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- PDB-6e8d: Crystal structure of the Bacillus subtilis sliding clamp-MutL complex. -

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基本情報

登録情報
データベース: PDB / ID: 6e8d
タイトルCrystal structure of the Bacillus subtilis sliding clamp-MutL complex.
要素Beta sliding clamp,DNA mismatch repair protein MutL
キーワードDNA BINDING PROTEIN / Complex
機能・相同性
機能・相同性情報


mismatch repair complex / mismatched DNA binding / DNA polymerase III complex / DNA strand elongation involved in DNA replication / mismatch repair / 3'-5' exonuclease activity / DNA replication / DNA-directed DNA polymerase activity / ATP hydrolysis activity / DNA binding ...mismatch repair complex / mismatched DNA binding / DNA polymerase III complex / DNA strand elongation involved in DNA replication / mismatch repair / 3'-5' exonuclease activity / DNA replication / DNA-directed DNA polymerase activity / ATP hydrolysis activity / DNA binding / ATP binding / cytoplasm
類似検索 - 分子機能
DNA mismatch repair protein, MutL / MutL, C-terminal domain, regulatory subdomain / MutL C terminal dimerisation domain / MutL, C-terminal, dimerisation / MutL, C-terminal domain superfamily / MutL, C-terminal domain, dimerisation subdomain / MutL C terminal dimerisation domain / DNA mismatch repair protein family, N-terminal / DNA mismatch repair protein, S5 domain 2-like / DNA mismatch repair, conserved site ...DNA mismatch repair protein, MutL / MutL, C-terminal domain, regulatory subdomain / MutL C terminal dimerisation domain / MutL, C-terminal, dimerisation / MutL, C-terminal domain superfamily / MutL, C-terminal domain, dimerisation subdomain / MutL C terminal dimerisation domain / DNA mismatch repair protein family, N-terminal / DNA mismatch repair protein, S5 domain 2-like / DNA mismatch repair, conserved site / DNA mismatch repair protein MutL/Mlh/Pms / DNA mismatch repair protein, C-terminal domain / DNA mismatch repair proteins mutL / hexB / PMS1 signature. / DNA mismatch repair protein, C-terminal domain / DNA polymerase III, beta sliding clamp / DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / DNA polymerase III beta subunit / : / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
類似検索 - ドメイン・相同性
Beta sliding clamp / DNA mismatch repair protein MutL / Beta sliding clamp
類似検索 - 構成要素
生物種Bacillus subtilis (枯草菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.34 Å
データ登録者Guarne, A. / Almawi, A.W.
引用ジャーナル: Nucleic Acids Res. / : 2019
タイトル: Binding of the regulatory domain of MutL to the sliding beta-clamp is species specific.
著者: Almawi, A.W. / Scotland, M.K. / Randall, J.R. / Liu, L. / Martin, H.K. / Sacre, L. / Shen, Y. / Pillon, M.C. / Simmons, L.A. / Sutton, M.D. / Guarne, A.
履歴
登録2018年7月28日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02019年5月1日Provider: repository / タイプ: Initial release
改定 1.12019年5月22日Group: Data collection / Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.22020年10月7日Group: Derived calculations
カテゴリ: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
改定 1.32024年3月13日Group: Data collection / Database references / カテゴリ: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Beta sliding clamp,DNA mismatch repair protein MutL
B: Beta sliding clamp,DNA mismatch repair protein MutL
C: Beta sliding clamp,DNA mismatch repair protein MutL
D: Beta sliding clamp,DNA mismatch repair protein MutL
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)229,7167
ポリマ-229,4394
非ポリマー2763
3,063170
1
A: Beta sliding clamp,DNA mismatch repair protein MutL
C: Beta sliding clamp,DNA mismatch repair protein MutL
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)114,9965
ポリマ-114,7202
非ポリマー2763
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-11 kcal/mol
Surface area42180 Å2
手法PISA
2
B: Beta sliding clamp,DNA mismatch repair protein MutL
D: Beta sliding clamp,DNA mismatch repair protein MutL


分子量 (理論値)分子数
合計 (水以外)114,7202
ポリマ-114,7202
非ポリマー00
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-12 kcal/mol
Surface area41690 Å2
手法PISA
単位格子
Length a, b, c (Å)59.020, 83.890, 128.260
Angle α, β, γ (deg.)80.30, 83.57, 89.96
Int Tables number1
Space group name H-MP1

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要素

#1: タンパク質
Beta sliding clamp,DNA mismatch repair protein MutL


分子量: 57359.852 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Bacillus subtilis (枯草菌) / 遺伝子: B4417_2457, mutL, B4417_3449 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: A0A085C685, UniProt: A0A164SDM9, UniProt: P05649*PLUS
#2: 化合物 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 3 / 由来タイプ: 合成 / : C3H8O3
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 170 / 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: 2.71 Å3/Da / 溶媒含有率: 54.62 %
結晶化温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 100 mM HEPES pH 7.5, 25 % PEG 3,350, 200 mM ammonium sulfate.

