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- PDB-3ig2: The Crystal Structure of a Putative Phenylalanyl-tRNA synthetase ... -

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基本情報

登録情報
データベース: PDB / ID: 3ig2
タイトルThe Crystal Structure of a Putative Phenylalanyl-tRNA synthetase (PheRS) beta chain domain from Bacteroides fragilis to 2.1A
要素Phenylalanyl-tRNA synthetase beta chain
キーワードLIGASE / Phenylalanyl-tRNA / synthetase / PheRS / bacteroides / fragilis / PSI / MCSG / Structural Genomics / Midwest Center for Structural Genomics / Protein Structure Initiative / Aminoacyl-tRNA synthetase / ATP-binding / Magnesium / Metal-binding / Nucleotide-binding / Protein biosynthesis / RNA-binding / tRNA-binding
機能・相同性
機能・相同性情報


phenylalanine-tRNA ligase complex / phenylalanine-tRNA ligase / phenylalanine-tRNA ligase activity / phenylalanyl-tRNA aminoacylation / tRNA binding / magnesium ion binding / ATP binding
類似検索 - 分子機能
Phenylalanine-tRNA ligase, class IIc, beta subunit, bacterial type / Phenylalanly tRNA synthetase, tRNA-binding-domain / tRNA synthetase, B5-domain / tRNA synthetase B5 domain / B5 domain profile. / tRNA synthetase B5 domain / B3/4 domain / Ferrodoxin-fold anticodon-binding domain / Ferrodoxin-fold anticodon-binding domain superfamily / Ferredoxin-fold anticodon binding domain ...Phenylalanine-tRNA ligase, class IIc, beta subunit, bacterial type / Phenylalanly tRNA synthetase, tRNA-binding-domain / tRNA synthetase, B5-domain / tRNA synthetase B5 domain / B5 domain profile. / tRNA synthetase B5 domain / B3/4 domain / Ferrodoxin-fold anticodon-binding domain / Ferrodoxin-fold anticodon-binding domain superfamily / Ferredoxin-fold anticodon binding domain / Ferredoxin-fold anticodon binding (FDX-ACB) domain profile. / Ferredoxin-fold anticodon binding domain / Phenylalanyl tRNA synthetase beta chain, core domain / Phenylalanyl tRNA synthetase beta chain CLM domain / B3/B4 tRNA-binding domain / Phenylalanyl-tRNA synthetase-like, B3/B4 / Phenylalanine-tRNA ligase, class IIc, beta subunit / B3/4 domain / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Putative DNA-binding domain superfamily / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Nucleic acid-binding, OB-fold / 2-Layer Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
Phenylalanine--tRNA ligase beta subunit / Phenylalanine--tRNA ligase beta subunit
類似検索 - 構成要素
生物種Bacteroides fragilis (バクテリア)
手法X線回折 / シンクロトロン / 解像度: 2.09 Å
データ登録者Stein, A.J. / Sather, A. / Hendricks, R. / Keigher, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
引用ジャーナル: To be Published
タイトル: The Crystal Structure of a Putative Phenylalanyl-tRNA synthetase (PheRS) beta chain domain from Bacteroides fragilis to 2.1A
著者: Stein, A.J. / Sather, A. / Hendricks, R. / Keigher, L. / Joachimiak, A.
