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- PDB-5whv: Crystal structure of ArtB -

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データを開く


IDまたはキーワード:

読み込み中...

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基本情報

登録情報
データベース: PDB / ID: 5whv
タイトルCrystal structure of ArtB
要素ArtB protein
キーワードTOXIN / bacterial toxin / glycan
機能・相同性OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta / metal ion binding / DI(HYDROXYETHYL)ETHER / ArtB protein
機能・相同性情報
生物種Salmonella enterica subsp. enterica serovar Typhimurium str. DT104 (サルモネラ菌)
手法X線回折 / 分子置換 / 解像度: 2.303 Å
データ登録者Gao, X. / Galan, J.E.
引用ジャーナル: Nat Microbiol / 年: 2017
タイトル: Evolution of host adaptation in the Salmonella typhoid toxin.
著者: Gao, X. / Deng, L. / Stack, G. / Yu, H. / Chen, X. / Naito-Matsui, Y. / Varki, A. / Galan, J.E.
履歴
登録2017年7月18日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年10月25日Provider: repository / タイプ: Initial release
改定 1.12017年12月6日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.22019年1月9日Group: Data collection / Derived calculations / カテゴリ: pdbx_struct_conn_angle / struct_conn
改定 1.32023年10月4日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
改定 1.42024年11月20日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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: ArtB protein
B: ArtB protein
C: ArtB protein
D: ArtB protein
E: ArtB protein
F: ArtB protein
G: ArtB protein
H: ArtB protein
I: ArtB protein
J: ArtB protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)173,44658
ポリマ－169,10010
非ポリマー4,34648
水12,358686
1
A: ArtB protein
B: ArtB protein
C: ArtB protein
D: ArtB protein
E: ArtB protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)86,35826
ポリマ－84,5505
非ポリマー1,80821
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area14290 Å2
ΔGint-112 kcal/mol
Surface area23100 Å2
手法PISA
2
F: ArtB protein
G: ArtB protein
H: ArtB protein
I: ArtB protein
J: ArtB protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)87,08832
ポリマ－84,5505
非ポリマー2,53827
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area16710 Å2
ΔGint-112 kcal/mol
Surface area24340 Å2
手法PISA
単位格子
Length a, b, c (Å)140.872, 94.231, 125.230
Angle α, β, γ (deg.)90.00, 103.62, 90.00
Int Tables number5
Space group name H-MC121

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要素

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タンパク質 , 1種, 10分子 ABCDEFGHIJ

#1: タンパク質
ArtB protein / Subtilase cytotoxin subunit B-like protein


分子量: 16910.010 Da / 分子数: 10 / 由来タイプ: 組換発現
由来: (組換発現) Salmonella enterica subsp. enterica serovar Typhimurium str. DT104 (サルモネラ菌)
遺伝子: ArtB, ERS157243_04891 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q404H3

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非ポリマー , 5種, 734分子

#2: 化合物...
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / ジエチレングリコ-ル


分子量: 106.120 Da / 分子数: 21 / 由来タイプ: 合成 / 式: C4H10O3
#3: 化合物
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / 2-モルホリノエタンスルホン酸


分子量: 195.237 Da / 分子数: 7 / 由来タイプ: 合成 / 式: C6H13NO4S / コメント: pH緩衝剤*YM
#4: 化合物
ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 11 / 由来タイプ: 合成 / 式: Cl
#5: 化合物
ChemComp-CA / CALCIUM ION / カルシウムジカチオン


分子量: 40.078 Da / 分子数: 9 / 由来タイプ: 合成 / 式: Ca
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 686 / 由来タイプ: 天然 / 式: H2O

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詳細

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: 2.39 Å3/Da / 溶媒含有率: 48.5 %
結晶化温度: 297 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: peg 200, calcium chloride / PH範囲: 5.5

