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- PDB-5hej: Pentameric ligand-gated ion channel ELIC mutant F116A -

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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: 5hej
タイトルPentameric ligand-gated ion channel ELIC mutant F116A
要素Gamma-aminobutyric-acid receptor subunit beta-1
キーワードTRANSPORT PROTEIN / Pentameric ligand-gated ion channels / Membrane protein / Ligand-gated ion channel
機能・相同性
機能・相同性情報


extracellular ligand-gated monoatomic ion channel activity / regulation of membrane potential / transmembrane signaling receptor activity / neuron projection / signal transduction / identical protein binding / membrane
類似検索 - 分子機能
Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 ...Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Distorted Sandwich / Up-down Bundle / Mainly Beta / Mainly Alpha
類似検索 - ドメイン・相同性
Gamma-aminobutyric-acid receptor subunit beta-1
類似検索 - 構成要素
生物種Dickeya dadantii (バクテリア)
手法X線回折 / シンクロトロン / 解像度: 3.5 Å
データ登録者Bertozzi, C. / Dutzler, R.
資金援助 スイス, 1件
組織認可番号
Swiss National Science Foundation スイス
引用ジャーナル: Plos Biol. / : 2016
タイトル: Signal Transduction at the Domain Interface of Prokaryotic Pentameric Ligand-Gated Ion Channels.
著者: Bertozzi, C. / Zimmermann, I. / Engeler, S. / Hilf, R.J. / Dutzler, R.
履歴
登録2016年1月6日登録サイト: RCSB / 処理サイト: PDBE
改定 1.02016年3月2日Provider: repository / タイプ: Initial release
改定 1.12016年3月16日Group: Database references
改定 1.22019年9月11日Group: Data collection / Refinement description / カテゴリ: refine_ls_shell / Item: _refine_ls_shell.R_factor_R_free
改定 1.32024年5月8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: Gamma-aminobutyric-acid receptor subunit beta-1
B: Gamma-aminobutyric-acid receptor subunit beta-1
C: Gamma-aminobutyric-acid receptor subunit beta-1
D: Gamma-aminobutyric-acid receptor subunit beta-1
E: Gamma-aminobutyric-acid receptor subunit beta-1
F: Gamma-aminobutyric-acid receptor subunit beta-1
G: Gamma-aminobutyric-acid receptor subunit beta-1
H: Gamma-aminobutyric-acid receptor subunit beta-1
I: Gamma-aminobutyric-acid receptor subunit beta-1
J: Gamma-aminobutyric-acid receptor subunit beta-1


分子量 (理論値)分子数
合計 (水以外)368,02910
ポリマ-368,02910
非ポリマー00
00
1
A: Gamma-aminobutyric-acid receptor subunit beta-1
B: Gamma-aminobutyric-acid receptor subunit beta-1
C: Gamma-aminobutyric-acid receptor subunit beta-1
D: Gamma-aminobutyric-acid receptor subunit beta-1
E: Gamma-aminobutyric-acid receptor subunit beta-1


分子量 (理論値)分子数
合計 (水以外)184,0155
ポリマ-184,0155
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area23740 Å2
ΔGint-156 kcal/mol
Surface area67360 Å2
手法PISA
2
F: Gamma-aminobutyric-acid receptor subunit beta-1
G: Gamma-aminobutyric-acid receptor subunit beta-1
H: Gamma-aminobutyric-acid receptor subunit beta-1
I: Gamma-aminobutyric-acid receptor subunit beta-1
J: Gamma-aminobutyric-acid receptor subunit beta-1


分子量 (理論値)分子数
合計 (水以外)184,0155
ポリマ-184,0155
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area23680 Å2
ΔGint-152 kcal/mol
