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- PDB-5heu: Pentameric ligand-gated ion channel ELIC mutant A257Y -

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データを開く


IDまたはキーワード:

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基本情報

登録情報
データベース: PDB / ID: 5heu
タイトルPentameric ligand-gated ion channel ELIC mutant A257Y
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 / transmembrane signaling receptor activity / 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 / 分子置換 / 解像度: 3.2 Å
データ登録者Bertozzi, C. / Dutzler, R.
資金援助 スイス, 1件
組織認可番号国
Swiss National Science Foundation スイス
引用ジャーナル: Plos Biol. / 年: 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1月10日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)367,86910
ポリマ－367,86910
非ポリマー00
水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)183,9355
ポリマ－183,9355
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area23020 Å2
ΔGint-131 kcal/mol
Surface area67020 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)183,9355
ポリマ－183,9355
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area23080 Å2
ΔGint-131 kcal/mol
Surface area67060 Å2
手法PISA
単位格子
Length a, b, c (Å)105.000, 266.610, 110.710
Angle α, β, γ (deg.)90.00, 110.47, 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: 36786.906 Da / 分子数: 10 / 変異: A257Y / 由来タイプ: 組換発現
由来: (組換発現) Dickeya dadantii (strain 3937) (バクテリア)
株: 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: 3.95 Å3/Da / 溶媒含有率: 68.83 %
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: X06SA / 波長: 0.978 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2013年7月14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: 0.978 Å / 相対比: 1
反射解像度: 3.2→50 Å / Num. obs: 93158 / % possible obs: 99.3 % / 冗長度: 3.9 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 15.2
反射 シェル解像度: 3.2→3.3 Å / 冗長度: 3.8 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.3 / % possible all: 99.2

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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
精密化構造決定の手法: 分子置換
開始モデル: 2yn6

2yn6


解像度: 3.2→29.939 Å / SU ML: 0.47 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 27.52 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2467 4689 5.04 %
Rwork0.2197 --
obs0.2211 93029 99.48 %
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: 3.2→29.939 Å
タンパク質核酸リガンド溶媒全体
原子数24980 0 0 0 24980
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00325650
X-RAY DIFFRACTIONf_angle_d0.58434960
X-RAY DIFFRACTIONf_dihedral_angle_d13.47715020
X-RAY DIFFRACTIONf_chiral_restr0.0443900
X-RAY DIFFRACTIONf_plane_restr0.0044460
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.23630.41121600.37632945X-RAY DIFFRACTION99
3.2363-3.27440.4071380.34882951X-RAY DIFFRACTION99
3.2744-3.31430.38251470.33182893X-RAY DIFFRACTION99
3.3143-3.35620.33672150.30742935X-RAY DIFFRACTION99
3.3562-3.40030.36661040.29432963X-RAY DIFFRACTION99