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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: 回転陽極 / タイプ: RIGAKU / 波長: 1.5418 Å
検出器タイプ: RIGAKU SATURN 944 / 検出器: CCD / 日付: 2014年8月21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: 1.5418 Å / 相対比: 1
反射解像度: 2.3→50 Å / Num. obs: 68092 / % possible obs: 96.59 % / 冗長度: 3.6 % / Net I/σ(I): 17.42

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解析

ソフトウェア
名称バージョン分類
PHENIX1.8.1_1168精密化
HKL-2000データ収集
HKL-2000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
開始モデル: 4RHR

4rhr


解像度: 2.303→31.124 Å / SU ML: 0.22 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 23.21 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.213 3416 5.02 %
Rwork0.1666 --
obs0.169 68081 96.58 %
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: 2.303→31.124 Å
タンパク質核酸リガンド溶媒全体
原子数9548 0 251 686 10485
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00810026
X-RAY DIFFRACTIONf_angle_d1.18913503
X-RAY DIFFRACTIONf_dihedral_angle_d14.9823605
X-RAY DIFFRACTIONf_chiral_restr0.0691414
X-RAY DIFFRACTIONf_plane_restr0.0061732
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3032-2.33610.27151060.22072457X-RAY DIFFRACTION88
2.3361-2.3710.34831400.21322649X-RAY DIFFRACTION95
2.371-2.4080.30591490.20142678X-RAY DIFFRACTION95
2.408-2.44750.25671450.20332607X-RAY DIFFRACTION96
2.4475-2.48970.22821130.20512732X-RAY DIFFRACTION95
2.4897-2.53490.2681100.20542659X-RAY DIFFRACTION96
2.5349-2.58370.3041360.20472689X-RAY DIFFRACTION96
2.5837-2.63640.27491310.19952674X-RAY DIFFRACTION96
2.6364-2.69370.21421600.1832638X-RAY DIFFRACTION96
2.6937-2.75630.23011430.18952667X-RAY DIFFRACTION97
2.7563-2.82520.24471400.19882693X-RAY DIFFRACTION96
2.8252-2.90150.25911540.20022653X-RAY DIFFRACTION96
2.9015-2.98680.2651470.19332682X-RAY DIFFRACTION97
2.9868-3.08320.26311310.18182672X-RAY DIFFRACTION97
3.0832-3.19320.24041450.17592732X-RAY DIFFRACTION98
3.1932-3.3210.19771490.1642704X-RAY DIFFRACTION98
3.321-3.47190.19091530.15972727X-RAY DIFFRACTION98
3.4719-3.65470.18891510.14282751X-RAY DIFFRACTION98
3.6547-3.88330.17681460.13592742X-RAY DIFFRACTION99
3.8833-4.18250.1891430.13942726X-RAY DIFFRACTION98
4.1825-4.60210.1451480.11342761X-RAY DIFFRACTION99
4.6021-5.26530.15691620.1222769X-RAY DIFFRACTION98
5.2653-6.62320.20631430.17322794X-RAY DIFFRACTION99
6.6232-31.12670.20661710.18572809X-RAY DIFFRACTION98
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)
12.2575-0.459-0.67931.8103-0.21042.8318-0.0228-0.2739-0.43060.15380.0975-0.12290.19930.3279-0.00810.16260.0686-0.01020.19410.05370.2348122.2093-223.4774272.9268
24.1779-0.5536-0.86951.76430.04251.66510.02120.0472-0.6004-0.3068-0.0793-0.08710.44030.27620.06110.27460.0746-0.00910.17090.00080.2652118-230.3318266.7999