Surface area67420 Å2
手法PISA
単位格子
Length a, b, c (Å)105.168, 266.994, 111.002
Angle α, β, γ (deg.)90.00, 110.25, 90.00
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質
Gamma-aminobutyric-acid receptor subunit beta-1


分子量: 36802.902 Da / 分子数: 10 / 由来タイプ: 組換発現
由来: (組換発現) Dickeya dadantii (strain 3937) (バクテリア)
: 3937 / 遺伝子: Dda3937_00520 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: E0SJQ4

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実験情報

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実験

実験手法: X線回折

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試料調製

結晶マシュー密度: 3.97 Å3/Da / 溶媒含有率: 69.04 %
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 / pH: 6.5 / 詳細: PEG 4000, 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: SLS / ビームライン: X06DA / 波長: 0.98 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2012年2月28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: 0.98 Å / 相対比: 1
反射解像度: 3.5→50 Å / Num. obs: 71671 / % possible obs: 99.4 % / 冗長度: 3.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.2
反射 シェル解像度: 3.5→3.6 Å / 冗長度: 3.6 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.10_2155: ???)精密化
XDSデータ削減
XDSデータスケーリング
PHASER位相決定
精密化解像度: 3.5→29.999 Å / SU ML: 0.5 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 29.58 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2545 3615 5.05 %
Rwork0.2133 --
obs0.2155 71528 99.36 %
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: 3.5→29.999 Å
タンパク質核酸リガンド溶媒全体
原子数24880 0 0 0 24880
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00225530
X-RAY DIFFRACTIONf_angle_d0.54334780
X-RAY DIFFRACTIONf_dihedral_angle_d13.63314940
X-RAY DIFFRACTIONf_chiral_restr0.0443880
X-RAY DIFFRACTIONf_plane_restr0.0044430
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5002-3.54620.33551660.32912442X-RAY DIFFRACTION94
3.5462-3.59470.3775810.30422636X-RAY DIFFRACTION100
3.5947-3.64590.31332070.2872557X-RAY DIFFRACTION99
3.6459-3.70030.4545690.28172703X-RAY DIFFRACTION99
3.7003-3.7580.31572200.28472527X-RAY DIFFRACTION100
3.758-3.81950.3259520.26682683X-RAY DIFFRACTION100
3.8195-3.88520.31072370.26742527X-RAY DIFFRACTION99
3.8852-3.95570.3371170.26252741X-RAY DIFFRACTION99
3.9557-4.03160.32842690.24862454X-RAY DIFFRACTION99
4.0316-4.11370.797920.24582758X-RAY DIFFRACTION99
4.1137-4.20290.29142870.23482446X-RAY DIFFRACTION99
4.2029-4.300400.21952736X-RAY DIFFRACTION99
4.3004-4.40760.26912870.212481X-RAY DIFFRACTION100
4.4076-4.526400.19042755X-RAY DIFFRACTION100
4.5264-4.65910.23762880.17892477X-RAY DIFFRACTION100
4.6591-4.808900.17492775X-RAY DIFFRACTION100
4.8089-4.980.24442880.18232463X-RAY DIFFRACTION100
4.98-5.178500.19662752X-RAY DIFFRACTION100
5.1785-5.41280.27632870.19352473X-RAY DIFFRACTION100
5.4128-5.696400.19442762X-RAY DIFFRACTION100
5.6964-6.05060.2452870.20352466X-RAY DIFFRACTION100
6.0506-6.513300.21682801X-RAY DIFFRACTION100
6.5133-7.16070.26912700.22812478X-RAY DIFFRACTION100
7.1607-8.17850.3251180.21112768X-RAY DIFFRACTION100
8.1785-10.23550.17921570.15852613X-RAY DIFFRACTION99