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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: CLSI / ビームライン: 08B1-1 / 波長: 0.97951 Å
検出器タイプ: RAYONIX MX300HE / 検出器: CCD / 日付: 2016年5月27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: 0.97951 Å / 相対比: 1
反射解像度: 2.34→48.255 Å / Num. obs: 98638 / % possible obs: 97.1 % / 冗長度: 2.2 % / Net I/σ(I): 13.4
反射 シェル解像度: 2.34→2.42 Å

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解析

ソフトウェア
名称バージョン分類
PHENIX1.9_1692精密化
XDSデータ削減
XDSデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.34→48.255 Å / SU ML: 0.38 / 交差検証法: FREE R-VALUE / σ(F): 1.96 / 位相誤差: 29.65 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2502 1349 1.37 %
Rwork0.2159 --
obs0.2164 98638 97.07 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
精密化ステップサイクル: LAST / 解像度: 2.34→48.255 Å
タンパク質核酸リガンド溶媒全体
原子数13451 0 18 170 13639
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00413867
X-RAY DIFFRACTIONf_angle_d0.73218895
X-RAY DIFFRACTIONf_dihedral_angle_d15.2114989
X-RAY DIFFRACTIONf_chiral_restr0.0292348
X-RAY DIFFRACTIONf_plane_restr0.0032422
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.42360.34291340.33029678X-RAY DIFFRACTION97
2.4236-2.52070.36211350.31639721X-RAY DIFFRACTION97
2.5207-2.63540.38281350.30719732X-RAY DIFFRACTION97
2.6354-2.77430.34691340.28879749X-RAY DIFFRACTION97
2.7743-2.94810.2711360.25559748X-RAY DIFFRACTION97
2.9481-3.17570.29671350.23579691X-RAY DIFFRACTION97
3.1757-3.49520.24911350.21339798X-RAY DIFFRACTION97
3.4952-4.00070.22591340.19189656X-RAY DIFFRACTION97
4.0007-5.03970.19291340.16769697X-RAY DIFFRACTION97
5.0397-48.26550.22391370.19769819X-RAY DIFFRACTION98
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)
10.7957-0.22070.00850.61150.54340.54030.0945-0.0680.00440.11030.0508-0.19050.12960.14880.03530.171-0.0157-0.07650.1942-0.00840.28598.11225.1846153.5608
20.2405-0.06850.35210.15830.31740.37130.10770.3839-0.2768-0.2144-0.0516-0.01990.104-0.0934-00.33350.05760.10840.31450.03510.603521.6831-8.9946138.1155
30.70340.084-0.01450.5648-0.44610.6656-0.03050.09650.1011-0.8322-0.0924-0.3520.60660.01450.87350.80410.18560.02170.6044-0.0110.39821.3941-10.4726123.2484
40.5002-0.27940.04250.1474-0.090.64680.1272-0.2272-0.1352-0.3575-0.1824-0.25420.2207-0.0874-0.02110.40980.0859-0.00530.2852-0.0470.384220.5174-8.8161131.1898
50.835-0.0508-1.09160.63280.15851.44710.21290.08750.1113-0.7813-0.1228-0.43390.0165-0.17880.14171.2690.15580.31330.75440.03950.698726.52268.9547104.7173
60.21410.0588-0.14710.1466-0.34570.48280.29440.1170.0977-0.6135-0.206-0.197-0.34520.25070.23881.19620.14360.25630.8867-0.00070.576625.61328.436499.8334
71.02120.2733-0.54980.375-0.04530.32760.1914-0.2861-0.0811-0.7055-0.2232-0.22380.2840.0608-0.57810.99650.2330.1280.70160.08540.414526.3058-1.1353109.644
80.2826-0.1867-0.08020.28520.28490.3576-0.2052-0.0210.193-0.40730.28530.2178-0.04650.3342-0.0561.0331-0.2063-0.17250.9090.21021.032511.0636-2.160899.2202
