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- PDB-3qi0: Structural, thermodynamic and kinetic analysis of the picomolar b... -

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データを開く


IDまたはキーワード:

読み込み中...

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基本情報

登録情報
データベース: PDB / ID: 3qi0
タイトルStructural, thermodynamic and kinetic analysis of the picomolar binding affinity interaction of the beta-lactamase inhibitor protein-II (BLIP-II) with class A beta-lactamases
要素Beta-lactamase inhibitory protein II
キーワードHYDROLASE INHIBITOR / enzyme-inhibitor complex / BSGC / beta-propeller / beta-lactamase / protein:protein interaction
機能・相同性
機能・相同性情報


: / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / 7 Propeller / Methylamine Dehydrogenase; Chain H / Mainly Beta
類似検索 - ドメイン・相同性
Beta-lactamase inhibitory protein II
類似検索 - 構成要素
生物種Streptomyces exfoliatus (バクテリア)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.8 Å
データ登録者Brown, N.G. / Chow, D.C. / Sankaran, B. / Zwart, P. / Prasad, B.V.V. / Palzkill, T.
引用ジャーナル: J.Biol.Chem. / : 2011
タイトル: Analysis of the binding forces driving the tight interactions between beta-lactamase inhibitory protein-II (BLIP-II) and class A beta-lactamases.
著者: Brown, N.G. / Chow, D.C. / Sankaran, B. / Zwart, P. / Prasad, B.V. / Palzkill, T.
履歴
登録2011年1月26日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02011年7月20日Provider: repository / タイプ: Initial release
改定 1.12012年2月29日Group: Database references
改定 1.22024年2月21日Group: Data collection / Database references / Derived calculations
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Beta-lactamase inhibitory protein II
B: Beta-lactamase inhibitory protein II
C: Beta-lactamase inhibitory protein II
D: Beta-lactamase inhibitory protein II
E: Beta-lactamase inhibitory protein II
F: Beta-lactamase inhibitory protein II
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)173,52841
ポリマ-170,1666
非ポリマー3,36235
3,585199
1
A: Beta-lactamase inhibitory protein II
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)29,0338
ポリマ-28,3611
非ポリマー6727
181
タイプ名称対称操作
identity operation1_555x,y,z1
2
B: Beta-lactamase inhibitory protein II
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)29,1299
ポリマ-28,3611
非ポリマー7698
181
タイプ名称対称操作
identity operation1_555x,y,z1
3
C: Beta-lactamase inhibitory protein II
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)28,7455
ポリマ-28,3611
非ポリマー3844
181
タイプ名称対称操作
identity operation1_555x,y,z1
4
D: Beta-lactamase inhibitory protein II
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)28,9377
ポリマ-28,3611
非ポリマー5766
181
タイプ名称対称操作
identity operation1_555x,y,z1
5
E: Beta-lactamase inhibitory protein II
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)29,1299
ポリマ-28,3611
非ポリマー7698
181
タイプ名称対称操作
identity operation1_555x,y,z1
6
F: Beta-lactamase inhibitory protein II
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)28,5533
ポリマ-28,3611
非ポリマー1922
181
タイプ名称対称操作
identity operation1_555x,y,z1
7
D: Beta-lactamase inhibitory protein II
F: Beta-lactamase inhibitory protein II
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)57,49010
ポリマ-56,7222
非ポリマー7698
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-82 kcal/mol
Surface area19750 Å2
手法PISA
8
B: Beta-lactamase inhibitory protein II
C: Beta-lactamase inhibitory protein II
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)57,87514
ポリマ-56,7222
非ポリマー1,15312
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-113 kcal/mol
Surface area19650 Å2
手法PISA
9
E: Beta-lactamase inhibitory protein II
ヘテロ分子

A: Beta-lactamase inhibitory protein II
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)58,16317
ポリマ-56,7222
非ポリマー1,44115
362
タイプ名称対称操作
identity operation1_555x,y,z1
crystal symmetry operation3_545-x,y-1/2,-z+1/21
Buried area3080 Å2
ΔGint-151 kcal/mol
Surface area19750 Å2
手法PISA
10
A: Beta-lactamase inhibitory protein II
ヘテロ分子

B: Beta-lactamase inhibitory protein II
C: Beta-lactamase inhibitory protein II
D: Beta-lactamase inhibitory protein II
E: Beta-lactamase inhibitory protein II
F: Beta-lactamase inhibitory protein II
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)173,52841
ポリマ-170,1666
非ポリマー3,36235
1086
タイプ名称対称操作
crystal symmetry operation3_545-x,y-1/2,-z+1/21
identity operation1_555x,y,z1
Buried area13770 Å2
ΔGint-368 kcal/mol
Surface area53140 Å2
手法PISA
単位格子
Length a, b, c (Å)114.606, 114.737, 173.827
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11A
21B
31C
41D
51E
61F

NCSドメイン領域:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A43 - 310
2114B43 - 310
3114C43 - 310
4114D43 - 310
5114E43 - 310
6114F43 - 310