10.2355-29.99970.16751260.21122639X-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)
11.81630.66460.6441.5004-0.28920.27450.7462-0.2317-0.03910.54680.310.50631.0311-0.3161.34070.6106-0.1803-0.39110.7709-0.05260.3694-118.39-61.8754-65.3789
20.80660.22350.07790.693-0.7970.95310.3475-0.0937-0.5159-0.24080.06050.2440.0715-0.46250.00680.8029-0.0817-0.21280.8467-0.03030.6407-119.0392-57.9038-65.6991
34.1308-1.8834-1.560.86750.71240.5849-0.5867-0.93870.34290.4441-0.0386-1.17920.91920.3497-0.04961.8235-0.4229-0.32670.85120.03631.4299-119.2766-67.1857-42.7307
40.9178-0.6274-0.2271.12210.02931.0613-0.5483-0.4350.26110.6727-0.35971.2739-1.1834-0.5996-0.1040.94830.0986-0.44241.0644-0.05241.1866-132.0047-51.4886-63.8318
50.3620.4207-0.04411.4602-0.09470.00120.23930.19290.19980.36130.01221.11040.47870.0109-0.40820.8657-0.0803-0.01650.92630.20540.6951-124.2397-55.2363-45.0484
60.03540.0277-0.060.1319-0.02370.2504-0.0475-0.1726-0.35340.69010.04440.5304-0.30210.1004-0.00021.1091-0.04350.19830.93010.00330.6035-117.5516-39.9875-14.5034
71.26120.6064-1.01941.05280.55732.2837-0.01680.1157-1.04980.6409-0.21140.19420.7567-0.73070.19860.6652-0.08850.06521.20070.05220.3507-124.1403-36.3257-21.7111
80.4049-0.3013-0.02130.1823-0.01090.0546-0.1645-0.3081-0.16660.1047-0.55420.3416-0.2032-0.02050.10192.07410.59410.30331.23510.03880.739-131.9896-38.6261-8.7006
90.9587-0.5556-0.55291.14520.00580.73340.2441-0.34010.5341-0.33520.78410.5143-0.030.03871.53791.16180.15110.2786-1.1465-1.0095-0.1272-93.2314-68.2559-61.1727
101.56390.2329-0.5372.0868-0.0050.3340.06010.09-0.0278-0.406-0.0236-0.2359-0.2277-0.08990.00020.79090.0417-0.04730.4973-0.09130.4199-97.2507-67.5263-61.0908
110.43670.6236-0.72410.8922-1.04131.2276-0.4404-0.48180.6233-0.5842-0.871-1.2892-0.6524-0.1356-0.31631.1197-0.2164-0.35531.2404-0.25681.4312-85.3053-65.3126-39.5318
121.3114-0.0639-1.1350.82280.00260.9677-0.31690.2401-0.15530.6638-0.09890.78410.3073-0.2678-0.01950.96860.04940.00960.7534-0.05661.1635-107.0323-76.4751-55.3831
13-0.0865-0.11820.15450.70280.20010.0696-0.3344-0.42790.02090.51530.01180.42240.5547-0.66210.08691.04160.156-0.26810.8608-0.11270.5938-98.3911-66.1432-39.7699
140.3979-0.11870.51670.66721.02442.7967-0.1793-0.2054-0.24931.3391-0.3377-0.1706-0.3371.252-0.08041.56640.06740.03720.55550.0480.3722-106.1942-47.3527-11.5486
151.4346-0.18660.41250.0473-0.09030.1064-0.2656-0.4938-0.34340.06170.1557-0.1281-0.7218-0.03690.01291.16090.22410.02160.93010.05190.4459-112.7633-53.8772-16.4542
161.22020.43120.07750.198-0.06490.15050.2923-2.2224-0.69941.570.08750.4472-0.3425-0.745-0.10452.4990.42380.05241.5668-0.28641.4383-111.2734-58.5367-1.817
172.57090.7995-0.23220.5328-0.91091.01490.7669-0.3950.0478-0.1704-0.2845-0.9609-0.97630.22880.07330.6070.23390.26080.4368-0.01670.5917-78.6695-46.698-64.5055
180.4730.22280.75751.8596-0.22471.0501-0.079-0.1255-0.089-0.2838-0.077-0.44950.2621-0.3950.00130.83930.05230.14330.5958-0.02760.6934-80.6195-50.0484-63.3022