履歴
登録2009年7月27日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02009年9月1日Provider: repository / タイプ: Initial release
改定 1.12011年7月13日Group: Advisory / Version format compliance
改定 1.22017年11月1日Group: Refinement description / カテゴリ: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
改定 1.32024年10月30日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Phenylalanyl-tRNA synthetase beta chain
B: Phenylalanyl-tRNA synthetase beta chain
C: Phenylalanyl-tRNA synthetase beta chain
D: Phenylalanyl-tRNA synthetase beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)96,8755
ポリマ－96,8504
非ポリマー241
水4,648258
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
2
A: Phenylalanyl-tRNA synthetase beta chain
D: Phenylalanyl-tRNA synthetase beta chain


分子量 (理論値)分子数
合計 (水以外)48,4252
ポリマ－48,4252
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-13 kcal/mol
Surface area18970 Å2
手法PISA
3
B: Phenylalanyl-tRNA synthetase beta chain

C: Phenylalanyl-tRNA synthetase beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)48,4503
ポリマ－48,4252
非ポリマー241
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area2230 Å2
ΔGint-18 kcal/mol
Surface area19050 Å2
手法PISA
単位格子
Length a, b, c (Å)48.496, 60.335, 78.805
Angle α, β, γ (deg.)99.040, 100.370, 105.080
Int Tables number1
Space group name H-MP1
詳細Author states that the biological unit is the same as asymmetric unit.

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要素

#1: タンパク質
Phenylalanyl-tRNA synthetase beta chain / Phenylalanine--tRNA ligase beta chain / PheRS


分子量: 24212.604 Da / 分子数: 4 / 断片: Core Domain / 由来タイプ: 組換発現
由来: (組換発現) Bacteroides fragilis (バクテリア)
株: NCTC 9343 / 遺伝子: BF2565, BF2590, pheT / プラスミド: pMCSG19 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3)
参照: UniProt: Q64T65, UniProt: Q5LC76*PLUS, phenylalanine-tRNA ligase
#2: 化合物 ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Mg
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 258 / 由来タイプ: 天然 / 式: H2O
Has protein modificationY

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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: 2.26 Å3/Da / 溶媒含有率: 45.6 %
結晶化温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 20% PEG 3350, 0.2M Magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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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: APS / ビームライン: 19-ID / 波長: 0.9794 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2009年6月15日
放射モノクロメーター: Double crystal / プロトコル: SINGLE WAVELENGTH / 散乱光タイプ: x-ray
放射波長波長: 0.9794 Å / 相対比: 1
反射解像度: 2.09→50 Å / Num. obs: 47621 / % possible obs: 98 % / 冗長度: 2.6 % / Rmerge(I) obs: 0.068 / Χ2: 3.826 / Net I/σ(I): 15.9
反射 シェル
解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.182.60.24147651.453197.3
2.18-2.262.60.19247011.589197.3
2.26-2.372.60.16647201.74197.6
2.37-2.492.60.13547831.889197.9
2.49-2.652.60.11247402.122197.9
2.65-2.852.60.09648192.805198.3
2.85-3.142.60.07147363.447198.4