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要素

#1: タンパク質
Beta-lactamase inhibitory protein II


分子量: 28360.947 Da / 分子数: 6 / 断片: unp residues 41-311 / 由来タイプ: 組換発現
由来: (組換発現) Streptomyces exfoliatus (バクテリア)
遺伝子: bliB / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: O87916
#2: 化合物...
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 35 / 由来タイプ: 合成 / : SO4
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 199 / 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: 3.36 Å3/Da / 溶媒含有率: 63.37 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7
詳細: 2.0 M ammonium sulfate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: ALS / ビームライン: 5.0.1 / 波長: 0.9774 Å
検出器タイプ: ADSC QUANTUM 210 / 検出器: CCD / 日付: 2009年12月9日
放射モノクロメーター: Single crystal, cylindrically bent Si(220)
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: 0.9774 Å / 相対比: 1
反射解像度: 2.8→50 Å / Num. all: 57635 / Num. obs: 57289 / % possible obs: 99.4 % / Observed criterion σ(I): -3
反射 シェル解像度: 2.8→2.85 Å / % possible all: 90.1

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解析

ソフトウェア
名称バージョン分類
HKL-2000データ収集
PHASER位相決定
REFMAC5.5.0102精密化
HKL-2000データ削減
HKL-2000データスケーリング
精密化構造決定の手法: 分子置換 / 解像度: 2.8→50 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.88 / SU B: 25.616 / SU ML: 0.229 / 交差検証法: THROUGHOUT / ESU R Free: 0.322 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor反射数%反射Selection details
Rfree0.24251 2898 5.1 %RANDOM
Rwork0.1952 ---
obs0.19758 54285 99.29 %-
溶媒の処理イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.4 Å / 溶媒モデル: MASK
原子変位パラメータBiso mean: 27.105 Å2
Baniso -1Baniso -2Baniso -3
1--1.22 Å20 Å20 Å2
2--0.37 Å20 Å2
3---0.85 Å2
精密化ステップサイクル: LAST / 解像度: 2.8→50 Å
タンパク質核酸リガンド溶媒全体
原子数11443 0 175 199 11817
拘束条件
Refine-IDタイプDev idealDev ideal target
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02111829
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.93516175
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.04951605
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7225.946444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.202151590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3011518
X-RAY DIFFRACTIONr_chiral_restr0.1040.21765
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219048
X-RAY DIFFRACTIONr_mcbond_it0.8251.57851
X-RAY DIFFRACTIONr_mcangle_it1.711212310
X-RAY DIFFRACTIONr_scbond_it3.05833978
X-RAY DIFFRACTIONr_scangle_it5.4654.53865
Refine LS restraints NCS