190.11920.0247-0.03310.1052-0.07750.06190.02490.74020.24590.7616-0.19760.694-0.9137-0.0589-0.00081.9254-0.37240.61610.8956-0.17481.7155-75.7837-33.2336-45.8325
200.6927-0.09950.16713.57860.69642.442-0.5487-0.6558-0.75121.061-0.90491.12471.22730.3575-0.25110.93680.18440.24140.64890.05761.1767-74.4316-60.6764-55.5627
210.6363-0.0235-0.66770.570.18560.6639-0.0435-0.8034-0.60321.14050.3616-0.26480.99210.839-0.0920.92530.06680.0750.9029-0.1081-79.1676-45.4695-42.3829
220.54690.4293-0.36830.7527-0.09780.3594-0.3455-0.6562-0.25950.55590.3787-0.42790.10120.3161-0.01260.8580.2503-0.13110.9213-0.05750.3049-95.2586-39.161-12.2282
230.95610.26920.09230.4057-0.06610.06460.2386-0.1554-0.25480.534-0.0245-0.5127-0.44030.69240.01071.04290.0522-0.2951.05820.08080.5728-91.9276-48.5503-15.4325
240.1575-0.30420.08180.4534-0.22910.1191-0.9591-0.0501-0.84380.1849-0.26460.3285-0.66550.63470.00251.01750.12950.0772.1827-0.07291.1753-85.0383-45.2701-2.1077
250.63640.4387-0.01991.2888-0.58092.41170.0697-0.0610.21540.2292-0.3507-0.4351-0.4249-0.5631-0.53240.54240.04710.08510.54860.12420.3392-94.8412-26.9118-70.6164
261.08160.06330.3671.39810.04931.17090.0634-0.03160.2097-0.0863-0.0901-0.12140.4131-0.2175-0.0290.77640.15820.1290.51180.09070.4088-92.137-29.5318-69.0855
272.7752-0.5594-2.7661.227-0.86634.4624-0.1848-0.513-0.7593-0.14420.0051.3330.2582-0.8432-0.26760.36160.6032-0.15811.7920.48081.0485-103.8984-15.0904-52.7945
280.47050.60730.26094.1809-1.73861.29230.32860.09090.23761.7062-0.1635-0.4548-0.25660.36790.18610.57010.1022-0.16610.90130.06710.9321-79.1043-25.7226-63.9136
290.38440.49490.01260.7619-0.00720.3650.5249-0.34690.75580.26050.6586-0.6303-0.66820.16831.71131.03220.17390.24650.72860.01340.9172-93.0142-21.544-49.2229
300.43990.04660.570.06790.03520.6103-0.2584-1.05230.51961.6165-0.39690.5827-0.0615-0.5994-2.27712.444-0.20910.60370.7279-0.17810.1868-99.7688-26.5324-15.5143
310.5506-0.67840.22240.6857-0.12820.110.1315-0.85220.4112-0.54230.4407-0.5134-0.25090.06910.00820.9912-0.185-0.03631.1154-0.21780.7865-90.3668-27.5534-19.9352
320.72590.36910.30930.13650.10380.1254-0.1134-0.87730.1654-0.1150.0736-0.0244-0.22970.9120.00021.4258-0.26240.12661.4307-0.07971.2086-89.3844-16.8282-8.9324
332.93130.10071.61070.45180.33591.2214-0.0413-0.63631.0004-0.326-0.01510.649-0.0011-1.3398-0.14390.9090.0747-0.1940.64030.25630.454-119.3964-36.2284-71.2644
342.3421-0.24650.68871.2724-0.88750.6485-0.22710.142-0.0392-0.06650.23580.61960.43070.1318-0.01550.73040.1112-0.12060.86780.11880.4797-115.8882-34.3074-70.6954
352.1635-2.8869-1.02653.91171.43820.6670.39980.187-1.6344-0.2098-0.75540.15110.4822-0.2449-0.75941.6789-0.2920.45111.47990.65331.5331-130.9503-35.9584-51.1505
361.01360.40190.28090.84790.34871.17690.6884-0.51770.52850.5443-0.07180.7379-0.75620.76030.05511.00910.159-0.0181.04010.19670.7377-114.6055-19.9024-69.137
370.1333-0.37180.0240.8204-0.26580.3847-0.11970.38280.45850.0525-0.05090.0531-0.2706-1.45930.03330.8650.01270.18031.01690.04930.8089-120.953-27.4775-51.0076
