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- PDB-6qyq: Crystal structure of human thymidylate synthase (hTS) variant R175C -

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基本情報

登録情報
データベース: PDB / ID: 6qyq
タイトルCrystal structure of human thymidylate synthase (hTS) variant R175C
要素(Thymidylate synthase) x 4
キーワードTRANSFERASE / human thymidylate synthase / folate pathway / R175C / interface variant
機能・相同性
機能・相同性情報


thymidylate synthase / Interconversion of nucleotide di- and triphosphates / sequence-specific mRNA binding / thymidylate synthase activity / folic acid binding / tetrahydrofolate interconversion / dTTP biosynthetic process / dTMP biosynthetic process / DNA biosynthetic process / G1/S-Specific Transcription ...thymidylate synthase / Interconversion of nucleotide di- and triphosphates / sequence-specific mRNA binding / thymidylate synthase activity / folic acid binding / tetrahydrofolate interconversion / dTTP biosynthetic process / dTMP biosynthetic process / DNA biosynthetic process / G1/S-Specific Transcription / mRNA regulatory element binding translation repressor activity / methylation / mitochondrial inner membrane / negative regulation of translation / mitochondrial matrix / mitochondrion / nucleus / cytoplasm / cytosol
類似検索 - 分子機能
Thymidylate Synthase; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / 2-Layer Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
Chem-FFO / Thymidylate synthase
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.25 Å
データ登録者Pozzi, C. / Mangani, M.
資金援助1件
組織認可番号
European UnionLSH-2005-2.2.0-8
引用ジャーナル: Molecules / : 2019
タイトル: Structural and Functional Characterization of the Human Thymidylate Synthase (hTS) Interface Variant R175C, New Perspectives for the Development of hTS Inhibitors.
著者: Pozzi, C. / Ferrari, S. / Luciani, R. / Costi, M.P. / Mangani, S.
履歴
登録2019年3月9日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02019年4月17日Provider: repository / タイプ: Initial release
改定 1.12024年1月24日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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

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集合体

登録構造単位
A: Thymidylate synthase
C: Thymidylate synthase
B: Thymidylate synthase
D: Thymidylate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)150,76816
ポリマ-149,1034
非ポリマー1,66512
8,539474
1
A: Thymidylate synthase
B: Thymidylate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)75,4809
ポリマ-74,5512
非ポリマー9297
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-90 kcal/mol
Surface area23380 Å2
手法PISA
2
C: Thymidylate synthase
D: Thymidylate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)75,2887
ポリマ-74,5512
非ポリマー7365
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-79 kcal/mol
Surface area23330 Å2
手法PISA
単位格子
Length a, b, c (Å)96.490, 96.520, 139.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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要素

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タンパク質 , 4種, 4分子 ACBD

#1: タンパク質 Thymidylate synthase / TSase


分子量: 37252.613 Da / 分子数: 1 / 変異: R175C / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TYMS, TS, OK/SW-cl.29 / プラスミド: pQE80L / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P04818, thymidylate synthase
#2: タンパク質 Thymidylate synthase / TSase


分子量: 37298.637 Da / 分子数: 1 / 変異: R175C / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TYMS, TS, OK/SW-cl.29 / プラスミド: pQE80L / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P04818, thymidylate synthase
#3: タンパク質 Thymidylate synthase / TSase


分子量: 37298.703 Da / 分子数: 1 / 変異: R175C / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TYMS, TS, OK/SW-cl.29 / プラスミド: pQE80L / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P04818, thymidylate synthase
#4: タンパク質 Thymidylate synthase / TSase


分子量: 37252.613 Da / 分子数: 1 / 変異: R175C / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TYMS, TS, OK/SW-cl.29 / プラスミド: pQE80L / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P04818, thymidylate synthase

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非ポリマー , 4種, 486分子

#5: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 6 / 由来タイプ: 合成 / : SO4
#6: 化合物
ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 4 / 由来タイプ: 合成 / : Cl
#7: 化合物 ChemComp-FFO / N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid / [6S]-5-FORMYL-TETRAHYDROFOLATE / 6S-FOLINIC ACID / l-ロイコボリン