32.74631.54541.45066.21042.29551.5441-0.048-0.3132-0.3548-0.66520.0448-0.126-0.2535-0.18840.00160.23940.0210.05160.16180.04390.1467114.5815-216.4645268.4004
44.7833-1.9836-0.80726.7107-3.29484.5133-0.2008-0.4467-0.15450.11920.24330.14220.39940.0044-0.07560.16770.028-0.01970.3120.03210.1098116.3796-221.2509279.3996
52.84991.2246-1.42912.13460.64892.5014-0.3777-0.4847-0.6803-0.03850.1176-0.28380.72110.57440.3020.30980.1420.04990.31680.06890.3767128.4496-231.442269.8735
61.86050.10670.66464.0324-0.8930.5165-0.336-0.6308-0.270.3425-0.03120.4113-0.09060.28240.19250.16880.07930.06460.32180.1090.2201111.8766-221.1353282.7041
72.152-2.4389-2.55657.73324.47957.90270.44690.7840.2061-1.313-0.3834-0.1033-0.445-0.5767-0.11540.4389-0.00440.04240.45960.03910.1958118.6966-202.6415236.878
82.3878-0.9586-0.78331.1272-0.4294.72320.3196-0.07930.0026-0.6024-0.41950.2451-0.1333-0.58170.12710.2720.0762-0.09540.2720.02770.206399.8092-204.3103245.8527
97.11252.6637-0.59691.4603-0.951.31240.0290.4523-0.0571-0.70750.00980.44740.12-0.0572-0.11030.32440.0921-0.11220.2561-0.04860.2188100.2597-207.941242.8996
102.7656-0.3196-0.11913.3317-2.18181.4607-0.09290.96241.2265-2.74910.25810.5133-0.7229-0.1749-0.13291.0537-0.144-0.11610.36890.15850.8098110.035-190.4089241.0194
113.28811.0540.42974.32030.78041.33680.15960.3134-0.0851-0.131-0.11590.13720.1651-0.0655-0.04490.1950.0095-0.03410.1555-0.00830.1417107.7181-208.7624246.302
126.95860.35230.38055.07622.83086.1883-0.29270.52950.6015-0.8927-0.0265-0.1051-0.8963-0.1590.24330.32360.02310.03010.19580.06970.2262115.6567-200.2271243.3946
133.9207-0.93242.42692.25180.29531.8775-0.11590.80140.5642-0.56860.14620.1785-0.22290.05440.11030.40590.0215-0.14560.59990.05820.2748100.1013-204.0481234.107
144.0964-0.7666-0.09874.2007-0.31454.03820.32730.4730.45070.0349-0.1385-0.5918-0.56820.6236-0.07280.3379-0.05250.07220.27070.0690.2468121.1646-200.7857243.776
153.58810.71-1.09423.22661.49423.2780.182-0.1267-0.253-0.4719-0.1987-1.10560.09220.6655-0.08610.20210.04170.07170.46450.00070.2947135.1805-219.3779258.8674
163.0185-0.72-0.25931.3382-1.59012.350.00750.5312-0.2452-0.27110.0393-0.09830.32810.4308-0.06010.27090.01040.07640.2569-0.03850.16121.3214-212.1463246.03
171.5279-1.00450.4154.52451.25474.0917-0.17920.0228-0.0756-0.38710.2865-0.54190.04770.7901-0.1310.23820.03040.06530.3508-0.03140.1987128.6275-214.5229250.4335
180.92221.81340.70145.92812.59871.6670.01-0.14570.0307-0.3777-0.1424-0.009-0.1019-0.27440.11880.1826-0.01450.02920.2223-0.02710.1881119.0505-211.6593257.9904
192.3198-0.86650.11841.38150.61426.7843-0.10010.0012-0.1382-0.08450.1979-0.23780.26691.0625-0.17560.1772-0.05440.0660.2693-0.00910.2368131.0651-215.7653252.5899
200.89640.3802-0.33170.5738-1.61655.52110.00280.1097-0.0402-0.3010.0435-0.1848-0.00070.5481-0.00880.31150.00040.0810.3659-0.02690.1799128.6056-214.6259247.2319