380.4493-0.15690.32110.0347-0.1930.4687-0.0319-0.19830.02271.0407-0.20170.76840.0929-0.5682-0.05561.15910.2868-0.02560.8097-0.01120.3469-113.6748-27.0213-17.0077
391.8165-0.38960.25420.6561-0.38620.32680.0012-0.2285-0.3431.01140.03420.33020.1425-0.0727-0.00061.33910.0170.18770.73080.00670.6613-110.3451-20.0084-23.9073
400.3820.1968-0.13420.5503-0.09550.05960.04230.4257-0.35630.9623-0.13810.0619-0.23580.47780.00041.4415-0.0788-0.08361.63530.07620.6219-118.5825-12.6714-13.102
41-0.06290.4351-0.20382.7912-0.94771.452-0.29370.0385-0.43030.89550.2586-0.4104-0.0202-0.1212-0.17230.594-0.06110.21880.82530.06120.5312-99.3977-129.4674-20.015
420.5428-0.62120.08841.25050.4541.6665-0.32240.19530.05660.22580.35820.1345-0.0164-0.012-0.01740.64830.10370.14230.56360.16420.7127-99.6796-125.505-19.1943
431.59350.18690.7430.10440.0760.33690.62550.51310.1401-1.35230.68450.24360.45020.61970.10722.1983-0.68030.55431.6347-0.19711.1023-76.8533-134.9215-20.5749
441.93540.43140.16792.21070.5490.1904-0.1471-0.084-0.76430.8796-0.2914-0.5298-0.4552-0.32070.13221.57720.15070.27291.40140.34180.5469-97.1328-119.6502-6.1072
450.1299-0.0763-0.14770.54250.07590.3506-0.307-0.70760.09771.9882-0.2111-0.207-0.42660.4454-0.19520.86930.1589-0.09561.06140.25831.0777-78.7861-123.088-14.9884
460.1786-0.1013-0.25130.3436-0.00110.39050.00830.12480.28970.1242-0.1404-0.8780.11540.2608-0.09030.6095-0.1117-0.36321.02450.31281.4534-48.6277-107.6329-22.6512
470.3521-0.1978-0.21450.5834-0.40061.0341-0.1437-1.13930.00120.23880.04310.17030.2970.4724-0.00320.6494-0.0262-0.23961.1403-0.01091.0324-55.4661-104.2306-15.488
480.01620.0331-0.1440.18710.39120.83760.6869-0.46380.79320.7592-0.7404-0.00940.08861.2180.00161.2131-0.1823-0.05191.40830.0521.114-42.071-106.8396-8.4471
490.90670.63861.15192.41740.80792.5956-0.34310.9985-0.0235-0.21090.6167-0.2511-0.11720.39611.10470.46950.0236-0.00960.34540.16330.8442-96.6665-134.9206-45.6251
500.2898-0.38570.42912.3671-0.16391.9297-0.1619-0.25270.2082-0.2024-0.01060.14880.2053-0.1737-0.0140.6361-0.12420.06050.6613-0.08240.7472-96.3707-134.3584-41.6295
510.08890.16610.03810.3990.08980.05530.04091.30370.6722-0.8171-1.53620.0583-0.9924-0.156-0.02311.8772-0.24610.10821.72210.35131.2793-75.4109-131.8061-54.5461
521.5595-0.01881.49880.1727-0.1011.85780.4078-0.6627-0.70810.4931-0.3563-0.9038-0.44720.3686-0.00091.1516-0.03060.28180.67540.07420.9822-90.1796-143.6859-32.2968
531.57-0.0557-0.07060.72970.26120.0784-0.47530.3963-0.05310.45490.78810.30210.14130.12420.07120.6129-0.07670.24750.7543-0.01060.886-74.9786-133.0634-41.4185
540.08790.2337-0.03520.49230.01790.4321-0.02090.26990.46870.2761-0.05820.41670.3670.6318-0.00080.49140.1621-0.02790.73390.08211.2673-46.3842-114.6251-34.4174
550.4389-0.3299-0.77870.6860.77621.45790.0935-0.35320.3899-0.4842-0.3242-0.22610.18530.1861-0.00360.48330.0778-0.04850.6970.08991.0864-50.9604-121.3397-27.862
560.07130.0341-0.1550.0173-0.10810.40630.0485-0.5563-0.56670.3536-0.16060.21790.08181.0969-0.00211.4625-0.36640.18821.4327-0.05492.3829-36.4848-125.9777-30.3178