3.14-3.592.60.05747924.474198.8
3.59-4.522.60.05148266.209199.1
4.52-502.60.064473912.709197.7

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解析

ソフトウェア
名称バージョン分類NB
DENZOデータ削減
SCALEPACKデータスケーリング
REFMACrefmac_5.5.0102精密化
PDB_EXTRACT3.004データ抽出
SBC-Collectデータ収集
HKL-3000データ削減
SHELX位相決定
MLPHARE位相決定
直接法位相決定
ARP/wARPモデル構築
Cootモデル構築
精密化解像度: 2.09→28.45 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.236 / WRfactor Rwork: 0.196 / SU B: 11.654 / SU ML: 0.14 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.234 / ESU R Free: 0.189 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD
詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
Rfactor反射数%反射Selection details
Rfree0.236 2416 5.1 %RANDOM
Rwork0.195 ---
obs0.197 47599 97.46 %-
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: 14.225 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.15 Å2
2--0 Å20.13 Å2
3---0.11 Å2
精密化ステップサイクル: LAST / 解像度: 2.09→28.45 Å
タンパク質核酸リガンド溶媒全体
原子数5992 0 1 258 6251
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226146
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.9518337
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1025765
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.1125.103292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.62115997
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6171518
X-RAY DIFFRACTIONr_chiral_restr0.090.2944
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024644
X-RAY DIFFRACTIONr_mcbond_it0.481.53803
X-RAY DIFFRACTIONr_mcangle_it0.86626041
X-RAY DIFFRACTIONr_scbond_it1.54732343
X-RAY DIFFRACTIONr_scangle_it2.3054.52289
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.093-2.1470.3031660.2293067360689.656
2.147-2.2060.271580.2173248350397.231
2.206-2.2690.2621750.2333153342097.31
2.269-2.3390.3081730.2343046330697.368
2.339-2.4150.2891730.2242990323797.714
2.415-2.4990.2871490.2272845306497.715
2.499-2.5930.3011540.2392783299797.998
2.593-2.6980.2491250.2162744292198.22
2.698-2.8160.2791240.222560273798.064
2.816-2.9520.2631300.2132482265998.232
2.952-3.110.2671400.22312248698.632
3.11-3.2960.245980.1932269239998.666
3.296-3.5210.2231160.1872105224698.887
3.521-3.7980.2031020.1821981210499.002
3.798-4.1530.1811090.161798192499.116
4.153-4.6310.17830.1461643174199.138
4.631-5.3240.18800.151455154699.288
5.324-6.4640.266750.2141217129999.461
6.464-8.9140.243610.199963103399.129
8.914-28.4490.21250.21252261489.088
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)
18.4814-4.35323.087424.2221-8.97299.06450.14590.00050.67960.5773-0.30160.1667-0.67920.38980.15580.2832-0.10090.01650.3349-0.09260.207912.824714.9521-51.6424
26.28390.5175-4.57595.69132.536313.27170.0156-0.5127-0.0040.4802-0.0898-0.2132-0.16050.76920.07420.2203-0.001-0.07170.36160.02620.184618.92453.7654-53.2411
39.2256.69388.50684.90565.26325.44770.07340.3868-0.53850.04020.2128-0.39580.12531.4858-0.28620.13160.02150.03460.1966-0.07830.228719.15957.0457-73.6744