211.7235-2.3806-1.45044.48853.6194.4712-0.2809-0.10990.52580.42090.5637-0.84-0.16870.9311-0.38480.2384-0.0051-0.0090.4837-0.03140.313135.1745-214.9386267.7539
223.11231.3025-0.00684.59822.29586.39120.0241-0.5139-0.51310.06430.02610.74340.0186-1.02590.01860.21450.03090.06160.44580.12810.559785.6546-216.3445274.7927
233.10910.10411.04770.4058-0.80162.0648-0.1728-0.3212-0.3975-0.02310.12930.11210.2886-0.02640.12790.2046-0.02470.03020.19030.09670.2154105.5751-222.8329275.7833
244.5741-1.144-0.70.3681-0.27642.265-0.0642-0.0738-0.2437-0.2067-0.07790.13490.27880.0030.07050.2908-0.03610.00080.15480.09690.2452103.0918-226.2506273.6704
258.15970.2893-1.14814.17710.12361.1697-0.2455-1.0344-0.74661.9031-0.61741.09510.3712-0.36790.7840.64770.0790.20790.414-0.02450.492295.3512-213.0366286.9578
261.4356-0.1411.84210.8163-0.88332.9995-0.0588-0.1823-0.27750.24050.20030.1705-0.1669-0.2268-0.0950.2906-0.01180.00120.12840.07420.341598.4417-223.6373275.1956
270.4136-0.37790.40690.3915-0.38360.42360.3177-0.1491-0.6654-0.42550.08520.74310.2662-0.0911-0.13080.2828-0.06910.02250.1420.08560.508495.7527-228.976267.0129
280.60171.23860.90113.88742.2331.64040.0342-0.0412-0.04780.04670.0770.0560.1133-0.0424-0.14850.17080.0435-0.00650.17390.02150.2756102.4232-213.9623268.8753
293.7411-1.269-0.26510.8372-1.18243.88910.0249-0.52070.10540.2820.0291.03950.1928-0.2614-0.08610.16970.0486-0.01880.22920.02450.326492.1723-213.1832275.3806
300.5608-0.83320.75563.1529-1.37961.0606-0.1581-0.1649-0.29580.2110.22580.54840.1409-0.1914-0.11710.2469-0.00340.07230.20850.09780.464496.0765-226.1985277.9599
319.20845.89251.00723.90430.46493.7470.2509-0.74951.30480.2725-0.39821.1271-0.9124-0.9376-0.0020.31730.10890.06220.4581-0.02460.585785.8309-205.8878273.8754
321.82140.08340.26312.9043.68836.7045-0.14920.15770.2927-0.18150.00630.1753-0.4117-0.7730.22280.26280.0044-0.15690.38570.03170.431988.1161-201.0456246.498
332.48490.21780.09960.4327-0.97772.9717-0.0334-0.0812-0.4159-0.27510.14630.60720.1123-0.4267-0.04230.1597-0.0049-0.12430.28780.02930.432489.4167-213.9777262.2547
347.78195.09873.18474.50190.7862.832-0.1115-0.82081.082-0.7214-0.68492.2706-0.4357-0.66150.42590.36020.146-0.15780.4145-0.03930.532684.0012-195.741261.1065
350.91480.24640.14462.17180.00541.22420.06150.0279-0.2657-0.11790.01970.22910.0766-0.1905-0.03320.1882-0.0164-0.12250.23620.00160.32194.4965-211.4398256.0893
368.96860.31562.77410.7988-1.29426.56-0.04940.05860.7248-0.4892-0.18870.646-0.3143-0.50130.21260.26960.082-0.05870.2301-0.01680.305491.5062-200.2891252.7723
371.67251.0893-0.25461.81391.11192.90320.08560.1895-0.1923-0.05120.11290.7515-0.2461-1.416-0.00070.1877-0.0454-0.13870.56810.06470.55379.809-213.4234258.5157