分子量: 473.439 Da / 分子数: 2 / 由来タイプ: 合成 / : C20H23N7O7
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 474 / 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: 2.21 Å3/Da / 溶媒含有率: 44.48 %
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: 8.3
詳細: 25 % saturated ammonium sulfate, 20 mM beta-mercaptoethanol and 0.1 M TRIS, pH 8.3

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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: ESRF / ビームライン: ID23-2 / 波長: 0.8726 Å
検出器タイプ: MARMOSAIC 225 mm CCD / 検出器: CCD / 日付: 2011年6月11日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.8726 Å / 相対比: 1
反射解像度: 2.25→38.35 Å / Num. obs: 57746 / % possible obs: 93 % / Observed criterion σ(I): 2 / 冗長度: 3.7 % / Biso Wilson estimate: 39.99 Å2 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.043 / Rrim(I) all: 0.085 / Net I/σ(I): 10
反射 シェル解像度: 2.25→2.37 Å / 冗長度: 3.6 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 8475 / Rpim(I) all: 0.179 / Rrim(I) all: 0.349 / % possible all: 94.7

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解析

ソフトウェア
名称バージョン分類
REFMAC5.8.0238精密化
MOSFLMデータ削減
SCALAデータスケーリング
MOLREP位相決定
精密化構造決定の手法: 分子置換
開始モデル: 1HVY
解像度: 2.25→36.7 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.924 / SU B: 14.456 / SU ML: 0.178 / 交差検証法: THROUGHOUT / ESU R: 0.337 / ESU R Free: 0.248
Rfactor反射数%反射Selection details
Rfree0.25072 2917 5.1 %RANDOM
Rwork0.18326 ---
obs0.18662 54740 92.53 %-
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: 1.2 Å
原子変位パラメータBiso mean: 46.493 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.03 Å2
精密化ステップサイクル: LAST / 解像度: 2.25→36.7 Å
タンパク質核酸リガンド溶媒全体
原子数9146 0 102 474 9722
拘束条件
Refine-IDタイプDev idealDev ideal target
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0129484
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8481.63812859
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5151144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.50221.811508
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.399151509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1571564
X-RAY DIFFRACTIONr_chiral_restr0.1340.21186
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027356
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.772.294600
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.9063.4165736
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2852.4464884
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.13630.30813853
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS精密化 シェル解像度: 2.25→2.308 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.533 229 -
Rwork0.492 4019 -
obs--93.51 %
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)
10.82520.04671.77540.17470.50354.9610.1504-0.27560.037-0.0350.1118-0.06770.0906-0.4345-0.26220.28830.01110.07360.27430.04850.2392-11.87282.013240.7344
29.24745.61952.963.45511.76980.9713-0.0084-0.15230.2327-0.0418-0.00950.23510.0484-0.11680.01790.3441-0.1208-0.05070.20460.14510.2799-17.5361-4.095528.0982