90.00850.02660.0148-0.00760.0128-0.02380.0986-0.1348-0.0748-0.10170.21070.14090.4102-0.4744-0.00021.4033-0.0066-0.16051.0232-0.00830.59285.2585-14.4581108.5298
100.0749-0.00920.04080.01410.02260.10620.1301-0.0872-0.0985-0.10760.1444-0.00270.0631-0.03260.03851.496-0.3013-0.63771.21610.06021.0187-5.0972-18.99598.2917
110.02620.00390.00220.02560.00520.0069-0.08860.3009-0.0594-0.1595-0.06970.26770.0233-0.31350.00012.69640.0952-0.5481.8121-0.02291.29070.3971-8.886593.6153
120.27830.0013-0.2330.3838-0.2580.3578-0.6846-0.10040.4793-0.22460.2326-0.13560.19030.2566-0.44041.42670.242-0.18270.86460.0190.64985.9028-8.8173104.3931
130.0187-0.1125-0.11950.82310.66430.93360.3352-0.12080.0761-0.29210.14060.3989-0.0658-0.2215-0.42241.30530.2128-0.21581.31750.32681.1987-3.2976-7.5327105.9113
14-0.00530.01970.00860.00470.0057-0.00390.0011-0.2050.23550.1679-0.04390.149-0.0868-0.2870.00032.38680.8023-0.24491.50230.03492.099-5.90531.9718100.3095
150.83780.1855-0.27540.77070.01671.86120.177-0.06460.1208-0.04260.08030.23120.00560.17880.89290.1874-0.0313-0.08040.24410.00460.374629.428945.199153.0818
160.1818-0.0508-0.25060.3778-0.4560.54010.11520.0891-0.0076-0.0390.0074-0.02010.1191-0.169200.2414-0.023-0.08520.27940.01590.368124.517145.7288153.6083
170.92310.15060.11070.8110.15790.3486-0.0188-0.05050.01980.05480.0182-0.05870.2871-0.02590.00330.1782-0.0307-0.03360.17960.02170.308522.908439.5656165.0799
181.725-1.60720.09211.4544-0.03810.60560.02510.3308-0.6580.41590.24590.60850.3924-0.35340.1680.7513-0.24620.10220.7844-0.0350.66319.560329.3027180.7601
190.48030.0132-0.12310.12110.54480.48470.24260.21-0.07740.0733-0.29510.37590.22180.1245-0.05170.2634-0.14610.04570.15880.01540.31714.947134.0699176.3841
200.1695-0.0027-0.03680.01620.02080.01440.2605-0.0025-0.02550.4222-0.0570.2865-0.23220.13740.09141.2461-0.030.30010.8490.02780.716412.809854.8097196.6985
210.56110.22360.14692.2296-1.71681.47880.0881-0.08820.26840.70460.21490.05460.3506-0.30590.3171.6323-0.22970.34060.8697-0.06590.70669.300747.8522206.8356
220.6361-0.7829-0.15381.03310.25330.1206-0.1052-0.3706-0.17650.74650.09140.5428-0.4972-0.3314-0.04391.2929-0.03210.29450.83150.05170.55610.66349.5277205.9789
230.7948-0.2194-0.27650.3366-0.09950.32450.13760.17390.65140.9061-0.39540.50690.58290.0867-0.49791.1198-0.09090.21530.735-0.03890.301713.500240.0167197.0649
24-0.0016-0.03110.03140.0128-0.0065-0.0198-0.3661-0.5478-0.25640.5952-0.2924-0.5750.08920.2276-0.00011.42870.498-0.36181.264-0.18321.189238.193223.6927202.5972
251.88210.5078-0.40680.1364-0.10910.0916-0.10161.1361-2.1144-0.50040.1809-0.83811.0532-0.0934-0.01132.20340.9745-0.23231.53390.59320.184833.388427.308206.3446
260.5560.24890.55430.10550.24390.55970.10690.4123-0.35070.12710.5395-0.23840.77860.44540.1171.38010.2018-0.40720.7996-0.05350.602830.470936.5851198.9176
270.5642-0.20370.16330.1267-0.10520.11560.18620.10970.01110.01790.3543-0.32440.0368-0.03780.10591.25770.0343-0.29410.9731-0.39740.978139.056533.862199.2501