383.4470.79220.29982.0070.86725.77720.13510.52870.264-0.3701-0.1207-0.0031-1.0365-0.39230.0890.31170.1144-0.120.32830.04060.328393.9243-197.4994248.5147
394.24173.6874-0.03177.398-2.84672.97320.22740.5548-0.0428-0.9311-0.14230.2464-0.184-0.0154-0.15420.37870.11090.00380.2424-0.00810.1145105.9002-181.6935261.4971
400.6234-0.54611.2041.2879-0.67162.3245-0.15750.46170.0142-0.24530.1152-0.2031-0.11860.3740.04170.21650.020.05080.1992-0.04520.1338117.9346-188.8294277.1424
411.0275-0.88350.84622.04750.15252.1301-0.05630.1084-0.1307-0.4020.1175-0.1202-0.04260.2267-0.0360.16810.02170.03980.1611-0.03510.0956114.2904-190.6152271.9075
421.2441-0.26390.37781.8433-0.58010.34920.01140.14360.0579-0.1552-0.0631-0.1586-0.14120.16090.05880.1811-0.00830.0220.1629-0.01150.0865114.2656-181.2311274.7049
433.1927-1.8834-1.95394.444-0.29132.55290.23960.05660.1752-0.4294-0.01360.1573-0.28950.1241-0.20630.1790.0086-0.05750.1473-0.02030.1244104.7552-184.4592268.0961
441.74860.5333-2.63612.7089-0.02925.83760.47660.6971-0.7885-0.5541-0.1251-0.3380.57331.65740.11360.30870.10870.0660.476-0.11490.2494122.2631-190.7256266.1533
453.9125-0.8513-1.11733.1623-0.07885.21530.34260.4125-0.3017-0.6578-0.27830.54-0.2211-0.53990.03570.27420.0895-0.06850.2224-0.0590.1767100.7357-180.9671266.3725
468.77433.2504-2.94764.35810.06567.1194-0.0976-0.445-0.37410.64990.241-0.44960.08140.3655-0.13450.2670.0283-0.06140.1547-0.00130.1918123.7689-183.5107310.1104
471.1961-1.1682-0.02922.20830.35983.0478-0.0589-0.28360.33760.2596-0.0192-0.2318-0.51640.13870.08810.1665-0.0223-0.06220.1945-0.0720.214114.7399-166.3552303.9832
480.96031.3736-0.92317.081-7.5078.31.0224-1.34910.5111.4352-1.10030.51470.2194-0.155-0.04230.5022-0.20170.01270.8451-0.00430.2564110.445-180.125317.1216
490.4805-0.88660.25922.10880.76943.40470.0112-0.14890.75090.3647-0.0047-0.1974-0.08520.3486-0.03540.1364-0.0402-0.02010.1888-0.04130.27123.4315-169.0812302.8261
506.00442.5136-2.53751.2789-1.10642.4976-0.00120.07180.3619-0.13040.21720.11550.18770.0743-0.27530.15880.0196-0.00240.09280.01370.1477112.3204-176.872298.09
516.34760.45142.73773.45991.27792.57940.253-0.19240.00550.96790.01430.17250.5237-0.1243-0.08750.23350.01730.03430.23210.04830.0799116.993-182.4735307.8549
522.1191-0.5157-0.28622.57970.91721.8671-0.6125-0.63760.48320.986-0.0838-0.4239-0.26540.4261-0.09750.399-0.0133-0.27060.1959-0.24930.3073120.564-164.813312.5917
534.63820.33170.84143.61610.43972.79010.2175-0.2992-0.5580.96490.1462-0.11590.52330.1032-0.19840.27930.0175-0.0590.16950.02680.1377119.0284-187.5484306.7273
546.25481.5887-0.51596.7954-1.75996.0633-0.25910.5386-0.2571-0.22790.3346-0.62830.65770.808-0.0320.22240.0974-0.07690.2727-0.07070.201124.7296-197.9175282.1535
551.0133-0.85680.2550.6839-0.25822.5763-0.05890.21740.280.36220.3152-0.16520.1010.355-0.11220.11570.0722-0.06050.1672-0.04370.2161122.5218-185.5709298.1573