43.3804-0.9054-0.58285.7965-0.73615.944-0.14860.1727-0.3658-0.42450.09210.50320.6221-0.51170.05650.19560.0042-0.03220.1796-0.02730.13728.79034.3226-78.9004
51.37121.0098-3.17741.7624-0.335311.71720.0154-0.0371-0.1615-0.1260.1512-0.329-0.0610.5441-0.16660.18760.0331-0.00120.1674-0.04430.198617.358.6641-80.9891
69.1512-6.65153.504912.7244-0.7443.48250.02370.4385-0.1417-0.0173-0.1505-0.5230.24460.56840.12680.17860.00150.01880.180.01240.147317.9883-0.7528-68.0167
75.5324-2.70720.92979.0794-3.03447.47650.1009-0.4884-0.21140.4326-0.2183-0.41110.37720.77560.11740.2169-0.0216-0.00230.28550.02540.11117.72242.8159-60.0097
822.33157.69786.61757.8243-1.230222.34520.019-0.33570.9741-0.2036-0.00930.9210.0657-2.0675-0.00970.14810.0448-0.01110.2339-0.02510.19465.541212.544-75.5175
96.1587-3.528120.31933.8563-12.810867.78740.0213-0.1593-0.0026-0.15670.29970.4680.1685-0.6564-0.3210.28930.0422-0.03090.2335-0.02640.29816.241617.0414-74.2346
106.2546-3.66690.335213.0636-3.90115.90020.1335-0.2311-0.4061-0.1406-0.25840.07070.52950.31650.12490.1277-0.02410.00430.20530.00370.083512.98820.5251-60.2152
1123.702431.2481.60241.8474-0.402710.68810.24740.4514-0.52080.17350.6546-0.30160.78440.09-0.9020.29540.10980.05780.36720.0850.738115.8041-20.5604-63.3705
120.19511.90610.792319.55948.06393.3347-0.0785-0.06580.0532-0.1064-0.26761.0711-0.0403-0.12140.34610.63370.02670.12740.4920.01520.66655.2783-14.4174-56.027
136.205-2.1785-1.33919.06865.09024.83880.1179-0.94780.03520.5317-0.04990.10090.03780.2592-0.0680.2791-0.09170.06120.3253-0.02130.13335.88513.1293-49.7398
142.6405-1.8136-0.91125.24897.647712.69120.10040.0416-0.3728-0.071-0.07920.15320.0277-0.2111-0.02120.253-0.05250.06010.2176-0.02660.1839-4.91211.4436-54.1992
1525.16766.197510.894818.866310.151234.4081-0.19121.030.4498-1.0385-0.05970.40040.2222-0.48880.25090.2170.01980.00110.1574-0.06830.22243.6616-5.4505-68.8752
1612.503-7.9977-2.276513.26680.95775.45360.11860.2168-0.0971-0.3702-0.33360.3606-0.1145-0.51330.2150.1655-0.06480.0220.2098-0.06660.1462-3.59311.4961-60.2862
177.079-5.0669-2.503410.16362.77362.05680.15120.233-0.4401-0.2506-0.33120.12070.1143-0.13950.17990.2216-0.00320.02880.16150.00630.17734.4675-2.9484-63.1069
188.85452.6313-4.67415.3339-5.399713.3342-0.28910.4211-0.8419-0.03870.06310.34290.30850.34980.2260.28050.03130.02830.2036-0.04810.268516.4092-10.1762-70.5084
1911.1162-8.9424-4.062421.36036.86356.8277-0.0313-0.1637-0.77050.2835-0.15260.70770.43680.17640.18390.1489-0.04370.01110.20950.00620.12919.4077-1.918-61.235
2040.19520.96315.468223.22661.450713.6154-0.21970.3372.9232-0.4596-0.85431.7869-0.9956-0.64911.0740.45510.1215-0.13770.2988-0.19340.51044.346413.2085-57.5502
217.49572.14464.11595.64973.344113.50020.09210.02340.10020.26160.1394-0.8526-0.29780.8474-0.23150.1475-0.0389-0.01160.1158-0.00240.230610.580221.1806-32.2129
2214.674-4.9633-7.64664.80352.33745.16070.20270.50930.4903-0.2861-0.0803-0.1037-0.2728-0.2493-0.12250.1484-0.0022-0.04630.1180.00140.0553-7.828429.12-33.8186