Ens-ID: 1 / : 1895 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDタイプRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.270.5
2BMEDIUM POSITIONAL0.270.5
3CMEDIUM POSITIONAL0.290.5
4DMEDIUM POSITIONAL0.280.5
5EMEDIUM POSITIONAL0.260.5
6FMEDIUM POSITIONAL0.350.5
1AMEDIUM THERMAL1.192
2BMEDIUM THERMAL1.422
3CMEDIUM THERMAL1.342
4DMEDIUM THERMAL1.062
5EMEDIUM THERMAL1.112
6FMEDIUM THERMAL3.172
LS精密化 シェル解像度: 2.792→2.864 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.327 182 -
Rwork0.269 3638 -
obs--91.61 %
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)
10.5747-1.3412-0.33693.17160.77590.2036-0.0235-0.03960.06640.10430.0661-0.0798-0.01040.0473-0.04260.1666-0.0578-0.01260.138-0.02880.20386.342310.464247.7864
24.0039-0.91618.63070.2119-1.973818.6133-0.56560.41020.30630.1494-0.0702-0.0841-1.20640.85430.63580.25970.0447-0.19440.35610.00820.16689.88125.971657.6379
34.5559-1.4268-3.68135.9351-1.36764.1341-0.1245-0.383-0.0764-0.15770.09470.01560.1750.3010.02980.0490.0532-0.06170.19080.03330.18928.9352-2.932954.0667
40.2536-0.2781-0.21941.01080.57210.34620.0068-0.00510.16190.07160.0546-0.02590.02250.0279-0.06140.134-0.0066-0.0520.12540.00920.17681.62941.876754.7038
50.2887-0.3477-0.45410.44440.57470.7455-0.0443-0.05350.045-0.00690.0848-0.0109-0.00230.1189-0.04050.1568-0.0157-0.03310.15770.03240.1794-5.98543.628258.5865
60.82730.0702-0.77730.0078-0.06210.74130.0219-0.0290.06080.00460.01250.0106-0.03810.0654-0.03450.1827-0.0142-0.07020.17230.02630.1376-3.3754-2.762253.2461
70.6638-0.5153-0.87620.45990.93572.2523-0.0393-0.1068-0.12-0.02010.07140.054-0.1510.0821-0.03210.13260.0535-0.04290.09940.03140.1678-6.5967-7.631855.4857
812.3966-6.6343-3.7736.38353.81022.2830.25150.41750.25840.0945-0.0728-0.33610.0513-0.0354-0.17860.25570.0274-0.02820.14150.03530.1613-15.99340.61549.3282
97.3176-1.8614-4.42850.78671.60063.3982-0.3956-0.1862-0.3263-0.11060.10750.1366-0.07840.1760.28810.1728-0.0044-0.00950.13140.09670.1013-15.0998-12.101351.1062
100.8489-0.9219-0.3021.14010.17440.5921-0.0641-0.05830.08340.01160.0591-0.1993-0.0435-0.09520.0050.15820.01180.00330.13130.02480.1674-8.021-8.326346.9404
112.33560.6484-0.89480.202-0.27580.37830.02520.1044-0.02720.00960.03020.0515-0.0258-0.0339-0.05540.21240.0474-0.05230.11330.00920.1832-12.9173-9.438941.2369
120.1007-0.18660.02994.29420.06260.01270.10860.03040.09480.0239-0.15720.09950.03110.00640.04860.2187-0.01930.03530.1490.01930.1667-6.9643-10.191936.6705
131.7609-1.5465-0.79132.2541.49621.09130.01660.04150.0470.0245-0.02090.03980.02190.03650.00430.1609-0.0332-0.02180.1036-0.02720.1489-6.1547-11.112531.7734
147.7455-11.9446-2.208919.79932.33831.4841-0.1314-0.20840.02820.04640.36250.15730.1306-0.0114-0.23110.13340.0049-0.01490.13450.06970.1686-6.0408-2.413125.2978
151.249-0.1432-0.20320.01970.02010.0375-0.0349-0.00370.10960.02320.03-0.0171-0.0216-0.0090.0050.22320.0258-0.06270.16250.01340.10370.7918-6.876431.1195
160.0470.2103-0.06243.4697-0.78460.20560.08250.00330.0222-0.2209-0.149-0.0941-0.00690.06380.06650.24080.01630.02850.1350.03450.15644.0474-1.883827.9562
171.615-0.8463-1.25870.50650.64990.98890.11550.04450.048-0.1406-0.09440.0247-0.0817-0.0056-0.02110.19920.0343-0.02050.156-0.00060.17428.9601-0.268633.1087
182.0921-2.5115-0.05573.0265-0.11793.16440.13360.0070.1228-0.1627-0.0292-0.1473-0.07030.2307-0.10440.1039-0.0094-0.00180.05070.01990.16213.83264.650636.8284
191.8272-0.4269-1.22331.35881.27241.59360.20.130.20020.3210.0791-0.23930.1667-0.0187-0.27910.1881-0.0245-0.02710.16370.0260.071614.3326-0.917343.5554
209.9105-3.3626.02161.974-3.37326.44840.0028-0.5528-0.14020.02240.05230.1587-0.1485-0.0775-0.05510.0787-0.0281-0.00630.1095-0.00870.17847.92633.62445.659
213.81381.2654-1.25040.4211-0.41430.41610.0172-0.0960.07280.0116-0.01430.01430.00540.0642-0.00290.14440.0211-0.02890.217-0.00530.137423.7122-24.573293.1887