280.0071-0.00770.02710.0227-0.0087-0.01690.10180.01930.0204-0.06380.0768-0.0222-0.20710.1-0.00011.56140.3576-0.20621.8259-0.25212.353943.122642.9216204.3991
290.4145-0.1784-0.03190.1298-0.23580.5606-0.1225-0.29-0.24130.19570.2420.341-0.0220.3540.0711.1634-0.00860.28610.7258-0.04440.485818.444434.8872103.0754
300.22270.00620.2808-0.01340.10980.7538-0.1401-0.09530.07740.17360.0026-0.17610.17590.0513-0.55320.98290.02010.20430.59510.02690.515913.480535.0325105.3489
310.7417-0.2838-0.24941.36210.58640.2734-0.24360.5589-0.3208-0.75140.1586-0.42030.23530.0129-0.42120.95220.11420.24440.6770.08360.360422.17627.141598.4853
320.3869-0.1388-0.31130.2059-0.40890.45150.14610.0331-0.0466-0.3359-0.1795-0.2599-0.24080.17440.12290.79840.00720.11860.54410.01210.36138.276140.9448112.0259
330.7029-0.10150.20590.66120.13220.72720.18830.1308-0.087-0.44-0.19160.0275-0.5031-0.27380.01340.66590.08390.1250.42310.00560.4408-5.265444.881129.2202
340.27540.1028-0.24590.60040.18921.31960.2661-0.05410.2424-0.294-0.0006-0.1345-0.5154-0.0080.19810.49690.07020.0820.24880.07310.3755-0.266844.1523126.3766
35-0.02010.00120.12020.0435-0.17630.91780.11340.17430.0999-0.47140.0974-0.28810.3972-0.2591-0.08710.2411-0.0211-0.07320.3839-0.08110.47981.79923.7368146.5282
360.3175-0.4658-0.04640.4467-0.78321.3506-0.0388-0.1646-0.2160.1910-0.0443-0.1814-0.30810.12870.216-0.0269-0.01480.3026-0.02780.5402-4.090327.9335155.7039
370.6306-0.45650.47120.4899-0.66250.6885-0.001-0.0241-0.11570.1059-0.1056-0.0622-0.0476-0.0871-0.00010.2628-0.00490.01650.2843-0.00580.4354-7.066735.0859146.084
380.66870.49340.19370.34110.11080.06890.4145-0.3012-0.40470.2078-0.2083-0.0543-0.1197-0.6088-0.04050.22540.0991-0.05190.4995-0.11180.53-22.025431.8513132.8512
390.00550.0046-0.00450.00470.00180.0005-0.0976-0.0935-0.2012-0.1248-0.03950.1218-0.02860.0166-0.063-0.2497-0.9114-1.08351.2389-0.96781.5341-37.365824.1066130.3685
400.0050.0072-0.0010.03330.02650.0048-0.0735-0.12520.0275-0.1095-0.0317-0.0833-0.00210.02840.04070.71810.0207-0.28581.66780.78791.7948-30.328128.7673134.2771
410.35070.41570.14190.9074-0.08820.27330.22220.2214-0.3934-0.29830.0239-0.22840.1899-0.00850.0870.4378-0.0007-0.07760.5771-0.13070.8147-19.018525.4855135.3798
420.02080.01130.04750.6306-0.25470.45750.39380.0189-0.1103-0.07740.26330.45650.12780.19860.65790.99630.2269-0.27030.8655-0.40841.367-21.522222.5291129.1797
430.27910.0560.2113-0.0392-0.00852.14610.21410.76660.59110.5624-0.0878-0.463-0.1473-0.2237-0.00891.337-0.12590.35050.5043-0.15080.605819.074374.964197.6072
440.61990.30040.39210.12490.17240.25890.3262-0.4262-0.25440.2520.1416-0.222-0.36040.40240.02731.6043-0.43120.31060.9147-0.12260.767733.4872.1399201.125
450.24250.02950.0520.2197-0.22180.19750.0358-0.45180.22240.4253-0.05310.2353-0.21120.48020.08341.2264-0.12490.27930.7651-0.11860.612226.239381.3534198.6583
460.4368-0.0435-0.15360.04590.13020.34690.7574-0.1865-0.1379-0.3602-0.36420.51740.2361-0.06950.04811.442-0.08320.4850.6624-0.14510.718818.055174.2764201.4798