237.76241.5378-4.082612.4205-11.694325.9627-0.2577-0.0545-0.38930.05370.2180.71690.9411-1.1170.03960.1576-0.0370.03790.1342-0.10220.2699-18.032522.5563-25.7926
2414.916-7.9401-7.316722.177214.612815.2276-0.2147-0.4241-0.54460.8052-0.30170.88860.547-0.42390.51640.1868-0.00780.03910.16760.07420.1392-15.918824.228-19.5065
253.6745-3.782-2.98545.65843.89593.01540.13520.12350.1265-0.2515-0.18830.1342-0.1528-0.30070.05310.0741-0.0018-0.02220.1523-0.01530.1372-13.926632.2745-27.6838
265.88433.98162.55492.83552.581529.334-0.30210.7667-0.1098-0.47790.432-0.0934-0.38540.6096-0.12990.64620.1738-0.00230.2603-0.04650.1531-9.123421.355-45.061
272.86930.6581-0.44137.70393.59256.5198-0.15950.423-0.1506-0.6656-0.0615-0.0332-0.1167-0.31830.2210.1112-0.00330.01060.0984-0.00060.0887-1.214920.298-37.9514
2815.92893.1593-1.68455.9682.28987.2447-0.1095-1.4215-0.08041.2667-0.07830.08820.496-0.03990.18790.4310.1977-0.00970.2987-0.03620.067-10.091831.1507-15.2077
292.3888-0.7019-0.79823.56772.71813.11670.0509-0.24010.11310.21790.2236-0.21830.02350.0693-0.27440.11520.01350.01710.0850.03330.0752-3.656324.9593-25.0327
3033.679424.6684-1.206227.86312.20861.9603-0.07950.0957-0.1152-0.330.19920.28360.4311-0.2013-0.11980.3587-0.0665-0.09750.2370.02410.166-14.49025.7812-43.8343
310.0191-0.30260.05996.1993-1.11080.20750.061-0.00130.00410.2381-0.07550.3240.01590.00230.01450.5539-0.13110.14560.6233-0.25950.5904-10.20580.0222-36.8639
3244.2682-12.51214.97753.5365-1.40740.56390.51761.2364-1.9661-0.1579-0.34570.55210.11590.1202-0.17191.72380.25490.11950.3856-0.51130.81371.30338.0548-32.4124
3316.2201-0.25799.634617.51695.423614.84460.05560.0242-0.2442-0.0936-0.0477-1.01890.06390.7543-0.00790.14680.02710.02840.13210.01670.15510.031412.5551-26.8819
3429.868627.7272-3.28426.2461-7.094232.69950.2004-0.1081-1.59910.0789-0.1907-1.45090.98160.7873-0.00970.40860.13940.21680.36850.1570.559.38267.4989-18.9103
3541.2922-3.820118.18844.4219-0.964312.80120.1099-0.0937-0.3562-0.32290.09090.18030.3393-0.5172-0.20080.2391-0.02470.02180.14690.040.1433-4.72716.6195-20.1313
369.3835-1.35797.48681.8449-1.295911.0236-0.3794-0.5180.15740.36650.09160.1933-0.2137-0.50930.28780.1865-0.02980.03910.12160.0230.127-6.269411.0286-21.2636
377.5771-0.80818.3032.47020.328110.8197-0.2195-0.5035-0.03630.2654-0.00310.1235-0.0852-0.52450.22270.1527-0.03950.01690.10620.01430.1185-5.989712.4915-26.0478
389.87772.8856-4.984819.47414.505411.30550.20620.26310.1155-0.157-0.09851.03830.2111-0.8669-0.10780.10840.0347-0.08250.25-0.02780.2494-17.707216.7009-37.5357
398.05813.458710.26893.52255.140216.75220.04310.0904-0.2704-0.17020.06490.06870.0748-0.3361-0.1080.0851-0.00230.0210.1147-0.02140.1064-7.796514.0328-35.5996
4024.821-0.81032.925519.702-3.243836.79520.2747-1.57840.51091.0501-0.38060.0225-0.38820.34730.10590.2149-0.0762-0.02190.2112-0.00810.11244.704220.8307-20.5369
4120.179915.60758.060513.34637.19124.2014-0.40740.9660.0015-0.24710.30150.4040.05840.08240.10580.31450.0295-0.060.2598-0.11130.31625.9542-26.9393-38.5254