30.34210.382-0.35690.8852-1.64693.79030.32940.299-0.13960.0660.16580.08440.44530.1861-0.49530.56550.3343-0.30810.4055-0.19750.2195-10.5577-6.99915.8183
40.21570.2862-0.47710.7824-0.66042.35170.14190.0194-0.03440.30640.160.1320.0746-0.2753-0.30180.37090.0108-0.02410.17540.05080.2837-8.8226.937434.08
52.33432.3776-1.67762.4763-1.61942.67070.01570.0741-0.1950.13580.1231-0.2347-0.010.1131-0.13880.30690.049-0.08160.1747-0.04530.27966.78514.299734.5461
60.4848-0.9578-0.18942.10840.08665.26320.01360.0562-0.00080.02550.0258-0.20810.15540.4196-0.03940.14350.0642-0.0540.2358-0.08740.345214.96754.45425.2382
72.90080.00210.73770.0766-0.84939.7066-0.30210.1415-0.0434-0.02710.0156-0.0260.27090.00680.28660.23720.0077-0.00760.2155-0.06920.240612.3325-0.480411.2227
81.4312-0.6809-1.29822.31161.7892.78030.17280.1691-0.09050.10220.1883-0.1243-0.29320.14-0.36110.1905-0.02470.00730.2493-0.07960.292812.41113.140116.0749
92.37010.4165-3.18870.2184-0.75474.57090.31590.02410.09310.1848-0.1465-0.028-0.65470.1924-0.16940.2506-0.20020.16970.2045-0.12620.424914.839521.540819.2778
101.0072-0.0736-0.39865.43523.06051.862-0.0548-0.07780.0447-0.14930.1678-0.1532-0.14070.1253-0.1130.489-0.01510.04710.0662-0.04570.26292.454728.83432.3533
110.4131-1.7903-0.487710.45351.0831.45280.06210.11980.06120.2263-0.1278-0.1508-0.1527-0.03030.06570.27310.06610.05290.29480.04590.2729-3.957726.438427.28
123.243-3.5149-2.54316.20115.92516.19530.1110.13310.1871-0.28180.0127-0.171-0.31640.095-0.12370.2615-0.04020.07520.30720.06280.20150.900216.621714.7887
133.4355-6.1725-3.860211.13027.06484.87660.03390.0004-0.293-0.0912-0.01120.4118-0.1434-0.2258-0.02270.1383-0.02650.06070.31710.01430.3575.677710.039312.2465
140.48180.81440.09731.40070.1450.23750.0776-0.022-0.06090.0543-0.0463-0.0934-0.0099-0.0493-0.03130.29660.02880.02110.1995-0.01760.2734-4.740714.005129.0702
151.39910.70251.16031.88611.36861.38960.05920.14840.00760.31260.0633-0.15160.12910.1083-0.12250.33070.0172-0.01240.1803-0.01480.25761.806413.925136.5591
161.01740.2250.09170.952-0.64750.50250.02110.010.1305-0.05390.00880.08320.0474-0.0032-0.02990.33290.02460.00420.1683-0.01280.2808-8.208110.724131.1511
170.9803-0.6542-0.60091.4051-2.16657.69230.1258-0.0473-0.0704-0.13580.14160.19810.3244-0.0629-0.26730.29580.0119-0.01120.14870.00780.2685-8.3787-9.171331.1639
181.93422.4343-0.0294.95480.96440.53170.121-0.42220.17920.6335-0.08740.15040.23010.2476-0.03360.44020.004-0.14020.2228-0.03730.13363.79919.171546.1257
191.61280.0812-2.15717.33441.1793.11160.1527-0.03310.05420.0765-0.0316-0.2659-0.19290.0459-0.12120.2162-0.027-0.04520.1843-0.04450.25213.830819.976437.1122
200.9313-0.2018-0.52253.35010.47860.3414-0.2839-0.103-0.05780.3860.2778-0.00590.20590.11250.00610.36250.0233-0.14390.1545-0.00040.20184.6308-0.310840.9698
212.81293.7645-3.70645.1528-5.14915.1975-0.2903-0.1089-0.0951-0.4158-0.0033-0.24490.4271-0.12480.29360.28080.01430.14230.3465-0.02770.2376-29.112110.107830.1193