225.54473.07673.18022.68360.6513.09480.00660.04210.08820.1882-0.11540.0042-0.22020.20190.10880.1526-0.0260.00390.0906-0.07590.110719.0207-14.676896.9126
234.17190.0032-0.60082.1371-4.21278.3964-0.2040.25020.08590.0950.1306-0.0194-0.1585-0.28250.07340.06160.0139-0.00150.1198-0.03760.183210.2589-18.322995.8963
241.4102-0.4704-1.00491.67011.42391.673-0.03410.04550.17940.08010.0877-0.1180.01570.1236-0.05360.107-0.0097-0.02190.1702-0.01280.153815.1021-17.581488.5327
250.00730.01140.01920.0359-0.14811.80060.02560.0046-0.0210.0591-0.0114-0.0344-0.09090.1722-0.01420.1324-0.0096-0.02680.1753-0.0320.208916.6521-13.5681.0071
260.0177-0.0378-0.09030.46060.83021.53940.02370.00940.02980.12860.1042-0.06880.19240.1299-0.12790.14860.0053-0.00440.1317-0.01160.169210.2281-18.975283.674
273.0513-0.5953-0.44131.85250.71750.30160.08580.27010.03220.0421-0.0467-0.0775-0.005-0.0097-0.03910.1021-0.00210.00340.1339-0.00290.12245.5821-16.652180.365
288.2417.3659-6.94836.584-6.21175.86320.0528-0.5411-0.37030.0151-0.4412-0.3402-0.010.44590.38840.19170.01340.01780.29040.00130.339913.904-22.412870.9978
293.2373-0.31425.68633.0733-2.064810.74120.1011-0.1444-0.06060.0005-0.0138-0.03510.1598-0.2433-0.08730.10950.0332-0.00870.1274-0.02160.11881.1289-20.957171.8394
300.0839-0.2417-0.16280.75590.49840.3427-0.0406-0.0121-0.04030.03490.00280.07680.0583-0.01980.03780.1352-0.00290.01110.1562-0.01990.16275.1689-25.236278.7053
310.0063-0.0010.09370.0031-0.00531.46110.01830.0101-0.00020.003-0.0167-0.01290.2710.0524-0.00160.12290.00180.01120.1627-0.02090.19753.9284-30.871573.7501
320.18440.17130.0310.26770.0860.0359-0.19810.02140.0261-0.14490.13810.1161-0.01270.05970.060.22410.01480.00950.21650.00120.20813.2722-35.424379.7882
330.2706-0.3848-0.38560.62030.78781.3387-0.0091-0.03350.030.06320.0558-0.03610.17940.0726-0.04660.0929-0.0017-0.01830.1282-0.00870.17162.1203-40.417680.6155
3433.29596.0806-16.80821.1225-3.04118.5565-0.3855-0.2307-0.5919-0.0832-0.042-0.05460.14440.09590.42750.14880.0624-0.03560.094-0.02490.253110.7395-46.848180.651
350.78620.2596-1.00780.1357-0.42551.4839-0.111-0.0513-0.0874-0.01920.0256-0.03790.09410.03150.08540.11660.00340.04530.1386-0.03540.21926.4288-41.222387.3615
361.37270.566-0.43550.2348-0.17570.1687-0.0551-0.0394-0.1312-0.02020.0011-0.05530.07970.0450.05390.14360.02290.01840.1443-0.00380.193311.6276-44.346490.5236
371.43330.8785-1.40231.0372-1.56052.7192-0.1797-0.0277-0.1322-0.07610.0927-0.01750.10640.09030.0870.0990.0013-0.00180.15970.01440.138512.9385-39.367195.7493
381.6806-0.8074-0.95481.7951-0.27190.9224-0.1467-0.142-0.11960.1356-0.0128-0.09970.05450.12250.15950.06060.00020.00610.1646-0.01210.12818.0441-35.6629100.5224
392.16441.10382.84831.09621.14053.93130.0743-0.02030.0437-0.0532-0.11530.06880.14230.03910.0410.05010.0534-0.01210.2177-0.02570.156612.1403-28.8157101.0736
400.50691.24910.70673.10121.73480.9989-0.08350.01610.0404-0.1868-0.02160.0683-0.12670.01310.10510.0603-0.0092-0.04760.209-0.0070.196216.8378-26.666794.799
414.2294-0.4878-0.79130.3468-0.61171.8605-0.02510.01330.0795-0.0642-0.0216-0.03750.1360.07120.04670.1476-0.014-0.02120.1177-0.00570.140216.8135-28.491363.0699
423.04130.41562.30870.11150.21081.9536-0.0793-0.6109-0.0678-0.1085-0.1199-0.14090.1293-0.38640.19920.2140.10850.20930.16390.09140.336119.9524-18.468965.6609
4310.8597-1.6935-1.56520.26470.24320.22690.11680.51230.0953-0.0293-0.0907-0.0136-0.0039-0.0726-0.02610.1640.0265-0.0020.0360.0380.12515.5113-15.613257.563
440.7734-0.3957-0.80755.7975-1.07191.2397-0.0247-0.14410.0857-0.04910.114-0.05580.04710.1562-0.08930.1430-0.01320.1448-0.03160.100222.4811-20.682756.631
451.19190.869-0.04262.10840.22210.1263-0.0479-0.1724-0.1165-0.08370.06320.04450.03780.1235-0.01530.16330.00790.02090.1494-0.01650.146830.8146-21.991254.7702
460.58440.2431-0.74530.1093-0.32190.9719-0.0110.0606-0.0366-0.0093-0.0232-0.01360.041-0.02410.03430.17130.0067-0.0210.2098-0.01130.135923.8035-20.214349.6719
