[日本語] English
- PDB-6qxs: Crystal structure of Enteroccocus faecalis thymidylate synthase (... -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 6qxs
タイトルCrystal structure of Enteroccocus faecalis thymidylate synthase (EfTS) in complex with FdUMP
要素(Thymidylate synthase) x 2
キーワードTRANSFERASE (転移酵素) / Enteroccocus faecalis thymidylate synthase / EfTS / folate pathway (葉酸) / inhibitor (酵素阻害剤) / FdUMP
機能・相同性
機能・相同性情報


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / メチル化 / 細胞質
類似検索 - 分子機能
Thymidylate Synthase; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / 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 / 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE / Thymidylate synthase
類似検索 - 構成要素
生物種Enterococcus faecalis (乳酸球菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.88 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 Comparison ofEnterococcus faecalisand Human Thymidylate Synthase Complexes with the Substrate dUMP and Its Analogue FdUMP Provides Hints about Enzyme Conformational Variabilities.
著者: Pozzi, C. / Ferrari, S. / Luciani, R. / Tassone, G. / Costi, M.P. / Mangani, S.
履歴
登録2019年3月7日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02019年4月10日Provider: repository / タイプ: Initial release
改定 1.12019年7月10日Group: Data collection / カテゴリ: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
改定 2.02019年11月20日Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
カテゴリ: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
改定 2.12024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

-
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

-
集合体

登録構造単位
A: Thymidylate synthase
B: Thymidylate synthase
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)147,41110
ポリマ-145,6204
非ポリマー1,7916
5,891327
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)73,7445
ポリマ-72,8482
非ポリマー8963
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-33 kcal/mol
Surface area24590 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)73,6685
ポリマ-72,7722
非ポリマー8963
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-39 kcal/mol
Surface area24390 Å2
手法PISA
単位格子
Length a, b, c (Å)72.040, 94.840, 97.000
Angle α, β, γ (deg.)90.00, 94.01, 90.00
Int Tables number4
Space group name H-MP1211

-
要素

-
タンパク質 , 2種, 4分子 ABCD

#1: タンパク質 Thymidylate synthase / / TSase


分子量: 36462.094 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Enterococcus faecalis (strain ATCC 700802 / V583) (乳酸球菌)
: ATCC 700802 / V583 / 遺伝子: thyA, EF_1576 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q834R3, thymidylate synthase
#2: タンパク質 Thymidylate synthase / / TSase


分子量: 36385.977 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Enterococcus faecalis (乳酸球菌) / : ATCC 700802 / V583 / 遺伝子: thyA, EF_1576 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q834R3, thymidylate synthase

-
非ポリマー , 4種, 333分子

#3: 化合物 ChemComp-UFP / 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE / FdUMP / Fluorodeoxyuridylate


タイプ: DNA linking / 分子量: 326.172 Da / 分子数: 2 / 由来タイプ: 合成 / : C9H12FN2O8P / コメント: 阻害剤*YM
#4: 化合物 ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン / 硫酸塩


分子量: 96.063 Da / 分子数: 2 / 由来タイプ: 合成 / : SO4
#5: 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
#6: 水 ChemComp-HOH / water /


分子量: 18.015 Da / 分子数: 327 / 由来タイプ: 天然 / : H2O

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 2.27 Å3/Da / 溶媒含有率: 45.81 %
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: 7.5 / 詳細: 2.2-2.5 M ammonium sulfate and 0.1 M HEPES, pH 7.5

-
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: Diamond / ビームライン: I24 / 波長: 0.96861 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2017年2月16日
放射モノクロメーター: Si(111) / 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: 0.96861 Å / 相対比: 1
反射解像度: 2.88→96.76 Å / Num. obs: 28081 / % possible obs: 95.1 % / Observed criterion σ(I): 2 / 冗長度: 2.2 % / Biso Wilson estimate: 30.71 Å2 / CC1/2: 0.956 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.123 / Rrim(I) all: 0.198 / Net I/σ(I): 4.2
反射 シェル解像度: 2.88→3.04 Å / 冗長度: 2.2 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 2 / Num. unique obs: 4058 / CC1/2: 0.845 / Rpim(I) all: 0.289 / Rrim(I) all: 0.466 / % possible all: 94.7