223.8903-0.7568-0.84891.1813-0.03240.23570.0094-0.23730.00220.15390.01620.1446-0.0419-0.0133-0.02560.24390.06680.08770.407-0.01140.1608-23.521723.396636.7993
231.2171.7409-2.79377.0028-0.14829.69470.2745-0.3872-0.05390.4826-0.51720.066-0.55580.92720.24270.2603-0.06660.01190.24070.09070.2895-14.130937.233832.3346
240.9236-0.2532-0.84550.07660.22320.80380.14860.13260.1665-0.04390.001-0.0742-0.0793-0.2105-0.14960.2707-0.03580.04120.35090.04050.2618-23.365816.508424.7315
252.42584.3492-0.45177.8024-0.79680.1251-0.14750.05360.0397-0.30810.06540.0941-0.006-0.1390.08210.23030.23750.02420.5431-0.12960.2322-32.601525.962317.766
262.748-1.207-0.61830.66540.01060.6661-0.10850.45810.18070.1517-0.0289-0.1406-0.2178-0.39090.13740.56320.1656-0.08930.30860.01470.1431-20.832331.42567.9949
2712.100610.65961.804211.5102-0.46462.2784-0.21220.08890.0337-0.12610.0573-0.1779-0.07410.00090.15480.26510.0193-0.00640.12540.01020.2862-13.848143.034316.0865
2811.7132-9.49140.15647.6962-0.1520.13830.48080.1758-0.0075-0.3724-0.19890.042-0.18330.0783-0.28190.7195-0.27430.0090.1169-0.00080.6945-6.847743.65312.581
290.1814-0.7433-0.38885.27523.25972.0848-0.1926-0.0747-0.0253-0.32550.2158-0.0104-0.40930.0682-0.02330.75330.06390.05250.20670.00290.135-9.291827.77828.7366
300.99750.90580.73396.2953-0.27960.7202-0.14390.4093-0.17780.00510.2387-0.4316-0.16290.2801-0.09480.3421-0.03630.09690.34120.01070.148-7.820821.01453.0499
311.2696-1.8425-0.26897.6606-0.05622.28080.15640.2203-0.07410.081-0.0213-0.19370.0219-0.141-0.13520.216-0.00040.00460.2117-0.01060.2493-7.94119.439512.1812
322.43424.1823-2.89197.2247-4.99593.54050.07350.04050.06380.17950.11040.1987-0.19640.108-0.18390.2859-0.08420.12170.4185-0.02760.2654-3.525829.703916.4202
331.41871.67281.07013.55223.34933.5930.31630.1468-0.1352-0.1134-0.139-0.2657-0.355-0.3096-0.17720.33280.06520.070.16860.06050.2051-13.026815.62316.5134
340.4446-0.1495-0.20.86930.51551.54580.07780.10870.052-0.06560.086-0.133-0.1286-0.2414-0.16380.26990.06120.03410.26730.03950.2211-19.722319.050619.7384
350.4187-0.523-0.39771.13861.04171.29830.1380.07490.08620.04790.0212-0.10270.0361-0.24-0.15920.24430.10350.0740.34170.05950.2285-21.526318.444218.8511
363.52214.53571.80717.20320.17434.33480.0757-0.63580.10430.1867-0.6367-0.1733-0.092-0.63180.5610.17490.04970.12520.3373-0.07010.2193-34.309127.444933.073
372.96120.1262-0.82572.51284.46978.3307-0.5909-0.02770.26870.0256-0.28470.5360.2788-0.46160.87560.2140.0822-0.01070.4033-0.0450.1555-35.597915.725614.5435
382.0398-2.87352.96994.8813-4.40644.3891-0.17030.19690.0188-0.27690.1131-0.1428-0.13970.14070.05720.5112-0.02250.06610.518-0.04160.0802-23.422817.0091-2.0282
390.89610.01950.06180.00730.00290.0108-0.02360.23220.3383-0.0162-0.01420.0348-0.0071-0.02450.03780.14390.1327-0.08980.3894-0.04980.2503-35.997521.075611.4778
4010.27231.33660.60482.28742.90243.87360.31950.30270.3024-0.0602-0.31170.0842-0.0709-0.3622-0.00780.24840.21540.08530.2581-0.00180.2414-30.465434.217524.8644