470.1827-0.0045-0.2950.0858-0.00520.41640.091-0.17050.12350.4236-0.18860.3943-0.26720.00420.01111.2536-0.15440.36180.7981-0.2210.642615.268468.6743206.7482
480.76450.2213-0.4430.16330.59990.37540.2330.00380.3930.4905-0.3203-0.1419-0.31950.1088-0.54980.7983-0.12860.11720.3931-0.05160.246235.390482.7395186.1632
490.96770.2325-0.62920.2054-0.2420.57290.325-0.17990.11670.4366-0.0721-0.0411-0.80640.13960.11470.8709-0.07720.08490.5315-0.04440.584939.850290.9029174.6523
500.897-0.7022-0.25470.90260.28810.18410.0894-0.0471-0.6660.3675-0.05750.6359-0.47550.09870.1940.9306-0.06830.12210.5371-0.09720.462932.151185.1621183.661
510.0537-0.575-0.73460.3804-0.3720.561.05221.27970.13370.153-0.03310.0163-0.27670.54330.24120.4955-0.52180.2023-0.70930.03690.453740.709786.0926176.4431
520.18050.2944-0.32170.3804-0.4690.72640.3029-0.12460.13780.71160.36110.299-0.0098-0.21620.16280.2311-0.0323-0.10660.41010.00050.401734.333266.3342158.6068
530.1248-0.0063-0.07830.25450.02280.012-0.11610.2004-0.1946-0.18910.0696-0.23270.02750.0211-0.00060.2306-0.0223-0.03430.33220.00250.550141.097566.2742150.7224
540.27920.10050.11330.38980.12910.11920.10580.00270.1267-0.0158-0.13260.0655-0.09680.084900.3275-0.0160.01830.319-0.010.435740.588278.3499156.6061
550.17380.14420.00960.0867-0.07840.0640.3122-0.0687-0.4071-0.4524-0.30040.3987-0.30020.07890.00040.35780.035-0.03390.3199-0.03110.572547.199776.8171159.9685
560.38790.2132-0.74972.1988-0.08451.57250.4312-0.6109-0.61810.5841-0.1243-1.1626-0.35420.966-0.10320.4811-0.174-0.22710.78590.12570.85459.032272.5823171.8091
570.010.0020.00280.0052-0.00060.0232-0.10720.2746-0.1613-0.1546-0.0804-0.01420.16570.06030.00021.2025-0.1567-0.06181.3077-0.11712.301374.452765.6967176.7702
580.01130.001-0.02170.0126-0.02760.034-0.1576-0.2431-0.06880.1344-0.01710.13690.1343-0.0809-0.00010.6170.035-0.10131.9778-0.25391.972368.195472.1092171.4508
590.321-0.0863-0.35760.2673-0.02850.4882-0.0482-0.38690.2340.32320.1541-0.376-0.04830.38960.0692-0.3436-0.0012-0.41570.50040.00331.039760.914571.6682169.8639
600.0575-0.02550.19360.14510.08150.62840.37460.2537-0.79660.3919-0.2732-0.0460.0332-0.02080.28390.5135-0.1529-0.22310.49990.31370.979454.70763.9759172.7826
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 25:154 )A25 - 154
2X-RAY DIFFRACTION2( CHAIN A AND RESID 155:179 )A155 - 179
3X-RAY DIFFRACTION3( CHAIN A AND RESID 180:230 )A180 - 230
4X-RAY DIFFRACTION4( CHAIN A AND RESID 231:293 )A231 - 293
5X-RAY DIFFRACTION5( CHAIN A AND RESID 294:331 )A294 - 331
6X-RAY DIFFRACTION6( CHAIN A AND RESID 332:363 )A332 - 363
7X-RAY DIFFRACTION7( CHAIN A AND RESID 364:411 )A364 - 411
8X-RAY DIFFRACTION8( CHAIN A AND RESID 415:420 )A415 - 420
9X-RAY DIFFRACTION9( CHAIN A AND RESID 421:430 )A421 - 430
10X-RAY DIFFRACTION10( CHAIN A AND RESID 431:439 )A431 - 439
11X-RAY DIFFRACTION11( CHAIN A AND RESID 440:447 )A440 - 447
12X-RAY DIFFRACTION12( CHAIN A AND RESID 448:472 )A448 - 472
13X-RAY DIFFRACTION13( CHAIN A AND RESID 473:486 )A473 - 486
14X-RAY DIFFRACTION14( CHAIN A AND RESID 487:503 )A487 - 503