-
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: 3UWL
解像度: 2.88→96.76 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.867 / SU B: 40.085 / SU ML: 0.384 / 交差検証法: THROUGHOUT / ESU R Free: 0.463
Rfactor反射数%反射Selection details
Rfree0.25169 1350 4.8 %RANDOM
Rwork0.19992 ---
obs0.20251 26635 94.42 %-
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: 38.774 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.16 Å2
2--0.11 Å20 Å2
3----0.08 Å2
Refine analyzeLuzzati coordinate error obs: 0.344 Å
精密化ステップサイクル: LAST / 解像度: 2.88→96.76 Å
タンパク質核酸リガンド溶媒全体
原子数9670 0 120 327 10117
拘束条件
Refine-IDタイプDev idealDev ideal target
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01210064
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.6413681
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.83351208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.55722.724547
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.12151553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3511549
X-RAY DIFFRACTIONr_chiral_restr0.130.21263
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027910
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_it1.7742.2184856
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.0433.3186056
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8952.2945208
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.94228.61415014
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: 2.88→2.955 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.296 119 -
Rwork0.291 1942 -
obs--95.2 %
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)
12.4482-3.963-0.49456.89271.92062.7350.2127-0.0868-0.0913-0.43590.2265-0.0327-0.22750.2274-0.43920.1453-0.0333-0.0060.1203-0.03540.206216.42824.83239.0033
23.07683.08053.23669.6736-0.23125.2354-0.1411-0.025-0.1022-0.13670.2037-0.165-0.1585-0.1531-0.06260.10410.02690.02730.1179-0.04050.183720.0377-12.14827.0328
30.26140.00290.17610.13280.05340.1395-0.13580.1335-0.11260.05990.12890.1906-0.07980.13450.00690.1980.00850.10740.19750.10940.344419.889-0.802915.2242
41.0462-0.147-0.63950.81721.9624.7945-0.4738-0.14480.1227-0.168-0.07380.2585-0.2672-0.14750.54750.29140.1176-0.09960.12660.07630.28216.80527.501222.9783
50.6333-1.61830.1995.72-0.45710.0642-0.09790.1501-0.02020.27550.1121-0.208-0.02780.0639-0.01420.13530.0050.00540.2424-0.00990.159910.3918-0.758435.3728
61.9549-2.16161.83123.446-2.75692.22330.32210.0481-0.1830.028-0.09810.29370.03590.0854-0.2240.1934-0.00010.03220.25990.02490.19135.831-5.593638.5961
74.37910.0741-1.33260.33850.1270.5089-0.11590.2919-0.60930.01080.0201-0.1442-0.0505-0.08170.09570.26180.00530.05680.0778-0.04340.19256.1654-18.130433.9708
82.1641.45180.86121.38460.69140.38680.4049-0.03740.1170.1306-0.39440.06160.1514-0.1162-0.01050.25550.1377-0.05910.33640.01860.2408-0.5397-25.889436.6333