410.49150.05151.61731.19431.22177.08190.05620.001-0.0013-0.20580.20010.1206-0.32550.0961-0.25620.19490.00260.07410.32960.05590.240922.145235.959664.2949
424.47442.036-5.30649.50893.602210.51310.1479-0.15280.2869-0.47470.21030.0886-0.53160.3706-0.35820.2366-0.06370.09610.2605-0.03160.219228.13441.898375.8103
438.452-5.0962-3.01136.03997.245911.1829-0.2237-1.5296-1.04770.02731.2536-0.0022-0.15521.424-1.02990.0298-0.05010.11540.6158-0.17190.540431.476736.683387.2239
440.98550.1397-0.4920.1259-0.26042.15530.13670.22210.0933-0.00010.1273-0.0649-0.2620.0108-0.2640.0997-0.00320.03710.4482-0.01490.254117.206332.95270.2962
453.9012.6998-2.50995.6696-1.39231.6517-0.0353-0.004-0.2112-0.2252-0.0736-0.11070.01640.03330.1090.1240.0492-0.06570.3973-0.08850.216422.838719.013167.4965
463.201-0.84871.48840.82070.71642.7750.2511-0.0612-0.07550.0567-0.061-0.0790.3645-0.2103-0.19010.2019-0.0064-0.09520.3133-0.03990.322513.603310.546578.163
470.0426-0.14960.51411.0765-1.21257.06660.02940.02460.0092-0.0152-0.0564-0.21710.24960.24930.02690.16780.0666-0.11270.2623-0.04780.292123.05339.934281.6535
482.07780.97891.54787.46431.14372.28030.07780.1179-0.17390.28910.07880.001-0.02350.1573-0.15650.2304-0.015-0.12250.2241-0.0090.223921.01649.66893.9188
490.7034-0.9524-0.19681.4608-0.25911.8425-0.0504-0.1049-0.00290.12510.26490.0141-0.1506-0.2259-0.21450.1552-0.0399-0.05680.36150.00910.2838.005315.552284.0566
507.7932-1.74583.0632.25131.53933.87970.2538-0.5177-0.4946-0.03280.1359-0.05070.1337-0.2454-0.38970.173-0.0701-0.08030.31890.09110.25847.88836.794989.999
514.2819-1.71083.45191.602-1.83163.01990.1269-0.1482-0.35480.1220.16730.15870.0216-0.2507-0.29420.0889-0.0309-0.07040.45330.03790.2712-2.36816.946377.1441
522.47451.075-0.2991.80291.96013.31120.18920.3647-0.06550.0607-0.0699-0.0784-0.0661-0.3685-0.11930.02250.0411-0.01110.46430.06450.3243-3.409628.458375.0526
534.9794-0.62814.57345.69151.88755.283-0.185-0.36990.15040.0135-0.05040.1874-0.1787-0.39490.23540.219-0.04610.00270.36190.05750.18457.396523.399989.4401
545.00720.87171.6964.8672-3.60623.8033-0.0491-0.05060.10710.0526-0.1145-0.1167-0.070.07550.16370.20930.0006-0.06270.26550.01410.24914.51219.384991.0454
551.33170.72310.33750.44820.3230.4539-0.07240.0593-0.072-0.03770.051-0.0341-0.0408-0.00070.02140.11810.0324-0.02030.38810.01550.26359.746529.228274.4704
561.43430.68410.78920.52570.86111.77850.02920.2010.02930.06540.02270.02860.09510.0889-0.05180.10130.017-0.02480.3998-0.00760.264410.982125.263969.2181
572.30770.1714-0.36091.14740.06210.7570.01450.15890.19920.03470.0393-0.1551-0.01870.198-0.05380.00360.01410.00930.464-0.01210.211529.602330.899369.0558
588.58110.481-2.28190.0317-0.07851.47830.0686-0.01240.1118-0.0191-0.01260.0128-0.084-0.1403-0.0560.2204-0.0078-0.03140.2595-0.04590.22557.830412.878258.105
596.05241.8185-0.7040.6298-0.6252.367-0.03910.4104-0.4489-0.06540.1304-0.0690.1339-0.2125-0.09130.19930.0031-0.09520.2812-0.12740.26869.683311.843663.4406