4220.1305-2.0994-3.91992.25710.69143.379-0.3314-0.2969-0.7624-0.09020.0656-0.18220.39320.21410.26580.14320.0124-0.01640.0733-0.00960.151430.3672-21.9798-25.3917
439.91315.734-2.113918.43682.38441.31180.461-1.32190.54860.8133-0.1582-0.47070.03520.4205-0.30280.18440.01720.0240.31-0.07910.120512.5758-14.048-16.2088
4412.5386-15.857217.723120.9851-20.579928.6835-1.70220.43831.46951.8793-0.9397-1.5147-3.0503-0.16432.64190.69490.1230.21020.1903-0.0040.996112.1314-4.2041-21.1583
459.294211.215-1.636114.019-1.1732.73470.08760.19561.2822-0.1160.15951.1942-0.5689-0.1369-0.24710.27590.11370.07470.17080.10180.71078.7717-8.8726-25.13
4611.5686-0.6431-5.1267.33930.66039.9090.0035-0.65910.08290.6191-0.015-0.015-0.17560.07830.01150.14890.00380.01010.1013-0.03070.09884.6661-17.3755-15.5719
4715.19185.01485.09984.19735.62277.87430.2336-0.8037-0.03660.1789-0.1552-0.02050.1152-0.1022-0.07850.28380.0330.0690.1392-0.01390.104721.7394-14.3897-19.063
4814.5424-0.0842-12.29014.370913.994655.1325-0.4225-2.1222-0.09790.0399-0.12160.02390.12351.57770.54410.3949-0.1682-0.34790.45180.22980.38234.4908-15.9024-18.3827
4919.8070.0847-3.9793.3672-0.00643.2874-0.2635-0.061-0.691-0.32460.19610.15650.2057-0.08080.06740.14510.00080.0060.0788-0.0290.106724.0915-20.7803-27.899
5015.5789-4.28713.450713.5380.554610.61010.30611.11920.608-0.3589-0.16910.7307-0.0776-0.4913-0.1370.17690.05040.06490.47050.19960.26469.8121-16.613-31.1825
514.07772.35711.14065.2447-0.23133.06930.0129-0.0898-0.00730.27910.0623-0.38-0.30350.2383-0.07520.13920.0170.02550.13-0.03570.102531.479-11.6323-24.7754
520.44981.86361.88548.08818.24578.4348-0.11530.1475-0.3247-0.41020.8564-0.8358-0.33350.8129-0.74110.5995-0.16380.0380.50860.18481.132446.3716-0.6489-22.8624
5319.1345-0.3177-2.230221.15550.84898.522-0.1975-0.33411.22130.5058-0.4015-0.8911-0.82850.80670.5990.2054-0.0661-0.0560.19430.06920.22436.1542-9.6066-31.0309
548.80524.48971.681414.66778.214517.0263-0.26850.8423-0.1966-0.76690.1838-0.8050.70960.64070.08470.203-0.00390.05530.24480.0150.177833.2684-15.3654-40.1899
557.013911.718317.682919.587429.545944.5827-0.23720.1087-0.0422-0.60550.2796-0.0868-0.80960.2528-0.04240.8977-0.15290.14880.79670.11980.179531.4927-7.4725-46.3542
561.0223-0.6091-2.10316.5402-0.640133.88150.09170.1850.610.25770.29190.5921-1.1865-0.7398-0.38360.24460.03220.05610.17030.11490.581123.5971-0.4068-29.9553
573.5340.81872.61223.82535.729716.30670.02180.23840.3752-0.39080.3130.2129-0.8816-0.086-0.33480.2255-0.0503-0.00320.13760.07420.2825.8471-2.3214-35.0581
583.00790.87531.73353.9822.977519.38550.0263-0.03940.58860.0559-0.17720.4099-0.1531-0.98930.15090.18840.0003-0.0140.10530.00320.262524.0237-5.005-28.3895
5934.51233.7016.289714.62642.789626.0716-0.0251-2.0620.38451.1397-0.0255-0.8818-0.07840.45170.05050.453-0.06570.01190.3444-0.06570.173826.5052-6.7611-11.8197
605.34260.92262.99178.25975.010415.2967-0.24860.2630.1913-0.5819-0.04470.3144-0.5753-0.26540.29330.0845-0.01640.02830.09360.0430.166525.7554-12.4958-31.4867