570.02280.21910.04550.89980.04842.2027-0.38560.65520.5605-0.44570.15740.0554-0.1060.51270.00010.746-0.053-0.18390.5579-0.11640.5899-100.672-112.9503-59.2411
581.5665-0.8277-0.11582.3499-0.85291.4513-0.3185-0.3181-0.5017-0.37790.20060.37860.12230.0043-0.03630.6389-0.1274-0.0650.5604-0.06450.7527-99.3689-116.3468-57.4904
590.09610.00860.09920.07430.08280.1376-0.1141-0.38280.11131.7409-0.3024-0.57880.0717-0.61010.00031.2995-0.1403-0.02541.0925-0.27731.7419-82.2175-99.3471-62.5519
601.4065-1.05880.03750.7715-0.16360.5080.80040.7557-0.69380.8914-0.3629-0.81350.18340.19890.1291.0081-0.1981-0.18051.004-0.34830.8327-91.9637-126.7583-64.4221
610.28820.01110.17030.5894-0.18090.0915-0.5160.592-0.0073-1.01660.1177-0.33680.60940.54080.04970.9055-0.043-0.03480.63960.16290.8652-78.5672-111.6995-59.8329
621.3668-0.4077-0.18970.11450.04380.20370.16090.83760.0720.08990.3312-1.8955-0.690.04550.03470.64-0.00190.06721.06270.09921.6309-45.1538-103.5119-50.0711
630.1446-0.09360.1240.4777-0.2150.19260.1807-0.46950.32480.4177-0.4919-0.38660.0832-0.2574-0.00020.83060.0810.01450.81410.03291.1386-49.4772-107.6897-41.3716
640.02620.0719-0.07030.5146-0.41842.24480.0536-1.0219-0.0056-0.1506-0.0926-1.0426-0.26520.0661-0.00150.4569-0.0844-0.08480.7051-0.13471.1816-51.0448-115.1716-48.5059
650.887-1.6297-0.97163.46082.08771.27740.03290.62270.5979-1.51571.1532-1.12441.51240.69560.75181.41-0.536-0.29991.89140.53511.3656-38.045-111.6407-56.0353
661.54690.2775-0.22361.1988-0.4630.7993-0.3847-0.32110.6735-0.35440.298-0.60940.0750.15460.18550.25010.1214-0.03570.50390.15451.0495-105.9075-93.7906-41.9614
670.5176-0.18570.30011.20480.46960.7452-0.212-0.473-0.0668-0.14350.0792-0.0487-0.12860.0726-0.02170.45950.0163-0.0480.53680.00930.9415-104.5356-96.2998-44.8577
681.16381.02570.2132.2515-0.86982.20260.4298-1.37830.39391.03090.3629-0.18170.19910.64221.72360.85890.49230.0032.2998-0.65640.224-87.7157-82.3124-33.3791
691.71891.3754-1.00941.2192-1.01130.76620.22390.6978-0.6665-0.44550.3697-1.94660.86850.4361-0.15390.6993-0.0054-0.37060.6921-0.01130.9636-100.0111-92.0021-57.9576
700.0830.0960.13430.4715-0.15490.0888-0.5595-0.19430.5743-0.70960.2369-0.2677-0.1682-0.0911-0.38740.6683-0.0028-0.3160.739-0.15531.1691-84.6681-88.3296-44.6584
712.40020.05780.94160.070.21921.0465-0.1765-0.0790.62840.1734-0.2632-0.9584-0.48251.0176-0.4820.5281-0.0342-0.16240.70620.39622.1739-49.2447-87.5115-39.6025
720.4236-0.20860.01120.1999-0.22230.3911-0.1357-0.442-0.68880.46580.36490.0516-0.08970.30620.1652-0.00070.3051-0.37290.70510.63612.4825-51.6364-97.8266-40.1013
730.0487-0.14380.13431.17750.22440.8642-0.0757-0.421-1.575-0.13030.23660.0103-0.19040.56550.00860.5925-0.1467-0.30060.93930.21111.0278-55.5711-94.1598-49.0861
740.03840.05820.07890.11260.17740.7007-0.65331.1689-0.41590.2437-0.2691-0.8461-0.06781.13820.00090.8129-0.015-0.2491.42540.18821.9656-44.5857-83.4071-50.2164
750.3448-0.0179-0.65060.25460.25291.7813-0.1319-1.13210.07340.50130.0948-0.0419-0.62310.51780.00190.4920.17480.09020.7324-0.02880.8451-105.1308-103.8422-17.5906