563.88752.38590.06413.27720.79512.07070.0502-0.1335-0.97460.25520.1203-1.71090.33620.1971-0.06210.14890.079-0.07380.20980.02140.3407123.392-191.8186295.7787
570.9944-1.0172-0.16051.03210.20271.40230.8737-0.01440.1271-0.09880.1709-0.9881-0.14970.58650.3109-0.93280.0587-0.27360.3648-0.03650.2167129.2835-184.7322289.0264
583.51813.016-1.12623.5231-1.24291.21680.1810.05290.28660.25980.0399-0.02390.00670.225-0.21770.0974-0.0021-0.00960.1125-0.01480.1713114.9565-185.2123289.3057
597.2836-4.1483-0.16913.95151.52115.48550.13050.4601-0.16170.15060.0727-0.11070.15430.2744-0.12750.19750.0023-0.04930.07850.00610.1121119.2178-196.128286.0681
603.91521.87190.3461.35490.61096.64970.0955-0.2217-0.28230.14360.0019-0.39740.14530.4678-0.08890.13010.0329-0.08240.2516-0.02860.2518132.7337-191.2687297.2611
610.22850.1925-0.16015.09760.94052.7489-0.00790.1768-0.1921-0.27120.04810.08810.22120.2044-0.02670.14580.0323-0.0210.1636-0.02960.1351117.1459-197.2814281.209
629.14593.2867-2.67328.48446.37818.2468-0.41270.5732-0.2691-0.39870.40050.0501-0.1310.01010.02880.25340.0149-0.04430.3138-0.0180.2212127.1846-204.4744273.0311
634.80514.29510.52878.618-0.43222.3679-0.00440.23660.6234-0.9755-0.05360.5488-0.6967-0.3810.04380.36690.11360.00990.21420.02780.237494.6477-156.1403277.163
641.9573-0.79481.46532.72330.75041.99130.2987-0.0145-0.0995-0.5724-0.2849-0.0004-0.22960.10510.03960.26780.0440.02390.10110.0260.0824104.4112-173.0931270.0284
653.6479-0.2736-1.44152.42960.55253.0628-0.20650.95660.7261-0.2550.12740.1984-0.1812-0.3327-0.02810.27050.0332-0.02540.21390.07640.168899.0709-169.0974269.8318
660.6581-0.76640.7182.32250.81433.15220.20150.0170.0936-0.4487-0.1454-0.3885-0.54070.0789-0.06050.25720.00260.05540.13470.02410.1291108.2794-162.5874271.5989
672.56721.8597-0.64251.3666-0.43771.0750.0516-0.1662-0.3222-0.0032-0.11180.0101-0.1369-0.00390.08570.14640.02630.03360.13180.0110.1508102.9938-171.4038281.5344
681.1947-1.89980.47995.9149-1.0884.23390.08640.3390.04890.23210.07210.2798-0.6606-0.6572-0.06810.1690.0584-0.01470.1406-0.01340.161694.3381-163.251278.6137
693.84561.7424-1.88291.05080.27986.11370.20370.47570.2701-0.64290.00640.1152-0.2754-0.0579-0.18360.36970.06580.01520.23980.03420.1539102.5589-164.4737262.2137
700.7050.68051.18564.8405-0.43912.75990.1655-0.09210.2838-0.0905-0.04960.853-0.4894-0.9305-0.09380.2460.11480.04140.27230.02620.254692.8033-160.07282.8482
717.42113.1159-1.19655.36240.6912.12310.4097-0.35190.650.9423-0.0140.0316-0.05540.0298-0.1090.34030.0450.00250.1793-0.11460.1777106.1071-156.4776307.2304
721.3108-0.46381.52321.38010.44592.66630.15090.17080.41140.04090.0979-0.1134-0.6265-0.2857-0.13710.25330.05720.03310.0909-0.01640.1796101.4172-159.3307286.8538