3.4003-3.44680.30831840.27822898X-RAY DIFFRACTION99
3.4468-3.49590.34851280.26822999X-RAY DIFFRACTION99
3.4959-3.5480.281610.25532907X-RAY DIFFRACTION99
3.548-3.60340.31361540.26822940X-RAY DIFFRACTION99
3.6034-3.66240.29611360.27062936X-RAY DIFFRACTION100
3.6624-3.72540.31432590.26512897X-RAY DIFFRACTION100
3.7254-3.7930.2857410.24683012X-RAY DIFFRACTION100
3.793-3.86580.28232750.24132846X-RAY DIFFRACTION100
3.8658-3.94460.3963360.23133073X-RAY DIFFRACTION100
3.9446-4.03010.24362530.21352854X-RAY DIFFRACTION100
4.0301-4.12370.29710.21163013X-RAY DIFFRACTION100
4.1237-4.22650.23362160.20892878X-RAY DIFFRACTION100
4.2265-4.34050.2495900.2032997X-RAY DIFFRACTION100
4.3405-4.46780.22751960.1992889X-RAY DIFFRACTION100
4.4678-4.61150.21181800.18182938X-RAY DIFFRACTION100
4.6115-4.77570.1851080.17153018X-RAY DIFFRACTION99
4.7757-4.96610.22782870.18362783X-RAY DIFFRACTION99
4.9661-5.19100.18753095X-RAY DIFFRACTION100
5.191-5.46310.22542880.18362832X-RAY DIFFRACTION100
5.4631-5.80300.18983107X-RAY DIFFRACTION100
5.803-6.24740.23412890.20532836X-RAY DIFFRACTION100
6.2474-6.869200.23333117X-RAY DIFFRACTION100
6.8692-7.84750.27362890.22652821X-RAY DIFFRACTION100
7.8475-9.828600.17153130X-RAY DIFFRACTION100
9.8286-29.94020.17242840.21892837X-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)
10.5092-0.24440.64840.6301-0.49970.51230.43470.0317-0.33730.32870.17670.24870.5939-0.27650.30420.4543-0.0128-0.15770.5393-0.07810.3463-118.0972-61.4076-64.2204
20.25380.11560.13670.871-0.44470.45410.1874-0.1821-0.3072-0.15280.00020.36270.0234-0.01700.4599-0.0372-0.14160.4757-0.0180.4325-118.7561-57.4155-64.3644
3-0.0093-0.01520.01740.05480.0073-0.0055-0.63170.1052-0.3729-1.26780.66090.53271.29910.0577-0.00011.4859-0.2575-0.0370.78520.04011.0747-119.1656-67.0899-41.7508
40.33360.80160.33231.77471.59862.883-0.1598-0.25540.32040.4194-0.62651.33151.0088-0.8872-1.3107-0.0378-0.0529-0.1490.58770.0090.631-128.0363-52.9556-54.0961
50.4201-0.33140.29450.64880.09950.3926-0.3310.1072-0.30530.2577-0.0080.5803-0.1229-0.0429-0.16140.77970.08430.26250.4940.05130.2003-119.8602-38.5466-16.2167
60.1979-0.01860.0088-0.02360.0418-0.0075-0.04650.3196-0.23370.60590.36310.0396-0.0905-0.23220.05471.9750.17690.29491.3040.0640.7531-132.0477-38.212-7.2695
70.4490.2798-0.28090.6062-0.29690.3214-0.00550.0490.213-0.20520.1261-0.02330.0571-0.13240.02490.61820.00510.02740.39220.00230.3764-93.6076-66.1653-64.0336
80.3062-0.44750.10610.5475-0.13850.0257-0.7011-0.1829-0.30.5061-0.290.81510.3765-0.0719-0.0010.77620.09580.00840.50440.00380.529-103.0887-66.6269-40.1933
90.2322-0.244-0.35281.7386-0.60981.3005-0.03780.11370.3106-0.8475-1.0451-0.51820.3586-0.1291-0.35510.8333-0.0364-0.0470.7712-0.12430.413-99.159-76.5045-62.2538
100.03350.03250.0080.03680.05510.0714-0.05970.2454-0.4008-0.191-0.6705-0.1944-0.5891-0.3835-0.00180.57310.06590.05310.7117-0.14480.8286-84.997-65.2892-38.4407