616.0686-7.08689.14059.571-5.413935.17940.2328-0.0122-0.27180.07670.13180.29671.89390.4668-0.36470.4168-0.07830.13310.39370.04750.594826.238814.4866-54.3452
6219.455-10.5958-0.803721.53784.62410.1666-0.1112-1.551-0.09821.4071-0.1802-0.2179-0.0979-0.0540.29140.3811-0.0229-0.05230.5216-0.03970.207823.486825.3503-49.6161
635.02690.39974.82241.42351.57629.1911-0.0584-0.56060.45120.0831-0.1720.1555-0.3774-1.06240.23050.23210.04290.0130.1929-0.0240.232214.957526.329-68.4049
6415.1358-2.72514.350313.94581.363916.23940.60551.12650.7664-1.01920.2901-0.1485-0.56850.903-0.89570.3791-0.04730.05560.32190.03340.348724.834431.0071-79.6668
6512.60872.4661.992111.46420.11997.2876-0.42390.61110.1816-0.64620.312-0.2693-0.37070.23420.11190.27270.03540.04890.19410.03270.101718.15220.9116-83.2832
662.83251.39610.83172.14352.12246.9435-0.1709-0.0770.3969-0.1754-0.11150.3365-0.4175-0.38660.28250.21630.0388-0.03360.13380.00850.229514.718926.659-73.5416
6712.3356-4.0044-2.244212.98134.6694.0422-0.0453-0.74170.25580.4558-0.31360.4458-0.7002-0.27130.35890.38850.02270.03950.35590.0150.365510.546338.4685-58.9551
684.3535-5.2322-2.459213.36927.840610.3691-0.0674-0.48170.3420.3308-0.10860.105-0.1887-0.5730.1760.1579-0.0148-0.00580.2284-0.04380.21919.528126.2425-60.3799
6911.4289-3.8232-9.51366.619813.758828.8955-0.51160.7441-0.1711-0.07130.5562-0.09110.02321.016-0.04460.33450.0320.16020.35410.03870.486225.223515.6885-79.4666
701.69481.63942.495711.92747.745611.78860.186-0.101-0.2549-0.31390.0327-0.46070.22330.2696-0.21880.13850.0223-0.00460.212-0.00310.214524.971118.914-66.944
711.6547-7.5261-4.409434.498820.200711.8610.0252-0.04870.20650.24170.3062-0.80430.04110.1158-0.33140.52910.0901-0.21150.3068-0.16190.558521.293536.9755-59.2994
7221.74111.25365.004720.3495-6.182610.41820.0615-0.2265-1.72090.4605-0.1250.69530.7829-0.64820.06350.2985-0.01880.10880.2915-0.0250.260427.188855.5512-50.8121
730.6895-3.49051.475522.91923.464826.13040.0871-0.08560.0944-1.09080.1237-0.5033-1.0879-0.7483-0.21080.4472-0.049-0.01330.5821-0.07520.668929.168143.7083-55.9716
744.6184-2.69653.072814.4748-2.76445.2992-0.0673-0.46290.1640.42070.1155-0.1543-0.21830.1739-0.04820.3145-0.0371-0.05880.3232-0.04870.23133.82428.6329-54.4063
7513.2585-9.19345.70659.0105-6.42456.99740.1140.62190.1738-0.0678-0.3437-0.3767-0.11490.68340.22970.3184-0.0716-0.01440.28280.01380.34835.871233.2454-67.6734
767.47262.012-7.19397.82477.602119.4264-0.46690.1271-0.7702-0.47490.4511-0.754-0.01480.48220.01580.36040.08960.02030.43850.03530.390237.44225.1136-67.354
7711.9998-10.3345-0.43459.53590.07730.1572-0.15830.02110.65110.06830.3447-0.16280.0293-0.1871-0.18650.4382-0.0118-0.11860.30080.08350.521924.504939.3855-69.6068
788.3608-9.3635-7.392618.394313.23929.65270.0741-0.03390.60750.084-0.06890.22220.031-0.0543-0.00520.4290.0573-0.12840.29170.01190.453414.517840.7297-69.014