94.8833-3.8741.15314.10521.55876.21350.0473-0.0915-0.17430.0786-0.03870.12780.2832-0.2873-0.00850.0278-0.0376-0.02490.1380.08290.2947-1.1672-15.077741.7625
100.3529-0.67060.2933.4524-4.55327.57720.0014-0.22410.0062-0.1370.13690.07230.25470.3438-0.13840.0766-0.0355-0.0130.22570.01570.214512.5262-13.672539.6794
110.0962-0.1907-0.5620.37961.11263.3896-0.01840.03970.01060.0444-0.0903-0.02740.154-0.23920.10870.0818-0.00850.02290.19430.00690.287325.6816-3.57942.286
120.1599-0.31570.08820.6542-0.17730.0514-0.051-0.0311-0.03890.15520.06480.0169-0.03830.0042-0.01370.1906-0.02340.02910.1963-0.00920.24628.877-1.316834.7762
130.2502-0.4904-0.48644.49660.68250.96950.0018-0.03280.0223-0.05730.06660.2245-0.0320.0682-0.06840.2202-0.01070.02890.15440.0470.162323.8525-0.415129.1053
140.2728-0.5379-0.11831.25850.80181.83050.0786-0.0873-0.0691-0.17440.1726-0.0018-0.1692-0.067-0.25120.1239-0.01820.02430.2106-0.00540.219219.58113.590623.7842
153.61131.17520.69112.27682.90523.9259-0.4516-0.2043-0.02480.04110.16150.21630.17890.30770.290.22220.0366-0.00010.16330.0050.170315.68468.000331.6752
161.0091.23191.79291.63092.01333.533-0.0745-0.12620.1006-0.1465-0.11570.1441-0.1548-0.36640.19020.15720.00640.01660.2107-0.03520.211718.94533.85422.4857
176.2016-2.75763.29411.7398-2.53728.9009-0.03170.2281-0.01510.04370.0820.07910.0071-0.1546-0.05030.1131-0.01090.00410.13540.00720.14296.5927-1.86937.3833
180.61160.6710.50136.52535.61674.8551-0.10.010.1266-0.4788-0.00230.1486-0.4483-0.01510.10220.24350.0262-0.01330.09860.05740.14516.11912.043914.1558
195.53322.77640.35061.40070.16510.03960.1807-0.41020.10760.0593-0.20360.05750.057-0.01580.02280.13770.0430.03010.251-0.020.13848.682510.970841.0549
203.1494-1.3037-0.21670.60990.23710.32610.01650.145-0.05140.0537-0.27130.13760.11-0.45530.25480.1844-0.16890.03760.6683-0.32380.27152.1126.907522.2388
211.8334-1.6054-0.95072.34463.06935.82570.09970.33460.25330.0011-0.2486-0.10630.1347-0.07250.1490.1144-0.05130.03120.23890.00990.169639.32313.260112.8394
220.4439-0.78590.87222.7054-0.70414.6762-0.1234-0.10530.0375-0.03380.07410.1541-0.1326-0.05550.04930.16180.0407-0.03190.15860.0080.162736.636820.529126.4367
230.49740.3556-0.00140.5910.02950.02120.00380.00070.0036-0.0222-0.04840.02140.02070.03520.04460.1544-0.01560.02930.24860.01470.164743.75495.44517.6239
241.01230.54790.54242.79411.57520.95090.06810.0396-0.05740.2909-0.0383-0.08950.1751-0.0202-0.02990.1589-0.00580.06150.20840.01830.192254.0779-6.393128.7414
252.4781.30681.26550.81231.34244.3789-0.0005-0.17910.06220.0095-0.09540.04080.0988-0.14410.09590.2178-0.0031-0.00170.16240.03450.144952.82123.598737.7026
260.17810.60790.31062.21191.64323.04120.0184-0.0373-0.05360.0675-0.0965-0.14810.02670.04770.07810.0987-0.019-0.00920.18180.01810.169658.05145.863347.1128