731.09940.49690.73272.7748-0.90963.72920.45460.03870.47490.0749-0.08940.0737-0.9831-0.4709-0.29590.29380.02160.07080.0975-0.00490.202499.641-157.0544293.0592
741.451-1.16560.91651.0916-0.92841.5179-0.06590.01490.2864-0.09110.0178-0.315-0.4970.11930.05780.2994-0.02610.05430.0890.00260.2486110.8925-155.2628291.8601
753.41691.3062-0.52911.1162-0.53370.39720.26970.12060.00020.1888-0.10020.0574-0.09220.0173-0.13270.21450.00460.0620.1206-0.00980.171105.1576-168.299293.3126
762.11580.8052.948.59913.11354.4449-0.0371-0.15870.11150.48310.19820.281-0.2608-0.2871-0.03670.19610.06540.04210.1449-0.00160.1133102.3187-161.6469303.1889
770.2779-0.24550.22390.3075-0.36151.24520.00090.01920.15860.19010.0452-0.0163-0.5052-0.0982-0.03120.32470.0330.06150.1207-0.02050.1996103.9508-151.8769293.5227
787.27053.232.19814.72174.82045.6950.071-1.6836-0.11940.0794-0.37040.39460.0948-0.73010.15760.37770.0266-0.01190.3685-0.04030.1797102.5662-164.8068312.1604
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 67 )
2X-RAY DIFFRACTION2chain 'A' and (resid 68 through 81 )
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 95 )
4X-RAY DIFFRACTION4chain 'A' and (resid 96 through 104 )
5X-RAY DIFFRACTION5chain 'A' and (resid 105 through 120 )
6X-RAY DIFFRACTION6chain 'A' and (resid 121 through 139 )
7X-RAY DIFFRACTION7chain 'B' and (resid 22 through 33 )
8X-RAY DIFFRACTION8chain 'B' and (resid 34 through 45 )
9X-RAY DIFFRACTION9chain 'B' and (resid 46 through 58 )
10X-RAY DIFFRACTION10chain 'B' and (resid 59 through 67 )
11X-RAY DIFFRACTION11chain 'B' and (resid 68 through 95 )
12X-RAY DIFFRACTION12chain 'B' and (resid 96 through 104 )
13X-RAY DIFFRACTION13chain 'B' and (resid 105 through 120 )
14X-RAY DIFFRACTION14chain 'B' and (resid 121 through 139 )
15X-RAY DIFFRACTION15chain 'C' and (resid 22 through 33 )
16X-RAY DIFFRACTION16chain 'C' and (resid 34 through 58 )
17X-RAY DIFFRACTION17chain 'C' and (resid 59 through 81 )
18X-RAY DIFFRACTION18chain 'C' and (resid 82 through 95 )
19X-RAY DIFFRACTION19chain 'C' and (resid 96 through 110 )
20X-RAY DIFFRACTION20chain 'C' and (resid 111 through 127 )
21X-RAY DIFFRACTION21chain 'C' and (resid 128 through 139 )
22X-RAY DIFFRACTION22chain 'D' and (resid 22 through 33 )
23X-RAY DIFFRACTION23chain 'D' and (resid 34 through 45 )
24X-RAY DIFFRACTION24chain 'D' and (resid 46 through 58 )
25X-RAY DIFFRACTION25chain 'D' and (resid 59 through 67 )
26X-RAY DIFFRACTION26chain 'D' and (resid 68 through 72 )
27X-RAY DIFFRACTION27chain 'D' and (resid 73 through 81 )
28X-RAY DIFFRACTION28chain 'D' and (resid 82 through 95 )
29X-RAY DIFFRACTION29chain 'D' and (resid 96 through 104 )
30X-RAY DIFFRACTION30chain 'D' and (resid 105 through 127 )
31X-RAY DIFFRACTION31chain 'D' and (resid 128 through 139 )
32X-RAY DIFFRACTION32chain 'E' and (resid 22 through 33 )
33X-RAY DIFFRACTION33chain 'E' and (resid 34 through 58 )