471.5055-2.2891.0665.1337-2.92941.79920.05520.05320.0633-0.1568-0.066-0.10380.08830.03880.01080.1589-0.03430.01340.0971-0.03170.180425.9893-16.93145.2555
485.35660.9441.11692.3285-1.94882.36320.2312-0.1367-0.04950.343-0.13670.0491-0.24540.0477-0.09450.1928-0.0084-0.03430.2284-0.02980.192831.2985-29.691342.7881
4914.57444.8518-6.66471.6168-2.21823.0484-0.01080.21840.2577-0.01420.10790.07430.0052-0.0907-0.09710.2092-0.05730.0180.1962-0.03720.135627.9997-20.065935.3649
501.18130.2456-0.56993.9658-0.36270.44970.00730.145-0.0682-0.03690.07620.06350.0912-0.0378-0.08350.1535-0.0175-0.02830.13260.02070.146221.5185-22.800940.7073
510.3278-0.2564-0.450.20090.35240.62960.02810.0928-0.0623-0.0252-0.08440.0433-0.0124-0.09770.05630.21020.0712-0.01410.175-0.00540.213520.8163-27.469234.9345
520.006-0.01930.04790.1839-0.31760.60970.02180.03050.00350.0721-0.06330.0145-0.05860.21190.04160.20990.0445-0.00870.18450.0430.188413.6383-28.188336.3877
530.11030.0039-0.43980.00520.03022.2218-0.09110.0307-0.0504-0.0281-0.0193-0.00350.0911-0.08310.11030.20240.006-0.01650.1277-0.03410.1699.6523-30.65134.536
540.1817-0.8097-0.22923.63251.02550.29030.07290.01520.0544-0.1302-0.033-0.2587-0.0425-0.0266-0.03990.2236-0.0121-0.04840.1411-0.00990.20538.1819-40.200938.106
550.2196-0.0745-0.00130.1769-0.12970.1292-0.08140.129-0.0070.0603-0.0106-0.09710.0212-0.00470.0920.17870.0093-0.04010.1111-0.00120.17175.3718-31.400141.4017
560.01220.00210.03790.02620.00570.11820.03110.0303-0.00260.0363-0.02510.05530.09610.0975-0.00610.1880.0127-0.00880.1255-0.03080.19322.621-35.840645.879
572.51130.19850.46090.03470.10580.7031-0.0218-0.0306-0.11270.0456-0.0048-0.01340.07790.04160.02650.15210.0191-0.02990.1023-0.01840.13772.5782-31.500251.8236
580.33390.4656-0.72180.6494-1.0091.5922-0.02660.0206-0.0327-0.02450.022-0.04250.0262-0.02590.00460.15130.0554-0.03960.0983-0.05590.16423.1697-30.639959.592
591.95321.02272.3970.53611.25522.9431-0.196-0.01840.1112-0.12090.01850.0604-0.2684-0.02160.17750.106-0.00850.01070.08560.01710.21015.5573-22.242858.5055
600.1688-0.02270.45410.0042-0.07861.50150.07190.0497-0.02950.00710.00550.0034-0.05460.2761-0.07750.1957-0.0293-0.01820.1801-0.00590.171112.7214-25.89158.4473
613.68632.07891.60391.66552.13393.87480.14740.11780.00460.00340.0159-0.0027-0.1102-0.1024-0.16330.07520.0218-0.01760.1463-0.00750.229742.5216-47.899169.7576
620.21550.8606-0.42813.4414-1.73761.0357-0.0039-0.04340.0713-0.2207-0.1270.25010.32860.05940.13090.33940.02390.25340.1375-0.09520.332152.4319-50.386866.8006
630.0295-0.09740.26390.64530.35187.9206-0.05330.0250.01560.3833-0.04190.04710.07570.43770.09530.233-0.02270.04320.1906-0.02810.237755.0406-42.095371.3337
640.01080.0872-0.08180.7217-0.67680.63480.00120.01050.0018-0.0270.03480.03690.0257-0.0326-0.03590.08610.0382-0.02160.2338-0.11020.16350.0755-41.22964.3649
650.3164-0.10390.64711.62971.19072.56580.07560.0382-0.0970.02010.06790.08070.13280.1018-0.14360.13060.0151-0.00220.22-0.01420.152449.0632-39.031956.0686
663.01190.9672-0.0311.8483-0.480.6111-0.23640.078-0.09250.0590.2120.2128-0.1652-0.04440.02440.0797-0.03160.02480.1978-0.07960.131150.9063-34.358163.1577
672.22271.50571.52111.14071.40962.5352-0.14970.10320.0436-0.06010.08370.09390.0250.05220.0660.04550.00070.01120.2332-0.040.161454.0755-29.6361.1079
6810.40920.7146-6.31190.15460.831819.0734-0.31780.2942-0.104-0.0168-0.0130.00880.1622-0.36920.33080.1623-0.03830.01810.1429-0.00140.249941.3149-27.531955.8005
691.6790.694.65040.29021.865813.2917-0.0148-0.03160.1437-0.0025-0.05790.09090.0895-0.04340.07270.1035-0.039-0.02960.2011-0.02560.243250.8974-19.716659.3344
702.968-0.29120.18381.26470.33180.1170.10460.04620.19470.1076-0.130.12380.0417-0.04470.02540.103-0.02350.01770.2098-0.01220.124948.0228-25.384765.6734
711.4386-0.81790.98550.4665-0.570.9599-0.0735-0.0049-0.11940.03460.02070.070.0958-0.04790.05270.1523-0.0264-0.00880.183-0.03130.192843.3356-19.591766.3504