276.0992-1.4589-0.82317.7223.24211.38290.08130.25030.3678-0.0105-0.0285-0.03220.0089-0.0616-0.05280.1403-0.0335-0.01030.16580.03890.150555.883917.102437.4753
289.1801-3.9554-2.68226.4781-2.19343.1336-0.26010.0810.38840.47210.0609-0.6164-0.1772-0.08350.19910.0961-0.0903-0.03070.1939-0.0210.190664.177112.940538.3622
291.7906-0.324-2.39440.09890.7456.15420.02210.1479-0.11430.0160.021-0.03640.05910.0155-0.04310.0735-0.0008-0.05230.1859-0.05730.238962.1222-3.969339.0015
300.49751.2094-0.15772.993-0.39110.05170.1124-0.05810.03430.1662-0.10920.0577-0.02360.0051-0.00320.2193-0.0120.04620.1612-0.01110.20843.2587-9.57934.5789
310.084-0.03480.67380.2974-0.12236.5307-0.0242-0.01910.0185-0.0318-0.0909-0.02630.1485-0.13130.11510.15460.01290.01090.1488-0.00680.161835.7149-17.990928.0151
320.6208-0.3746-0.32990.22760.20040.1792-0.0664-0.0026-0.16310.0425-0.020.09030.0285-0.02450.08630.1918-0.0527-0.00150.1963-0.03880.223431.6468-10.345527.0438
332.68131.12984.50721.94340.73048.69830.04470.1216-0.13010.42170.0544-0.0155-0.3350.0746-0.09910.18310.0355-0.0390.1789-0.04460.197139.3148-0.4731.4476
340.19440.1045-0.12150.1639-0.08490.08720.0959-0.0044-0.0060.0474-0.0630.0742-0.03970.0273-0.03290.18530.02640.01720.1903-0.02540.228238.9286-2.864617.3884
354.3524-5.52832.06637.0245-2.6250.98290.05190.15080.251-0.0539-0.188-0.33790.03570.06580.13610.15630.00970.01460.1508-0.0390.218438.5936-14.10728.9169
361.46632.61120.91555.0471.79490.6399-0.1491-0.03890.0296-0.45910.1480.0066-0.17130.06790.00110.2578-0.022-0.00760.17940.00670.169537.04457.147220.8598
372.0956-2.6273-2.54784.0673.31223.12480.1004-0.104-0.0243-0.0572-0.1203-0.1514-0.13990.08150.01990.1329-0.0574-0.02030.20530.0070.155148.346618.961616.6746
380.67160.97290.2211.6770.53260.2535-0.08010.1645-0.1603-0.06340.184-0.34230.05310.024-0.1040.17270.02110.07910.1837-0.04220.221849.1825-8.930110.0359
391.9099-0.6692-0.29920.6854-1.58486.4028-0.01280.0984-0.13110.0527-0.08110.0161-0.16660.2070.0940.1140.01110.01360.1821-0.01640.136254.7388-10.012813.2487
401.41480.22160.20830.04330.03610.0325-0.06560.02310.1511-0.02710.02710.0477-0.01210.00920.03840.1771-0.0079-0.00080.1560.00290.178953.802610.363216.9676
412.76622.9325-1.06343.1602-1.19710.5650.05980.10460.05020.11730.19890.1388-0.0738-0.0802-0.25870.08320.07910.04930.3367-0.00610.360215.397-44.732937.3443
421.633-0.4058-0.45440.74110.2830.199-0.0925-0.0408-0.09360.07190.14290.00130.02830.0002-0.05040.1572-0.0112-0.0070.18180.09540.180813.8988-47.513827.7651
430.06010.05730.05660.05630.05560.0549-0.06510.033-0.0217-0.0780.0546-0.0004-0.07720.04130.01050.1359-0.0179-0.03130.23330.12260.248710.5256-41.47817.6326
444.95562.53951.5452.73894.58610.5087-0.0167-0.13170.1307-0.11720.02640.0657-0.27460.1968-0.00970.16820.0286-0.0520.10440.04120.18645.2838-38.25711.039
