70X-RAY DIFFRACTION70(chain D and resid 72:77)D72 - 77
71X-RAY DIFFRACTION71(chain D and resid 78:82)D78 - 82
72X-RAY DIFFRACTION72(chain D and resid 83:87)D83 - 87
73X-RAY DIFFRACTION73(chain D and resid 88:94)D88 - 94
74X-RAY DIFFRACTION74(chain D and resid 95:101)D95 - 101
75X-RAY DIFFRACTION75(chain D and resid 102:107)D102 - 107
76X-RAY DIFFRACTION76(chain D and resid 108:113)D108 - 113
77X-RAY DIFFRACTION77(chain D and resid 114:118)D114 - 118
78X-RAY DIFFRACTION78(chain D and resid 119:123)D119 - 123
79X-RAY DIFFRACTION79(chain D and resid 124:130)D124 - 130
80X-RAY DIFFRACTION80(chain D and resid 131:134)D131 - 134

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万見について

-
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

-
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