110.2976-0.51570.17620.25130.4210.5212-0.2683-0.1481-0.86790.52090.05470.47750.3751-0.2506-0.14340.59910.0402-0.12170.38530.01040.3277-102.7773-71.3647-47.1723
121.0647-0.2685-0.22751.3068-0.61960.3224-0.18490.0146-0.11490.473-0.00830.04850.23130.0342-0.31220.88730.070.0750.44390.04050.3077-108.4757-49.8773-12.364
131.905-0.5218-1.19420.14460.33850.77530.1225-2.0756-0.71670.3039-0.1730.4295-0.1120.6667-0.11591.83890.12970.34771.23010.08040.8995-111.4487-58.5593-0.3136
140.7809-0.07610.25460.8514-0.1830.31760.256-0.2861-0.0591-0.0465-0.1821-0.5419-0.42080.4551-0.01910.4720.06330.12410.3807-0.07020.4624-78.4129-46.4428-63.166
15-0.02080.2580.12981.1077-0.64070.9808-0.1604-0.0825-0.1336-0.41850.0138-0.44990.3689-0.292-0.02130.48730.05150.06330.3792-0.02210.3983-80.4152-49.7664-61.8234
160.0573-0.10640.22340.1944-0.3930.8805-0.38370.5815-0.11950.82050.53841.80980.25620.34830.00111.0298-0.54370.39960.2578-0.28511.2131-75.3145-32.9855-44.6312
170.4581-0.1193-0.53580.549-0.60860.9671-0.1931-0.4447-0.12480.31130.2112-0.37360.43280.6784-0.08150.48920.0699-0.03870.63210.01650.7082-76.3884-53.3893-48.3132
180.3205-0.0229-0.49850.807-0.18420.5503-0.0227-0.1457-0.10540.4046-0.08450.02230.11970.3521-0.08060.63260.0805-0.12490.5903-0.00710.2008-93.7654-42.665-12.3729
190.05430.0213-0.00880.30380.02210.0044-0.0265-0.3308-0.7758-0.15620.3322-0.0953-0.78410.6345-0.00021.57260.20880.01961.7165-0.13151.028-84.8895-45.4435-0.4331
200.5045-0.1478-0.3510.9435-0.07580.17140.14490.05740.05130.0029-0.1396-0.3871-0.0685-0.3314-0.00780.46830.08160.08670.46340.04760.4144-94.483-26.6912-69.2535
210.14840.24830.31411.50550.11991.28030.0235-0.01660.018-0.084-0.0359-0.21470.3596-0.04790.14220.52940.10760.13480.3906-0.01890.3808-91.7828-29.2586-67.6014
222.26461.7357-2.52672.1762-1.53243.0742-0.8798-0.0656-0.5432-0.67660.2343-0.07760.51310.2594-0.13650.1750.4868-0.2071.54120.53030.6048-103.5355-14.7152-51.678
230.20080.22170.4207-0.05780.17381.04990.43680.26260.48940.09830.1123-0.3741-0.7119-0.1259-0.03410.57620.03930.17050.3134-0.04040.6524-85.2946-23.6573-55.926
240.56010.15980.26411.1222-0.92420.7719-0.1515-0.20140.21650.25190.1366-0.1119-0.00410.3607-0.15440.68820.00210.03410.4801-0.09240.2759-95.9522-26.8049-16.1405
250.30080.14840.15030.05230.0090.0984-0.2694-0.81880.30160.1056-0.34810.3139-0.2281-0.2158-0.00021.2537-0.15540.25481.2715-0.091.0354-88.8977-16.7893-7.2492
260.6120.26610.62890.21280.13740.8274-0.1315-0.44240.78120.119-0.31310.6387-0.0527-0.7671-0.36990.46280.2273-0.30250.47040.2609-0.0897-118.9507-35.9308-69.9304
270.6345-0.00980.34860.4164-0.43740.4308-0.09240.01770.0896-0.11470.25240.25050.07020.16190.04370.53630.085-0.0520.57010.09350.3194-115.4932-33.965-69.176
281.3341-1.14050.080.9831-0.08840.00880.45380.193-0.8096-0.6344-0.50540.3178-0.2160.7385-0.25250.6792-0.28070.29830.65581.1710.8865-130.7271-35.7721-49.9833