451.0361.69322.11053.24223.86284.71580.03310.16020.03250.33250.05150.01470.35710.1943-0.08460.214-0.0516-0.09240.2044-0.03610.29436.9598-24.58569.8214
460.058-0.22940.22477.1877-8.06099.067-0.02670.09020.02570.1318-0.203-0.1886-0.15060.15350.22980.11580.025-0.04850.212-0.06350.24871.7058-18.03576.9177
4717.95185.6811-8.39081.8014-2.65543.9220.2299-0.23810.27490.0625-0.09570.0908-0.10610.1101-0.13420.06220.0326-0.10380.13810.05730.3440.1203-28.84365.1064
480.1273-0.0346-0.99530.0240.2988.75340.0538-0.0154-0.01030.00140.05930.0169-0.03140.1589-0.1130.17390.0241-0.10360.20510.09120.29475.4635-29.502-2.1096
491.76461.4218-1.53671.146-1.23541.3815-0.0043-0.1112-0.0075-0.0005-0.08650.00460.06030.19460.09080.07580.13690.09520.26890.12210.278515.8312-31.90327.7858
507.34365.4958-2.96254.7998-1.59941.7530.05650.1194-0.1417-0.0713-0.098-0.1259-0.146-0.210.04150.18390.0141-0.02410.14210.04580.139527.9728-36.50055.6348
511.26640.96320.10296.6613-0.87520.16240.0404-0.01690.0868-0.0672-0.1239-0.370.02890.01250.08340.1836-0.02750.0450.1637-0.02180.186828.9641-47.43134.5627
520.76990.050.81090.01590.05780.86110.1175-0.03710.001-0.006-0.07430.00790.1261-0.0671-0.04310.10730.04040.05330.2757-0.00940.224531.6249-43.603413.5116
532.73771.51990.77625.63582.92321.5164-0.1303-0.22860.06710.06670.05160.16650.03450.03740.07870.2415-0.00810.10820.18120.07560.114222.6724-36.417117.9551
540.8129-0.1484-0.7977.7308-1.75021.4744-0.068-0.1325-0.1082-0.30750.07470.0820.10980.2123-0.00670.14060.01320.01450.1455-0.01760.163729.3448-56.646716.1066
550.5806-0.2185-0.50852.4006-1.00391.06310.21070.11130.2181-0.3221-0.0445-0.1233-0.0518-0.1115-0.16620.13750.01770.02210.2627-0.00570.208118.3031-46.876123.1959
564.7403-0.09512.29150.0197-0.05411.11150.18070.3635-0.12820.0334-0.06790.06940.07710.1917-0.11280.1983-0.06980.09790.2443-0.07850.337717.2521-52.719213.6916
570.5894-0.7088-0.0411.91560.54890.4332-0.006-0.03260.04870.13790.1813-0.00620.18880.0486-0.17520.1863-0.0202-0.04020.19860.02060.252220.6887-51.910220.2925
580.2303-0.3993-0.2446.18053.59092.245-0.06010.21830.12340.40180.0173-0.07490.1318-0.05460.04280.1217-0.0127-0.03760.25730.07350.23145.3118-44.395636.0545
591.42-0.8886-1.14650.72091.19642.3547-0.03220.4864-0.18530.0496-0.25050.14920.0364-0.25680.28270.1111-0.0734-0.03540.33450.03020.153210.3781-57.23389.1889
601.0724-0.1011-0.86320.05670.1270.75890.08230.3844-0.0001-0.0472-0.13160.0944-0.0864-0.4620.04920.06060.0409-0.11820.5202-0.06010.26382.5276-50.764220.6599
610.7718-0.312-0.05560.51131.62786.69690.0291-0.1685-0.11820.05330.11050.01560.26740.1999-0.13960.19960.0258-0.01110.15350.01570.160137.8821-58.429435.7007
621.82412.7526-1.09916.8696-2.8041.63380.06060.2646-0.32210.3342-0.11190.099-0.58810.09340.05130.4416-0.0524-0.03270.2359-0.08350.249936.4694-64.958721.7592