760.1414-0.0183-0.24931.3115-1.1391.6295-0.1775-0.3770.36710.51650.16390.37460.1022-0.23650.00290.56230.04620.16580.727-0.06870.8435-104.7505-101.871-21.1336
770.3228-0.3118-0.39850.3640.46760.6441-0.15390.13530.04210.1472-0.9966-0.58571.6846-0.1715-0.1071.42640.0375-0.10561.14410.41551.462-84.4339-104.0045-7.2031
784.82030.56220.82651.0383-1.00481.28611.22521.49551.58790.46330.4461-0.3524-0.93910.55850.41311.22090.5959-0.14321.3577-0.25161.0907-103.2743-87.4669-22.0428
790.85170.4231-0.3150.8124-0.30820.26530.0213-0.63810.2414-0.0519-0.2633-0.1534-1.05070.2078-0.01241.00750.1068-0.06041.3027-0.22550.9564-84.8205-95.231-16.9743
800.0340.0625-0.16560.0983-0.2570.7512-0.1287-0.44510.99990.0179-0.2376-0.54510.64090.4234-0.10630.6514-0.0129-0.22031.0936-0.28331.3369-51.2575-94.5285-26.0388
810.4305-0.192-0.1340.40080.38191.5456-0.3108-0.01830.07060.96140.1608-0.3132-0.2850.0815-0.00880.6452-0.0847-0.29420.7688-0.10671.1738-58.385-87.3866-28.7899
822.32741.47530.53333.33961.47690.65450.537-0.2589-0.6780.7151.1157-1.3436-1.2757-1.23780.38871.30250.3605-0.10321.93760.58791.7918-47.1083-80.3825-20.985
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 55 )
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 146 )
3X-RAY DIFFRACTION3chain 'A' and (resid 147 through 159 )
4X-RAY DIFFRACTION4chain 'A' and (resid 160 through 186 )
5X-RAY DIFFRACTION5chain 'A' and (resid 187 through 208 )
6X-RAY DIFFRACTION6chain 'A' and (resid 209 through 252 )
7X-RAY DIFFRACTION7chain 'A' and (resid 253 through 286 )
8X-RAY DIFFRACTION8chain 'A' and (resid 287 through 317 )
9X-RAY DIFFRACTION9chain 'B' and (resid 11 through 55 )
10X-RAY DIFFRACTION10chain 'B' and (resid 56 through 146 )
11X-RAY DIFFRACTION11chain 'B' and (resid 147 through 159 )
12X-RAY DIFFRACTION12chain 'B' and (resid 160 through 186 )
13X-RAY DIFFRACTION13chain 'B' and (resid 187 through 208 )
14X-RAY DIFFRACTION14chain 'B' and (resid 209 through 252 )
15X-RAY DIFFRACTION15chain 'B' and (resid 253 through 286 )
16X-RAY DIFFRACTION16chain 'B' and (resid 287 through 317 )
17X-RAY DIFFRACTION17chain 'C' and (resid 11 through 55 )
18X-RAY DIFFRACTION18chain 'C' and (resid 56 through 146 )
19X-RAY DIFFRACTION19chain 'C' and (resid 147 through 159 )
20X-RAY DIFFRACTION20chain 'C' and (resid 160 through 186 )
21X-RAY DIFFRACTION21chain 'C' and (resid 187 through 208 )
22X-RAY DIFFRACTION22chain 'C' and (resid 209 through 252 )
23X-RAY DIFFRACTION23chain 'C' and (resid 253 through 286 )
24X-RAY DIFFRACTION24chain 'C' and (resid 287 through 317 )
25X-RAY DIFFRACTION25chain 'D' and (resid 11 through 55 )
26X-RAY DIFFRACTION26chain 'D' and (resid 56 through 146 )
27X-RAY DIFFRACTION27chain 'D' and (resid 147 through 159 )
28X-RAY DIFFRACTION28chain 'D' and (resid 160 through 186 )
29X-RAY DIFFRACTION29chain 'D' and (resid 187 through 208 )
30X-RAY DIFFRACTION30chain 'D' and (resid 209 through 252 )
31X-RAY DIFFRACTION31chain 'D' and (resid 253 through 286 )
32X-RAY DIFFRACTION32chain 'D' and (resid 287 through 317 )
33X-RAY DIFFRACTION33chain 'E' and (resid 11 through 55 )