290.1301-0.20960.01030.92170.84011.15150.00170.14940.2791-0.00830.08010.1826-0.9693-0.6577-0.17250.57010.14770.05320.64920.12050.5729-117.2149-23.2907-59.5226
300.4141-0.02620.63170.5055-0.52760.90730.036-0.11460.04630.21450.02920.196-0.5395-0.0786-0.23670.73870.12940.11190.4875-0.02120.2521-112.1076-24.2361-18.5275
310.24890.0829-0.1170.02580.05130.2057-0.28740.0197-0.3291.1915-0.21590.79180.19160.47880.01771.59160.15460.171.24790.03560.5949-118.1459-12.2653-11.4596
32-0.09170.05190.0059-0.020.41530.7707-0.2184-0.00540.02080.11210.11350.06050.0499-0.0963-0.10010.3187-0.03080.13430.40950.06670.457-103.0956-128.8646-22.8797
33-0.00510.0607-0.05090.466-0.45590.3604-0.052-0.30730.74940.6340.008-0.2119-0.34530.09960.00010.79220.04780.05960.6382-0.00570.6943-81.1591-119.6817-13.1882
341.7560.3242-0.16220.30390.59791.64660.1266-0.9544-0.44190.26570.15080.84580.5955-0.54410.42880.2998-0.01660.18220.74480.08120.7595-104.0578-127.9616-11.1056
350.08390.0127-0.07230.1832-0.07960.07030.1124-0.01290.1402-0.97550.82380.57610.4783-0.6930.00831.2738-0.25820.36370.8759-0.00770.6507-77.0106-135.6132-21.1555
360.61730.6749-0.03930.47810.00470.24640.0196-0.5308-0.57320.6202-0.2884-0.2186-0.01870.11840.0480.61460.02740.05440.75650.07310.5612-88.8336-122.1686-10.6036
370.6917-0.2762-0.65690.9021-0.00860.70460.0292-0.50120.10480.56790.0228-0.24280.1072-0.07550.0493-0.50.0319-0.66610.54590.19960.5621-51.462-107.0466-19.5784
380.13670.1301-0.18460.88180.22320.26630.4151-0.40790.3343-0.0698-0.4465-1.01580.3610.70780.01580.9204-0.0557-0.30161.4683-0.01041.0931-41.8796-107.5355-7.8946
390.56230.3621-0.0361.3247-0.13841.0702-0.2010.73330.0322-0.35750.43710.04270.03650.38840.29810.4307-0.0051-0.06480.30050.07860.6384-96.593-134.5209-46.2601
400.4128-0.7103-0.12521.8241-0.080.4155-0.2112-0.22950.1065-0.13880.01630.20590.1696-0.0891-0.00930.3966-0.03980.01260.3643-0.03060.3925-96.1693-134.0837-42.226
410.02750.0369-0.00550.0528-0.02070.01230.41890.1131-0.5952-0.4277-1.10360.8551-0.3689-0.5477-0.00591.2001-0.2086-0.14980.8901-0.25610.6257-75.4396-131.3452-55.1974
420.45740.05460.17490.47510.29750.0855-0.3759-0.1153-0.2721-0.13630.139-0.21160.42690.1860.10560.57-0.03760.1460.45590.05620.5974-83.2744-138.6618-37.3867
430.28180.08650.37521.17230.47650.75760.1085-0.02180.0718-0.0271-0.1266-0.04640.19060.2819-0.06160.2490.077-0.02920.48370.08140.5937-48.2936-117.4029-31.9543
440.0598-0.0495-0.06550.02560.09430.0663-0.16910.7625-0.2921-0.118-0.26180.07910.63950.773300.7778-0.0370.00191.2569-0.14831.7974-36.1355-126.2299-30.2773
450.1812-0.33710.25370.7364-0.13930.02510.0362-0.1155-0.0337-0.2177-0.03880.1420.11560.0794-00.4438-0.0923-0.04920.40330.02740.4474-99.5933-114.5448-57.9453
460.0353-0.01480.02880.0162-0.02150.0215-0.3121-0.0075-0.08451.33170.17470.4004-0.0034-1.03860.00020.745-0.0271-0.08990.74280.07931.0666-82.3054-98.4179-62.0303
471.2554-0.40790.41740.21860.11180.15430.05960.7010.2878-0.3104-0.13730.1860.24240.23260.08390.5968-0.0273-0.0550.5246-0.08360.3317-85.8725-118.8513-62.3356