630.90010.0141-0.59161.93141.75141.9962-0.1332-0.0163-0.03580.1075-0.01460.13720.1874-0.02310.14780.20890.0258-0.0190.1630.04560.16236.6791-53.526729.3376
641.30950.7060.15172.0570.80780.33280.10050.0187-0.0616-0.024-0.0313-0.2065-0.0255-0.0307-0.06920.14160.0038-0.03010.27330.02040.198249.9046-46.487935.5044
650.3045-0.9649-0.59243.3982.03741.22820.07490.0343-0.0119-0.046-0.0238-0.1146-0.0597-0.0223-0.05110.1776-0.0033-0.03540.21390.00910.189254.075-38.283322.7369
660.34270.4021-1.03921.63560.19544.94450.04920.04360.02750.10070.00770.1002-0.171-0.1275-0.05690.17060.00430.01850.15480.00080.144955.9418-47.861710.3742
670.82181.2856-0.28282.5443-2.36817.07310.2075-0.15160.13980.3183-0.28430.1925-0.07290.17120.07690.10030.04780.02390.1935-0.01030.201662.5454-52.20434.6426
686.0583-5.4418-0.132910.09232.32240.94130.2890.5057-0.0508-0.0503-0.258-0.0340.0920.1057-0.0310.14850.0740.05070.21880.05580.150759.2699-61.865913.8299
692.91691.1256-0.019.6586-5.02752.73810.0896-0.26530.0197-0.4277-0.03490.12210.2544-0.0166-0.05470.07980.0449-0.00530.2409-0.01440.134765.6991-54.690714.5839
702.22931.33781.84348.48545.31233.8278-0.06370.16120.2545-0.03550.0241-0.1661-0.04480.10310.03960.11490.02330.02490.21450.0310.156165.7565-42.082815.1331
711.1264-2.42482.67425.31-5.82416.40350.0588-0.01380.0138-0.2944-0.0928-0.05450.27410.04150.0340.28040.14150.09940.2121-0.02090.135458.8257-37.64049.5271
722.57081.06130.10310.43910.04210.00450.0619-0.06010.05540.0332-0.04940.0286-0.00410.0017-0.01250.26570.0192-0.01390.1649-0.00220.161842.8983-34.86917.1485
730.05260.0764-0.61530.6428-0.97687.66570.01230.0117-0.00270.0328-0.03820.1043-0.04250.10050.02590.1396-0.0064-0.00610.1526-0.01320.175836.8796-26.784519.0545
740.96470.54960.460.31420.25980.2267-0.07110.04560.0776-0.0290.03470.039-0.0593-0.01340.03640.20620.06850.01120.19280.00610.180830.8468-32.772823.2767
750.18430.52130.67172.88222.73433.0970.0020.09460.04290.2399-0.18880.20130.36560.15240.18680.36070.04280.02910.2390.00850.136539.9389-43.094116.6348
760.0090.0787-0.04410.7712-0.41820.23030.00490.00770.00870.01360.0012-0.0104-0.0037-0.0241-0.00610.19930.00480.00020.1859-0.01560.203137.6573-42.170431.7428
772.80951.3906-0.53034.55222.62832.27660.0201-0.2339-0.05-0.14030.1044-0.2501-0.08750.1711-0.12450.22380.0176-0.00960.1501-0.04920.18936.152-34.333138.5138
782.3297-1.4337-0.2831.7885-1.26492.503-0.30910.1535-0.10650.3084-0.0515-0.0706-0.0610.12870.36050.19250.0370.00810.24450.05280.238442.8154-59.859427.318
790.1487-0.2752-0.27720.63150.77181.0701-0.1022-0.06160.03870.09230.0693-0.0233-0.02630.05110.03290.17490.0125-0.05360.22730.01060.178348.4666-39.685139.6785
802.26462.85282.68883.62553.4083.2063-0.24170.09110.02-0.27260.17470.0876-0.27150.14840.06710.20390.04980.03840.21940.0250.197352.7669-55.041433.5393
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 15
2X-RAY DIFFRACTION2A16 - 21