34X-RAY DIFFRACTION34chain 'E' and (resid 56 through 146 )
35X-RAY DIFFRACTION35chain 'E' and (resid 147 through 159 )
36X-RAY DIFFRACTION36chain 'E' and (resid 160 through 186 )
37X-RAY DIFFRACTION37chain 'E' and (resid 187 through 208 )
38X-RAY DIFFRACTION38chain 'E' and (resid 209 through 252 )
39X-RAY DIFFRACTION39chain 'E' and (resid 253 through 286 )
40X-RAY DIFFRACTION40chain 'E' and (resid 287 through 317 )
41X-RAY DIFFRACTION41chain 'F' and (resid 11 through 55 )
42X-RAY DIFFRACTION42chain 'F' and (resid 56 through 146 )
43X-RAY DIFFRACTION43chain 'F' and (resid 147 through 159 )
44X-RAY DIFFRACTION44chain 'F' and (resid 160 through 186 )
45X-RAY DIFFRACTION45chain 'F' and (resid 187 through 208 )
46X-RAY DIFFRACTION46chain 'F' and (resid 209 through 252 )
47X-RAY DIFFRACTION47chain 'F' and (resid 253 through 286 )
48X-RAY DIFFRACTION48chain 'F' and (resid 287 through 317 )
49X-RAY DIFFRACTION49chain 'G' and (resid 11 through 55 )
50X-RAY DIFFRACTION50chain 'G' and (resid 56 through 146 )
51X-RAY DIFFRACTION51chain 'G' and (resid 147 through 159 )
52X-RAY DIFFRACTION52chain 'G' and (resid 160 through 186 )
53X-RAY DIFFRACTION53chain 'G' and (resid 187 through 208 )
54X-RAY DIFFRACTION54chain 'G' and (resid 209 through 252 )
55X-RAY DIFFRACTION55chain 'G' and (resid 253 through 286 )
56X-RAY DIFFRACTION56chain 'G' and (resid 287 through 317 )
57X-RAY DIFFRACTION57chain 'H' and (resid 11 through 55 )
58X-RAY DIFFRACTION58chain 'H' and (resid 56 through 146 )
59X-RAY DIFFRACTION59chain 'H' and (resid 147 through 159 )
60X-RAY DIFFRACTION60chain 'H' and (resid 160 through 186 )
61X-RAY DIFFRACTION61chain 'H' and (resid 187 through 208 )
62X-RAY DIFFRACTION62chain 'H' and (resid 209 through 227 )
63X-RAY DIFFRACTION63chain 'H' and (resid 228 through 252 )
64X-RAY DIFFRACTION64chain 'H' and (resid 253 through 286 )
65X-RAY DIFFRACTION65chain 'H' and (resid 287 through 317 )
66X-RAY DIFFRACTION66chain 'I' and (resid 11 through 55 )
67X-RAY DIFFRACTION67chain 'I' and (resid 56 through 146 )
68X-RAY DIFFRACTION68chain 'I' and (resid 147 through 159 )
69X-RAY DIFFRACTION69chain 'I' and (resid 160 through 186 )
70X-RAY DIFFRACTION70chain 'I' and (resid 187 through 208 )
71X-RAY DIFFRACTION71chain 'I' and (resid 209 through 227 )
72X-RAY DIFFRACTION72chain 'I' and (resid 228 through 252 )
73X-RAY DIFFRACTION73chain 'I' and (resid 253 through 286 )
74X-RAY DIFFRACTION74chain 'I' and (resid 287 through 317 )
75X-RAY DIFFRACTION75chain 'J' and (resid 11 through 55 )
76X-RAY DIFFRACTION76chain 'J' and (resid 56 through 146 )
77X-RAY DIFFRACTION77chain 'J' and (resid 147 through 159 )
78X-RAY DIFFRACTION78chain 'J' and (resid 160 through 186 )
79X-RAY DIFFRACTION79chain 'J' and (resid 187 through 208 )
80X-RAY DIFFRACTION80chain 'J' and (resid 209 through 252 )
81X-RAY DIFFRACTION81chain 'J' and (resid 253 through 286 )
82X-RAY DIFFRACTION82chain 'J' and (resid 287 through 317 )

+
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