480.57850.03770.68290.4630.42920.82070.35610.3704-0.2763-0.0723-0.2673-0.38910.08920.06430.00020.34890.03030.05790.49180.10230.6154-49.1081-109.1346-46.11
490.1572-0.1416-0.06780.06790.01540.0886-0.416-0.36510.5195-1.0445-0.1521-0.65920.91870.8534-0.00021.2138-0.1003-0.03371.49550.35151.3047-37.6003-111.1923-55.8219
500.8284-0.28470.42620.1493-0.39380.1565-0.217-0.18930.4018-0.31670.1395-0.0844-0.04010.11450.17310.31150.0614-0.05760.40880.06760.5298-105.9189-93.7596-41.2966
510.1-0.34860.10541.04830.10470.39830.0523-0.1075-0.27560.0727-0.01620.02880.02720.00360.00250.2567-0.007-0.08710.3011-0.00360.5331-104.3926-96.0934-44.2249
520.4135-0.75470.47631.3374-0.9010.5957-0.0712-1.00910.02460.77390.32621.94090.4936-0.13090.04220.66390.3220.131.5708-0.09590.8283-87.9554-82.3085-32.2291
530.2716-0.22240.19740.1409-0.22840.1535-0.2776-0.08750.5791-0.19570.0440.0492-0.1539-0.0831-0.02220.4515-0.0408-0.16480.4153-0.05410.6263-93.0633-89.9368-50.8962
541.9016-0.1570.58651.2575-0.12021.274-0.33320.2224-0.2017-0.56220.0905-0.7004-0.28790.0494-0.5438-0.91040.0364-0.360.37280.21020.9819-52.7823-93.5296-42.5909
550.0045-0.02520.03510.1947-0.22530.2279-0.3035-0.01070.4797-0.20430.293-0.7272-0.21980.41390.00051.0505-0.1265-0.0390.98310.09441.837-44.2913-82.9841-49.3786
560.6223-0.7770.29780.8922-0.28181.0323-0.0148-0.68650.13420.7865-0.01910.1817-0.37130.287-0.05130.50570.10440.22210.5129-0.12440.6437-105.1232-104.5617-17.4029
570.20810.06670.25250.67260.10840.11780.0393-0.23980.13150.16850.24160.08370.38650.14710.05130.41610.01870.13050.47910.03820.6191-110.3719-108.34-22.0576
580.0746-0.0733-0.16430.630.33420.38440.233-0.3460.63720.29570.07190.0556-0.47030.134400.6160.0269-0.05220.5744-0.13140.6964-86.5176-92.7747-20.1181
590.21980.05330.14930.1878-0.07070.0846-0.40870.15290.80080.2311-0.1870.29970.3719-0.06020.00080.50680.00070.06850.5236-0.09890.7285-110.7755-95.4253-17.542
600.0664-0.0640.02930.0701-0.05250.02650.71740.08080.0440.2798-1.01260.26050.616-0.07610.00020.9950.0218-0.03591.30460.25490.977-84.6296-105.1007-6.7462
610.81920.4774-0.34630.2768-0.03280.41690.188-0.33310.92360.0752-0.0863-0.1043-0.6485-0.02990.05870.78660.1838-0.02470.7328-0.08280.6458-94.8607-91.8219-18.9769
620.22020.0576-0.17250.81680.07390.79250.0375-0.05480.27810.381-0.152-0.23140.03480.04830.02760.3298-0.0052-0.18310.4936-0.07250.7186-54.1839-92.1796-26.2716
630.10670.14080.02460.2866-0.21890.27490.1508-0.5561-0.18660.88540.3469-0.6378-0.1746-0.4206-0.00021.15070.0223-0.34751.5903-0.26361.524-46.8587-80.6087-19.8827
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 208 )
5X-RAY DIFFRACTION5chain 'A' and (resid 209 through 285 )
6X-RAY DIFFRACTION6chain 'A' and (resid 286 through 317 )
7X-RAY DIFFRACTION7chain 'B' and (resid 11 through 111 )
8X-RAY DIFFRACTION8chain 'B' and (resid 112 through 132 )
9X-RAY DIFFRACTION9chain 'B' and (resid 133 through 146 )