603.2240.74680.490.54470.42980.3446-0.24460.3565-0.05730.28260.0910.18970.25460.08490.15360.33850.04960.16370.4143-0.06650.181930.472823.560766.5296
616.2663.0784-1.43321.5127-0.70680.4332-0.0505-0.3162-0.2134-0.0166-0.1563-0.1059-0.0410.14550.20680.23480.0263-0.00170.25310.08290.292319.001452.158871.9423
622.06532.40890.35613.4608-0.12270.5765-0.31220.22330.0585-0.21230.23830.0092-0.32840.05790.07390.40140.04430.00090.25490.08450.12982.403748.780669.6209
633.96510.21655.22460.6729-1.998914.8683-0.56980.1001-0.0464-0.33960.2245-0.12460.3751-0.80250.34530.2978-0.22110.13960.42010.0160.2484-13.190738.511471.7328
640.2366-0.02940.39250.9295-0.68751.1004-0.19020.1821-0.03560.00610.25560.075-0.3380.0984-0.06540.3074-0.02580.02410.3460.02630.25537.403547.88379.6834
654.43742.9747-1.45834.1354-5.22168.9011-0.6597-0.31030.23220.0590.0563-0.1648-0.7475-0.39030.60350.32760.23610.01310.31130.01960.2391-2.218756.910786.968
664.18081.8084-1.17044.8873-1.30850.4856-0.14750.2052-0.00910.4560.1285-0.0143-0.0589-0.08420.0190.1810.1050.08470.494-0.04970.1159-4.375643.742597.0329
677.2191-1.4282-3.9543.38542.21942.83490.5559-0.08480.16020.1087-0.3917-0.1387-0.2183-0.1404-0.16420.18110.08950.10310.3855-0.04030.213-11.594647.67396.3814
682.69632.65532.64937.1985-1.92037.0791-0.2622-0.13620.0931-0.23440.20020.116-0.2805-0.45830.06190.11330.05150.04860.3286-0.04050.239-14.053541.619389.3846
696.0052-1.4763-9.045210.70032.198213.75510.0796-0.0125-0.20180.2495-0.22730.55650.02840.00260.14780.198-0.0717-0.10910.1837-0.09160.3757-20.201634.034386.4228
700.1605-0.437-0.33291.19380.91010.6996-0.07080.0139-0.07820.1778-0.04510.21480.115-0.02420.11590.1517-0.06830.17550.331-0.0850.4522-19.377531.460593.5753
715.2105-2.00781.85670.9803-0.81540.72140.3988-0.0837-0.241-0.0442-0.30160.12580.05490.0971-0.09730.1957-0.0750.00450.6499-0.04360.099-3.588433.42795.5641
7214.7347-4.8321-2.89563.40284.3376.92480.1779-0.0596-1.0480.1359-0.32950.33320.2706-0.54440.15150.1587-0.09640.0970.32340.01140.2244-9.772827.896899.4504
737.20241.2675-1.06491.3173-1.60081.9858-0.3502-0.2981-0.1290.21610.1256-0.1799-0.2869-0.21880.22460.3565-0.08270.09520.4309-0.01240.1051-0.88731.2756103.0044
742.9744-0.33120.93090.67551.09552.6080.3799-0.0094-0.3449-0.0164-0.0161-0.12470.0469-0.0936-0.36380.30310.0044-0.08010.26940.03380.254616.102534.193397.0956
752.47594.51271.70988.31783.11851.18090.2275-0.167-0.12390.3758-0.1418-0.27580.151-0.1133-0.08560.2013-0.020.03340.35190.02780.2367-0.818726.907888.5978
761.56441.4813-1.59381.4091-1.51641.6548-0.06030.14690.0391-0.05350.18910.03940.0415-0.2297-0.12880.11310.02420.06850.41240.1190.3368-1.280732.835287.4347
770.8653-0.42921.03380.5452-0.0512.20520.0188-0.0176-0.1062-0.01040.14340.0691-0.288-0.0151-0.16220.28410.08690.06360.3260.04530.19718.521444.237287.4215
782.79111.45832.98623.81981.8843.4558-0.54880.0746-0.03460.00370.39450.1684-0.6289-0.08110.15420.23620.13080.01780.38350.02580.2691-4.394154.499972.2854