720.25270.07670.30631.6846-0.14840.40840.0218-0.09550.023-0.1719-0.0425-0.0460.0577-0.10410.02070.1381-0.02090.03070.1846-0.04930.126442.5755-21.021873.5421
732.68381.2382.99622.22731.55083.3666-0.0154-0.1591-0.06430.01240.09830.1641-0.0039-0.153-0.08280.1116-0.01130.00510.1386-0.02550.167239.9308-19.493777.6079
740.1318-0.10780.07970.0933-0.06980.0525-0.08850.13340.10320.1245-0.0383-0.1035-0.09270.05530.12690.2328-0.0605-0.080.2819-0.02040.330.3848-23.123578.7666
752.7379-0.23750.64111.0044-0.18890.16950.07470.2212-0.1609-0.034-0.0220.01480.01370.0544-0.05270.0933-0.01970.03310.1707-0.02880.123939.4607-26.462981.9007
760.17730.2085-0.11620.6261-0.14640.0766-0.0801-0.0749-0.0704-0.13430.03980.07590.04840.04420.04030.08330.0363-0.00780.1824-0.00610.171734.8617-30.999984.2
770.98790.31860.84550.31380.84942.51-0.0201-0.0456-0.1134-0.02630.0180.02360.0333-0.08520.00210.1377-0.0134-0.0280.15610.00320.137239.1273-36.969584.1729
780.05640.3319-0.24692.0557-1.35271.3191-0.01850.02210.0123-0.11520.14450.10770.1138-0.1572-0.12610.13090.0224-0.02540.1528-0.02830.181240.0741-44.700383.431
790.01660.18680.1372.11271.55041.1393-0.00620.0138-0.0124-0.00580.1309-0.1545-0.01140.0829-0.12470.09380.06070.01320.22960.01720.152648.4475-43.500481.1875
800.0497-0.3587-0.05842.79980.3270.11840.00510.0313-0.0421-0.0486-0.18120.06420.005-0.0270.17610.0966-0.02380.01520.1948-0.03050.335144.898-43.333573.9721
813.135-0.06380.677310.26196.34584.09480.0208-0.01830.0939-0.15220.0318-0.1846-0.10370.0104-0.05260.1078-0.0048-0.02010.0992-0.03960.202224.0333-54.084443.4602
826.48995.2005-1.69316.6122-4.52824.5556-0.54250.0833-0.06940.61880.334-0.1877-1.2388-0.34440.20850.51850.0847-0.05720.0959-0.00640.131721.5494-50.82633.7464
834.91552.78745.21757.44113.78455.65870.2235-0.3465-0.3467-0.04910.1998-0.55250.1815-0.3171-0.42340.17250.03330.05470.1883-0.01220.079529.6367-54.790730.6439
841.30820.30250.60860.07170.13520.31930.14840.0714-0.13710.04490.0047-0.0160.03270.0981-0.15310.1849-0.0480.05390.2008-0.11450.20730.4309-48.030236.1676
852.6-1.25170.91770.613-0.43650.3271-0.0205-0.09070.0328-0.01660.0142-0.0267-0.0287-0.04170.00620.2514-0.04870.04530.1673-0.01110.178632.425-39.796137.7603
861.43550.954-1.53810.968-0.80323.44030.11360.001-0.2407-0.05920.0818-0.31710.0755-0.0226-0.19540.12540.0056-0.02280.1856-0.04280.192337.293-46.7335.7374
870.62140.3761.30380.23770.77773.7863-0.07180.07310.002-0.0330.08390.00960.00160.2435-0.0120.1549-0.01180.04880.2391-0.05650.110941.8888-44.210632.6467
884.09032.07282.87415.72717.59618.928-0.07550.2207-0.27350.18920.06860.2044-0.4217-0.80550.00690.0340.02220.02010.1915-0.0630.204343.8479-39.670645.5494
891.37292.56350.37434.80670.6920.1047-0.03380.0450.0175-0.07430.01030.0339-0.00990.03890.02360.104-0.01970.06930.3349-0.02370.273751.72-42.358435.9736
900.7373-0.5122-0.60991.37130.58210.57680.0516-0.02960.03780.11870.0557-0.2067-0.02590.1171-0.10730.10960.01830.04520.1743-0.05770.19246.2703-49.016638.4344
911.39141.27180.85961.19860.79650.5343-0.02490.0589-0.01890.01130.0775-0.1163-0.00080.0479-0.05260.16480.06090.00520.2131-0.08490.30452.1674-49.899942.7891
923.070.8015-1.54810.2328-0.6042.75070.1143-0.0002-0.0337-0.0220.0025-0.01870.41550.2469-0.11670.1230.05790.00690.1747-0.1110.296750.7069-57.006443.4176
931.57751.07050.06420.74930.03670.0049-0.04160.0877-0.3603-0.05380.0435-0.30660.00730.0135-0.00190.14250.09610.01850.2298-0.10730.325352.4556-61.307745.4437
944.1789-5.6159-6.6429.924512.366415.5372-0.0407-0.2886-0.26860.33810.3932-0.18650.49210.463-0.35250.27080.08480.00690.132-0.0190.24248.8243-63.138555.1682
950.5630.29770.48290.16250.2580.41590.080.0322-0.13480.04210.0076-0.0350.05980.0211-0.08760.21620.0831-0.03340.2062-0.09770.317645.6532-65.620146.1445
960.8430.41950.69770.69320.87473.31740.23860.144-0.11150.03770.0991-0.29770.07630.0351-0.33770.15430.0559-0.07180.0907-0.09440.255741.182-68.540950.3186