15X-RAY DIFFRACTION15( CHAIN B AND RESID 25:69 )B25 - 69
16X-RAY DIFFRACTION16( CHAIN B AND RESID 70:120 )B70 - 120
17X-RAY DIFFRACTION17( CHAIN B AND RESID 121:211 )B121 - 211
18X-RAY DIFFRACTION18( CHAIN B AND RESID 212:230 )B212 - 230
19X-RAY DIFFRACTION19( CHAIN B AND RESID 231:299 )B231 - 299
20X-RAY DIFFRACTION20( CHAIN B AND RESID 300:314 )B300 - 314
21X-RAY DIFFRACTION21( CHAIN B AND RESID 320:330 )B320 - 330
22X-RAY DIFFRACTION22( CHAIN B AND RESID 331:363 )B331 - 363
23X-RAY DIFFRACTION23( CHAIN B AND RESID 364:424 )B364 - 424
24X-RAY DIFFRACTION24( CHAIN B AND RESID 425:439 )B425 - 439
25X-RAY DIFFRACTION25( CHAIN B AND RESID 440:457 )B440 - 457
26X-RAY DIFFRACTION26( CHAIN B AND RESID 458:472 )B458 - 472
27X-RAY DIFFRACTION27( CHAIN B AND RESID 473:485 )B473 - 485
28X-RAY DIFFRACTION28( CHAIN B AND RESID 486:503 )B486 - 503
29X-RAY DIFFRACTION29( CHAIN C AND RESID 27:52 )C27 - 52
30X-RAY DIFFRACTION30( CHAIN C AND RESID 53:119 )C53 - 119
31X-RAY DIFFRACTION31( CHAIN C AND RESID 120:140 )C120 - 140
32X-RAY DIFFRACTION32( CHAIN C AND RESID 141:179 )C141 - 179
33X-RAY DIFFRACTION33( CHAIN C AND RESID 180:230 )C180 - 230
34X-RAY DIFFRACTION34( CHAIN C AND RESID 231:299 )C231 - 299
35X-RAY DIFFRACTION35( CHAIN C AND RESID 300:317 )C300 - 317
36X-RAY DIFFRACTION36( CHAIN C AND RESID 319:357 )C319 - 357
37X-RAY DIFFRACTION37( CHAIN C AND RESID 358:417 )C358 - 417
38X-RAY DIFFRACTION38( CHAIN C AND RESID 418:430 )C418 - 430
39X-RAY DIFFRACTION39( CHAIN C AND RESID 431:443 )C431 - 443
40X-RAY DIFFRACTION40( CHAIN C AND RESID 444:458 )C444 - 458
41X-RAY DIFFRACTION41( CHAIN C AND RESID 459:472 )C459 - 472
42X-RAY DIFFRACTION42( CHAIN C AND RESID 473:481 )C473 - 481
43X-RAY DIFFRACTION43( CHAIN D AND RESID 32:52 )D32 - 52
44X-RAY DIFFRACTION44( CHAIN D AND RESID 53:69 )D53 - 69
45X-RAY DIFFRACTION45( CHAIN D AND RESID 70:90 )D70 - 90
46X-RAY DIFFRACTION46( CHAIN D AND RESID 91:120 )D91 - 120
47X-RAY DIFFRACTION47( CHAIN D AND RESID 121:140 )D121 - 140
48X-RAY DIFFRACTION48( CHAIN D AND RESID 141:211 )D141 - 211
49X-RAY DIFFRACTION49( CHAIN D AND RESID 212:230 )D212 - 230
50X-RAY DIFFRACTION50( CHAIN D AND RESID 231:258 )D231 - 258
51X-RAY DIFFRACTION51( CHAIN D AND RESID 259:299 )D259 - 299
52X-RAY DIFFRACTION52( CHAIN D AND RESID 300:317 )D300 - 317
53X-RAY DIFFRACTION53( CHAIN D AND RESID 319:348 )D319 - 348
54X-RAY DIFFRACTION54( CHAIN D AND RESID 349:393 )D349 - 393
55X-RAY DIFFRACTION55( CHAIN D AND RESID 394:416 )D394 - 416
56X-RAY DIFFRACTION56( CHAIN D AND RESID 417:430 )D417 - 430
57X-RAY DIFFRACTION57( CHAIN D AND RESID 431:440 )D431 - 440
58X-RAY DIFFRACTION58( CHAIN D AND RESID 450:457 )D450 - 457
59X-RAY DIFFRACTION59( CHAIN D AND RESID 458:465 )D458 - 465
60X-RAY DIFFRACTION60( CHAIN D AND RESID 466:480 )D466 - 480

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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://pdbjlvh1.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