792.3141-0.11471.69371.5222-2.05025.9842-0.163-0.41870.25630.2133-0.02210.0654-0.7129-0.06090.18510.29180.14290.0030.2202-0.06740.14445.388656.138496.298
804.88698.04-1.096415.70220.5752.5462-0.27460.14150.2722-0.43530.24530.52810.0487-0.07380.02930.16330.1005-0.00470.26310.04570.2511-11.68951.471478.6968
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 37
2X-RAY DIFFRACTION2A38 - 44
3X-RAY DIFFRACTION3A45 - 53
4X-RAY DIFFRACTION4A54 - 73
5X-RAY DIFFRACTION5A74 - 92
6X-RAY DIFFRACTION6A93 - 111
7X-RAY DIFFRACTION7A112 - 122
8X-RAY DIFFRACTION8A123 - 149
9X-RAY DIFFRACTION9A150 - 160
10X-RAY DIFFRACTION10A161 - 173
11X-RAY DIFFRACTION11A174 - 179
12X-RAY DIFFRACTION12A180 - 185
13X-RAY DIFFRACTION13A186 - 192
14X-RAY DIFFRACTION14A193 - 221
15X-RAY DIFFRACTION15A222 - 244
16X-RAY DIFFRACTION16A245 - 255
17X-RAY DIFFRACTION17A256 - 272
18X-RAY DIFFRACTION18A273 - 285
19X-RAY DIFFRACTION19A286 - 292
20X-RAY DIFFRACTION20A293 - 311
21X-RAY DIFFRACTION21B24 - 32
22X-RAY DIFFRACTION22B33 - 46
23X-RAY DIFFRACTION23B47 - 53
24X-RAY DIFFRACTION24B54 - 73
25X-RAY DIFFRACTION25B74 - 83
26X-RAY DIFFRACTION26B84 - 109
27X-RAY DIFFRACTION27B110 - 119
28X-RAY DIFFRACTION28B120 - 128
29X-RAY DIFFRACTION29B129 - 143
30X-RAY DIFFRACTION30B144 - 172
31X-RAY DIFFRACTION31B173 - 180
32X-RAY DIFFRACTION32B181 - 192
33X-RAY DIFFRACTION33B193 - 204
34X-RAY DIFFRACTION34B205 - 231
35X-RAY DIFFRACTION35B232 - 262
36X-RAY DIFFRACTION36B263 - 272
37X-RAY DIFFRACTION37B273 - 282
38X-RAY DIFFRACTION38B283 - 292
39X-RAY DIFFRACTION39B293 - 304
40X-RAY DIFFRACTION40B305 - 312
41X-RAY DIFFRACTION41C24 - 37
42X-RAY DIFFRACTION42C38 - 43
43X-RAY DIFFRACTION43C44 - 53
44X-RAY DIFFRACTION44C54 - 73
45X-RAY DIFFRACTION45C74 - 87
46X-RAY DIFFRACTION46C88 - 99
47X-RAY DIFFRACTION47C100 - 116
48X-RAY DIFFRACTION48C117 - 130
49X-RAY DIFFRACTION49C131 - 143
50X-RAY DIFFRACTION50C144 - 152
51X-RAY DIFFRACTION51C153 - 171
52X-RAY DIFFRACTION52C172 - 179
53X-RAY DIFFRACTION53C180 - 185
54X-RAY DIFFRACTION54C186 - 194
55X-RAY DIFFRACTION55C195 - 221
56X-RAY DIFFRACTION56C222 - 254
57X-RAY DIFFRACTION57C255 - 279
58X-RAY DIFFRACTION58C280 - 285
59X-RAY DIFFRACTION59C286 - 299
60X-RAY DIFFRACTION60C300 - 312
61X-RAY DIFFRACTION61D23 - 28
62X-RAY DIFFRACTION62D29 - 46
63X-RAY DIFFRACTION63D47 - 53
64X-RAY DIFFRACTION64D54 - 74
65X-RAY DIFFRACTION65D75 - 83
66X-RAY DIFFRACTION66D84 - 98
67X-RAY DIFFRACTION67D99 - 108
68X-RAY DIFFRACTION68D109 - 114
69X-RAY DIFFRACTION69D115 - 122
70X-RAY DIFFRACTION70D123 - 128
71X-RAY DIFFRACTION71D129 - 143
72X-RAY DIFFRACTION72D144 - 149
73X-RAY DIFFRACTION73D150 - 162
74X-RAY DIFFRACTION74D163 - 179
75X-RAY DIFFRACTION75D180 - 185
76X-RAY DIFFRACTION76D186 - 201
77X-RAY DIFFRACTION77D202 - 255
78X-RAY DIFFRACTION78D256 - 274
79X-RAY DIFFRACTION79D275 - 306
80X-RAY DIFFRACTION80D307 - 312

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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