970.1154-0.44330.01591.7463-0.06830.1775-0.0677-0.0533-0.00520.18350.1953-0.05320.16420.0816-0.12760.25080.0731-0.05090.1278-0.06530.220135.2711-68.22846.0765
984.49140.56780.94271.93120.01180.20780.1578-0.4649-0.096-0.0281-0.1526-0.28290.056-0.1014-0.00510.1908-0.008-0.06350.1097-0.03960.152827.5141-67.789144.997
990.882-1.1897-0.08391.60980.11050.0115-0.0349-0.00570.15140.04930.0309-0.22750.0296-0.00670.00410.224-0.03430.0120.1391-0.050.139628.6454-65.023636.81
1000.88511.51080.89113.53223.62425.5502-0.1053-0.07810.0371-0.2005-0.03640.1061-0.21060.14730.14170.1290.0331-0.03340.1291-0.08610.2128.6262-58.023640.7858
1011.6052-0.2045-1.51186.5398-2.89652.97420.27860.0912-0.151-0.0887-0.3067-0.065-0.07470.16430.02810.40360.198-0.20240.1671-0.16190.577448.6135-78.512662.3363
1020.0736-0.24952.61990.8703-9.113895.52260.06180.0001-0.035-0.10130.00160.01090.95350.3193-0.06340.15820.0795-0.08360.07190.10320.719558.084-81.23166.3078
10313.8343-27.03499.868467.1665-7.110617.379-0.4596-0.7710.43151.48320.6607-1.39340.292-1.2174-0.20110.0739-0.0761-0.14920.28250.33880.604353.9754-80.889175.1234
1040.47160.71011.43791.07042.17144.6270.1310.0668-0.20320.13490.1332-0.29390.30450.3756-0.26420.25850.1556-0.10050.23470.1620.532854.6474-73.36870.7626
1055.83170.80070.04561.1956-1.885714.56910.13050.0655-0.4455-0.1913-0.2569-0.46050.1530.7010.12640.16830.0706-0.04450.19960.03950.335458.1549-65.590469.3936
10611.0027-6.34558.40644.8906-4.06257.3238-0.0205-0.2147-0.29080.24250.0780.1084-0.04130.1291-0.05760.2003-0.0467-0.11680.39360.11280.23953.0389-68.747475.6982
1073.9358-1.3772-1.78540.49160.62820.8116-0.1655-0.4616-0.19520.09630.11070.02010.08710.20880.05480.2267-0.0601-0.21690.4940.17820.251554.6061-65.543980.4912
1087.30796.0788-7.984918.8046-13.297611.9468-0.58760.4947-0.4977-1.34830.37080.31911.0814-0.50350.21680.3121-0.0685-0.07580.3584-0.00810.161848.5458-56.012472.4148
10918.080821.2574-10.006943.0945-17.95237.65340.0043-0.90750.86470.6420.1741-0.1531-0.23250.0367-0.17840.292-0.1303-0.07730.3993-0.06810.132449.7265-57.357485.0564
1106.7882-3.83816.67053.6235-4.0026.62580.5632-0.0053-0.2187-0.0517-0.39650.13010.52220.1628-0.16670.2058-0.1089-0.0450.4610.18260.10446.1135-64.307780.8337
1113.0342-0.3462-0.27516.5546-0.88070.15330.1124-0.3467-0.2040.4331-0.09820.0795-0.08550.0547-0.01410.2588-0.163-0.01740.475-0.03290.154840.2585-59.934782.0201
1120.3946-0.1358-0.10960.46521.14833.00860.0454-0.0298-0.0367-0.05170.019-0.0052-0.19350.1712-0.06450.3184-0.29450.04910.31220.03510.200335.7417-65.599482.4331
1134.5528-0.8132-3.09410.1570.56392.1146-0.00790.016-0.21520.0618-0.09940.04320.0529-0.07560.10730.4087-0.3776-0.04060.35930.00620.144530.9362-67.001182.9195
1144.21313.3084-8.167713.5104-10.613717.4635-0.06570.3099-0.29250.3418-0.30930.0913-0.0622-0.44090.3750.1221-0.14680.08130.34990.04390.232124.7981-66.855573.9435
1151.9035-0.0507-1.3222.7095-0.63891.0928-0.2046-0.3163-0.509-0.2715-0.04980.48410.26150.19480.25440.2547-0.206-0.05260.37330.14890.328430.5384-73.620178.3844
1164.026-2.9667-0.30452.27330.26640.0437-0.2634-0.4588-0.34820.27740.18420.32980.0471-0.03860.07910.3431-0.2581-0.09260.45520.02920.275127.7889-76.723973.0351
1175.0449-0.7826-0.06353.3168-2.58792.15860.13940.078-0.77050.3516-0.0040.1664-0.1956-0.0849-0.13550.3941-0.1863-0.1670.11610.12120.437233.0341-81.523171.496
1182.053-3.1668-0.50584.92150.80170.14120.4320.1846-0.3647-0.7202-0.37850.4106-0.0643-0.0804-0.05350.5165-0.0897-0.22170.09150.14620.694537.1322-85.898166.4646
11910.5179-6.24553.982610.6342-3.55661.9752-0.2788-0.1335-0.98310.15330.3565-0.9164-0.3020.2563-0.07770.3909-0.17840.00120.5183-0.00220.496743.7538-86.462472.303
1202.60913.09932.66663.68813.18432.7723-0.07010.1231-0.272-0.1490.1989-0.2835-0.17180.2297-0.12880.3023-0.029-0.11550.35660.31360.422745.2739-78.061367.6272
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 56