3X-RAY DIFFRACTION3A22 - 40
4X-RAY DIFFRACTION4A41 - 56
5X-RAY DIFFRACTION5A57 - 63
6X-RAY DIFFRACTION6A64 - 80
7X-RAY DIFFRACTION7A81 - 90
8X-RAY DIFFRACTION8A91 - 120
9X-RAY DIFFRACTION9A121 - 135
10X-RAY DIFFRACTION10A136 - 145
11X-RAY DIFFRACTION11A146 - 169
12X-RAY DIFFRACTION12A170 - 193
13X-RAY DIFFRACTION13A194 - 204
14X-RAY DIFFRACTION14A205 - 227
15X-RAY DIFFRACTION15A228 - 241
16X-RAY DIFFRACTION16A242 - 262
17X-RAY DIFFRACTION17A263 - 269
18X-RAY DIFFRACTION18A270 - 280
19X-RAY DIFFRACTION19A281 - 296
20X-RAY DIFFRACTION20A297 - 313
21X-RAY DIFFRACTION21B1 - 12
22X-RAY DIFFRACTION22B13 - 21
23X-RAY DIFFRACTION23B22 - 60
24X-RAY DIFFRACTION24B61 - 81
25X-RAY DIFFRACTION25B82 - 88
26X-RAY DIFFRACTION26B89 - 101
27X-RAY DIFFRACTION27B102 - 110
28X-RAY DIFFRACTION28B111 - 120
29X-RAY DIFFRACTION29B121 - 137
30X-RAY DIFFRACTION30B138 - 154
31X-RAY DIFFRACTION31B155 - 170
32X-RAY DIFFRACTION32B171 - 191
33X-RAY DIFFRACTION33B192 - 200
34X-RAY DIFFRACTION34B201 - 241
35X-RAY DIFFRACTION35B242 - 248
36X-RAY DIFFRACTION36B249 - 260
37X-RAY DIFFRACTION37B261 - 274
38X-RAY DIFFRACTION38B275 - 292
39X-RAY DIFFRACTION39B293 - 301
40X-RAY DIFFRACTION40B302 - 315
41X-RAY DIFFRACTION41C1 - 21
42X-RAY DIFFRACTION42C22 - 53
43X-RAY DIFFRACTION43C54 - 75
44X-RAY DIFFRACTION44C76 - 81
45X-RAY DIFFRACTION45C82 - 90
46X-RAY DIFFRACTION46C91 - 120
47X-RAY DIFFRACTION47C121 - 128
48X-RAY DIFFRACTION48C129 - 137
49X-RAY DIFFRACTION49C138 - 146
50X-RAY DIFFRACTION50C147 - 157
51X-RAY DIFFRACTION51C158 - 171
52X-RAY DIFFRACTION52C172 - 190
53X-RAY DIFFRACTION53C191 - 201
54X-RAY DIFFRACTION54C202 - 206
55X-RAY DIFFRACTION55C207 - 229
56X-RAY DIFFRACTION56C230 - 240
57X-RAY DIFFRACTION57C241 - 259
58X-RAY DIFFRACTION58C260 - 275
59X-RAY DIFFRACTION59C276 - 294
60X-RAY DIFFRACTION60C295 - 313
61X-RAY DIFFRACTION61D1 - 13
62X-RAY DIFFRACTION62D14 - 21
63X-RAY DIFFRACTION63D22 - 42
64X-RAY DIFFRACTION64D43 - 59
65X-RAY DIFFRACTION65D60 - 81
66X-RAY DIFFRACTION66D82 - 93
67X-RAY DIFFRACTION67D94 - 101
68X-RAY DIFFRACTION68D102 - 113
69X-RAY DIFFRACTION69D114 - 121
70X-RAY DIFFRACTION70D122 - 131
71X-RAY DIFFRACTION71D132 - 140
72X-RAY DIFFRACTION72D141 - 152
73X-RAY DIFFRACTION73D153 - 169
74X-RAY DIFFRACTION74D170 - 188
75X-RAY DIFFRACTION75D189 - 201
76X-RAY DIFFRACTION76D202 - 240
77X-RAY DIFFRACTION77D241 - 251
78X-RAY DIFFRACTION78D252 - 269
79X-RAY DIFFRACTION79D270 - 301
80X-RAY DIFFRACTION80D302 - 315

+
万見について

-
お知らせ

-
2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

-
2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

+
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

+
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

+
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。

-
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