7910.8726-2.64182.210910.65382.50710.00640.2240.41061.0007-0.4494-0.69290.1673-0.527-0.53960.46890.220.0013-0.060.16560.00530.293624.970934.3259-63.6876
8039.3226-15.95774.413314.27962.1422.5044-0.0132-0.6936-2.0152-1.16260.5716-0.1338-0.42690.079-0.55831.69550.23380.60780.22440.12160.600232.05318.7944-62.204
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A504 - 514
2X-RAY DIFFRACTION2A515 - 526
3X-RAY DIFFRACTION3A527 - 532
4X-RAY DIFFRACTION4A533 - 551
5X-RAY DIFFRACTION5A552 - 563
6X-RAY DIFFRACTION6A564 - 575
7X-RAY DIFFRACTION7A576 - 592
8X-RAY DIFFRACTION8A593 - 596
9X-RAY DIFFRACTION9A607 - 612
10X-RAY DIFFRACTION10A613 - 622
11X-RAY DIFFRACTION11A623 - 627
12X-RAY DIFFRACTION12A628 - 638
13X-RAY DIFFRACTION13A639 - 653
14X-RAY DIFFRACTION14A654 - 663
15X-RAY DIFFRACTION15A664 - 668
16X-RAY DIFFRACTION16A669 - 680
17X-RAY DIFFRACTION17A681 - 690
18X-RAY DIFFRACTION18A691 - 700
19X-RAY DIFFRACTION19A701 - 708
20X-RAY DIFFRACTION20A709 - 713
21X-RAY DIFFRACTION21B505 - 522
22X-RAY DIFFRACTION22B523 - 534
23X-RAY DIFFRACTION23B535 - 541
24X-RAY DIFFRACTION24B542 - 546
25X-RAY DIFFRACTION25B547 - 569
26X-RAY DIFFRACTION26B570 - 579
27X-RAY DIFFRACTION27B580 - 592
28X-RAY DIFFRACTION28B593 - 606
29X-RAY DIFFRACTION29B607 - 620
30X-RAY DIFFRACTION30B621 - 627
31X-RAY DIFFRACTION31B628 - 636
32X-RAY DIFFRACTION32B637 - 644
33X-RAY DIFFRACTION33B645 - 652
34X-RAY DIFFRACTION34B653 - 657
35X-RAY DIFFRACTION35B658 - 664
36X-RAY DIFFRACTION36B665 - 680
37X-RAY DIFFRACTION37B681 - 689
38X-RAY DIFFRACTION38B690 - 698
39X-RAY DIFFRACTION39B699 - 707
40X-RAY DIFFRACTION40B708 - 713
41X-RAY DIFFRACTION41C501 - 513
42X-RAY DIFFRACTION42C514 - 529
43X-RAY DIFFRACTION43C530 - 535
44X-RAY DIFFRACTION44C536 - 540
45X-RAY DIFFRACTION45C541 - 549
46X-RAY DIFFRACTION46C550 - 561
47X-RAY DIFFRACTION47C562 - 575
48X-RAY DIFFRACTION48C576 - 586
49X-RAY DIFFRACTION49C587 - 591
50X-RAY DIFFRACTION50C592 - 612
51X-RAY DIFFRACTION51C613 - 627
52X-RAY DIFFRACTION52C628 - 637
53X-RAY DIFFRACTION53C638 - 644
54X-RAY DIFFRACTION54C645 - 653
55X-RAY DIFFRACTION55C654 - 658
56X-RAY DIFFRACTION56C659 - 668
57X-RAY DIFFRACTION57C669 - 677
58X-RAY DIFFRACTION58C678 - 693
59X-RAY DIFFRACTION59C694 - 700
60X-RAY DIFFRACTION60C701 - 713
61X-RAY DIFFRACTION61D504 - 511
62X-RAY DIFFRACTION62D512 - 521
63X-RAY DIFFRACTION63D522 - 536
64X-RAY DIFFRACTION64D537 - 542
65X-RAY DIFFRACTION65D543 - 553
66X-RAY DIFFRACTION66D554 - 573
67X-RAY DIFFRACTION67D574 - 583
68X-RAY DIFFRACTION68D584 - 592
69X-RAY DIFFRACTION69D593 - 609
70X-RAY DIFFRACTION70D610 - 616
71X-RAY DIFFRACTION71D617 - 625
72X-RAY DIFFRACTION72D626 - 631
73X-RAY DIFFRACTION73D632 - 638
74X-RAY DIFFRACTION74D639 - 655
75X-RAY DIFFRACTION75D656 - 676
76X-RAY DIFFRACTION76D677 - 684
77X-RAY DIFFRACTION77D685 - 692
78X-RAY DIFFRACTION78D693 - 700
79X-RAY DIFFRACTION79D701 - 707
80X-RAY DIFFRACTION80D708 - 713

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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