2X-RAY DIFFRACTION2A57 - 63
3X-RAY DIFFRACTION3A64 - 70
4X-RAY DIFFRACTION4A71 - 87
5X-RAY DIFFRACTION5A88 - 101
6X-RAY DIFFRACTION6A102 - 114
7X-RAY DIFFRACTION7A115 - 128
8X-RAY DIFFRACTION8A129 - 134
9X-RAY DIFFRACTION9A135 - 140
10X-RAY DIFFRACTION10A141 - 156
11X-RAY DIFFRACTION11A157 - 175
12X-RAY DIFFRACTION12A176 - 194
13X-RAY DIFFRACTION13A195 - 207
14X-RAY DIFFRACTION14A208 - 216
15X-RAY DIFFRACTION15A217 - 231
16X-RAY DIFFRACTION16A232 - 249
17X-RAY DIFFRACTION17A250 - 275
18X-RAY DIFFRACTION18A276 - 291
19X-RAY DIFFRACTION19A292 - 301
20X-RAY DIFFRACTION20A302 - 310
21X-RAY DIFFRACTION21B43 - 56
22X-RAY DIFFRACTION22B57 - 63
23X-RAY DIFFRACTION23B64 - 70
24X-RAY DIFFRACTION24B71 - 87
25X-RAY DIFFRACTION25B88 - 101
26X-RAY DIFFRACTION26B102 - 114
27X-RAY DIFFRACTION27B115 - 128
28X-RAY DIFFRACTION28B129 - 134
29X-RAY DIFFRACTION29B135 - 140
30X-RAY DIFFRACTION30B141 - 156
31X-RAY DIFFRACTION31B157 - 175
32X-RAY DIFFRACTION32B176 - 194
33X-RAY DIFFRACTION33B195 - 207
34X-RAY DIFFRACTION34B208 - 216
35X-RAY DIFFRACTION35B217 - 231
36X-RAY DIFFRACTION36B232 - 249
37X-RAY DIFFRACTION37B250 - 275
38X-RAY DIFFRACTION38B276 - 291
39X-RAY DIFFRACTION39B292 - 301
40X-RAY DIFFRACTION40B302 - 310
41X-RAY DIFFRACTION41C42 - 56
42X-RAY DIFFRACTION42C57 - 63
43X-RAY DIFFRACTION43C64 - 70
44X-RAY DIFFRACTION44C71 - 87
45X-RAY DIFFRACTION45C88 - 101
46X-RAY DIFFRACTION46C102 - 114
47X-RAY DIFFRACTION47C115 - 128
48X-RAY DIFFRACTION48C129 - 134
49X-RAY DIFFRACTION49C135 - 140
50X-RAY DIFFRACTION50C141 - 156
51X-RAY DIFFRACTION51C157 - 175
52X-RAY DIFFRACTION52C176 - 194
53X-RAY DIFFRACTION53C195 - 207
54X-RAY DIFFRACTION54C208 - 216
55X-RAY DIFFRACTION55C217 - 231
56X-RAY DIFFRACTION56C232 - 249
57X-RAY DIFFRACTION57C250 - 275
58X-RAY DIFFRACTION58C276 - 291
59X-RAY DIFFRACTION59C292 - 301
60X-RAY DIFFRACTION60C302 - 310
61X-RAY DIFFRACTION61D42 - 56
62X-RAY DIFFRACTION62D57 - 63
63X-RAY DIFFRACTION63D64 - 70
64X-RAY DIFFRACTION64D71 - 87
65X-RAY DIFFRACTION65D88 - 101
66X-RAY DIFFRACTION66D102 - 114
67X-RAY DIFFRACTION67D115 - 128
68X-RAY DIFFRACTION68D129 - 134
69X-RAY DIFFRACTION69D135 - 140
70X-RAY DIFFRACTION70D141 - 156
71X-RAY DIFFRACTION71D157 - 175
72X-RAY DIFFRACTION72D176 - 194
73X-RAY DIFFRACTION73D195 - 207
74X-RAY DIFFRACTION74D208 - 216
75X-RAY DIFFRACTION75D217 - 231
76X-RAY DIFFRACTION76D232 - 249
77X-RAY DIFFRACTION77D250 - 275
78X-RAY DIFFRACTION78D276 - 291
79X-RAY DIFFRACTION79D292 - 301
80X-RAY DIFFRACTION80D302 - 310
81X-RAY DIFFRACTION81E42 - 56
82X-RAY DIFFRACTION82E57 - 63
83X-RAY DIFFRACTION83E64 - 70
84X-RAY DIFFRACTION84E71 - 87
85X-RAY DIFFRACTION85E88 - 101
86X-RAY DIFFRACTION86E102 - 114
87X-RAY DIFFRACTION87E115 - 128
88X-RAY DIFFRACTION88E129 - 134
89X-RAY DIFFRACTION89E135 - 140
90X-RAY DIFFRACTION90E141 - 156
91X-RAY DIFFRACTION91E157 - 175
92X-RAY DIFFRACTION92E176 - 194
93X-RAY DIFFRACTION93E195 - 207
94X-RAY DIFFRACTION94E208 - 216
95X-RAY DIFFRACTION95E217 - 231
96X-RAY DIFFRACTION96E232 - 249
97X-RAY DIFFRACTION97E250 - 275
98X-RAY DIFFRACTION98E276 - 291
99X-RAY DIFFRACTION99E292 - 301
100X-RAY DIFFRACTION100E302 - 310
101X-RAY DIFFRACTION101F42 - 56
102X-RAY DIFFRACTION102F57 - 63
103X-RAY DIFFRACTION103F64 - 70
104X-RAY DIFFRACTION104F71 - 87
105X-RAY DIFFRACTION105F88 - 101
106X-RAY DIFFRACTION106F102 - 114
107X-RAY DIFFRACTION107F115 - 128
108X-RAY DIFFRACTION108F129 - 134
109X-RAY DIFFRACTION109F135 - 140
110X-RAY DIFFRACTION110F141 - 156
111X-RAY DIFFRACTION111F157 - 175
112X-RAY DIFFRACTION112F176 - 194
113X-RAY DIFFRACTION113F195 - 207
114X-RAY DIFFRACTION114F208 - 216
115X-RAY DIFFRACTION115F217 - 231
116X-RAY DIFFRACTION116F232 - 249
117X-RAY DIFFRACTION117F250 - 275
118X-RAY DIFFRACTION118F276 - 291
119X-RAY DIFFRACTION119F292 - 301
120X-RAY DIFFRACTION120F302 - 309

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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