34X-RAY DIFFRACTION34chain 'E' and (resid 59 through 67 )
35X-RAY DIFFRACTION35chain 'E' and (resid 68 through 95 )
36X-RAY DIFFRACTION36chain 'E' and (resid 96 through 104 )
37X-RAY DIFFRACTION37chain 'E' and (resid 105 through 120 )
38X-RAY DIFFRACTION38chain 'E' and (resid 121 through 139 )
39X-RAY DIFFRACTION39chain 'F' and (resid 22 through 33 )
40X-RAY DIFFRACTION40chain 'F' and (resid 34 through 45 )
41X-RAY DIFFRACTION41chain 'F' and (resid 46 through 67 )
42X-RAY DIFFRACTION42chain 'F' and (resid 68 through 95 )
43X-RAY DIFFRACTION43chain 'F' and (resid 96 through 104 )
44X-RAY DIFFRACTION44chain 'F' and (resid 105 through 120 )
45X-RAY DIFFRACTION45chain 'F' and (resid 121 through 139 )
46X-RAY DIFFRACTION46chain 'G' and (resid 22 through 33 )
47X-RAY DIFFRACTION47chain 'G' and (resid 34 through 58 )
48X-RAY DIFFRACTION48chain 'G' and (resid 59 through 67 )
49X-RAY DIFFRACTION49chain 'G' and (resid 68 through 81 )
50X-RAY DIFFRACTION50chain 'G' and (resid 82 through 95 )
51X-RAY DIFFRACTION51chain 'G' and (resid 96 through 104 )
52X-RAY DIFFRACTION52chain 'G' and (resid 105 through 120 )
53X-RAY DIFFRACTION53chain 'G' and (resid 121 through 139 )
54X-RAY DIFFRACTION54chain 'H' and (resid 22 through 33 )
55X-RAY DIFFRACTION55chain 'H' and (resid 34 through 45 )
56X-RAY DIFFRACTION56chain 'H' and (resid 46 through 67 )
57X-RAY DIFFRACTION57chain 'H' and (resid 68 through 81 )
58X-RAY DIFFRACTION58chain 'H' and (resid 82 through 95 )
59X-RAY DIFFRACTION59chain 'H' and (resid 96 through 104 )
60X-RAY DIFFRACTION60chain 'H' and (resid 105 through 120 )
61X-RAY DIFFRACTION61chain 'H' and (resid 121 through 138 )
62X-RAY DIFFRACTION62chain 'H' and (resid 139 through 145 )
63X-RAY DIFFRACTION63chain 'I' and (resid 22 through 33 )
64X-RAY DIFFRACTION64chain 'I' and (resid 34 through 45 )
65X-RAY DIFFRACTION65chain 'I' and (resid 46 through 67 )
66X-RAY DIFFRACTION66chain 'I' and (resid 68 through 81 )
67X-RAY DIFFRACTION67chain 'I' and (resid 82 through 95 )
68X-RAY DIFFRACTION68chain 'I' and (resid 96 through 104 )
69X-RAY DIFFRACTION69chain 'I' and (resid 105 through 120 )
70X-RAY DIFFRACTION70chain 'I' and (resid 121 through 139 )
71X-RAY DIFFRACTION71chain 'J' and (resid 22 through 33 )
72X-RAY DIFFRACTION72chain 'J' and (resid 34 through 45 )
73X-RAY DIFFRACTION73chain 'J' and (resid 46 through 67 )
74X-RAY DIFFRACTION74chain 'J' and (resid 68 through 81 )
75X-RAY DIFFRACTION75chain 'J' and (resid 82 through 95 )
76X-RAY DIFFRACTION76chain 'J' and (resid 96 through 104 )
77X-RAY DIFFRACTION77chain 'J' and (resid 105 through 127 )
78X-RAY DIFFRACTION78chain 'J' and (resid 128 through 139 )

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万見について

-
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