10X-RAY DIFFRACTION10chain 'B' and (resid 147 through 159 )
11X-RAY DIFFRACTION11chain 'B' and (resid 160 through 208 )
12X-RAY DIFFRACTION12chain 'B' and (resid 209 through 285 )
13X-RAY DIFFRACTION13chain 'B' and (resid 286 through 317 )
14X-RAY DIFFRACTION14chain 'C' and (resid 11 through 55 )
15X-RAY DIFFRACTION15chain 'C' and (resid 56 through 146 )
16X-RAY DIFFRACTION16chain 'C' and (resid 147 through 159 )
17X-RAY DIFFRACTION17chain 'C' and (resid 160 through 208 )
18X-RAY DIFFRACTION18chain 'C' and (resid 209 through 285 )
19X-RAY DIFFRACTION19chain 'C' and (resid 286 through 317 )
20X-RAY DIFFRACTION20chain 'D' and (resid 11 through 55 )
21X-RAY DIFFRACTION21chain 'D' and (resid 56 through 146 )
22X-RAY DIFFRACTION22chain 'D' and (resid 147 through 159 )
23X-RAY DIFFRACTION23chain 'D' and (resid 160 through 208 )
24X-RAY DIFFRACTION24chain 'D' and (resid 209 through 285 )
25X-RAY DIFFRACTION25chain 'D' and (resid 286 through 317 )
26X-RAY DIFFRACTION26chain 'E' and (resid 11 through 55 )
27X-RAY DIFFRACTION27chain 'E' and (resid 56 through 146 )
28X-RAY DIFFRACTION28chain 'E' and (resid 147 through 159 )
29X-RAY DIFFRACTION29chain 'E' and (resid 160 through 208 )
30X-RAY DIFFRACTION30chain 'E' and (resid 209 through 285 )
31X-RAY DIFFRACTION31chain 'E' and (resid 286 through 317 )
32X-RAY DIFFRACTION32chain 'F' and (resid 11 through 111 )
33X-RAY DIFFRACTION33chain 'F' and (resid 112 through 132 )
34X-RAY DIFFRACTION34chain 'F' and (resid 133 through 146 )
35X-RAY DIFFRACTION35chain 'F' and (resid 147 through 159 )
36X-RAY DIFFRACTION36chain 'F' and (resid 160 through 208 )
37X-RAY DIFFRACTION37chain 'F' and (resid 209 through 285 )
38X-RAY DIFFRACTION38chain 'F' and (resid 286 through 317 )
39X-RAY DIFFRACTION39chain 'G' and (resid 11 through 55 )
40X-RAY DIFFRACTION40chain 'G' and (resid 56 through 146 )
41X-RAY DIFFRACTION41chain 'G' and (resid 147 through 159 )
42X-RAY DIFFRACTION42chain 'G' and (resid 160 through 208 )
43X-RAY DIFFRACTION43chain 'G' and (resid 209 through 285 )
44X-RAY DIFFRACTION44chain 'G' and (resid 286 through 317 )
45X-RAY DIFFRACTION45chain 'H' and (resid 11 through 146 )
46X-RAY DIFFRACTION46chain 'H' and (resid 147 through 159 )
47X-RAY DIFFRACTION47chain 'H' and (resid 160 through 208 )
48X-RAY DIFFRACTION48chain 'H' and (resid 209 through 285 )
49X-RAY DIFFRACTION49chain 'H' and (resid 286 through 317 )
50X-RAY DIFFRACTION50chain 'I' and (resid 11 through 55 )
51X-RAY DIFFRACTION51chain 'I' and (resid 56 through 146 )
52X-RAY DIFFRACTION52chain 'I' and (resid 147 through 159 )
53X-RAY DIFFRACTION53chain 'I' and (resid 160 through 208 )
54X-RAY DIFFRACTION54chain 'I' and (resid 209 through 285 )
55X-RAY DIFFRACTION55chain 'I' and (resid 286 through 317 )
56X-RAY DIFFRACTION56chain 'J' and (resid 11 through 55 )
57X-RAY DIFFRACTION57chain 'J' and (resid 56 through 111 )
58X-RAY DIFFRACTION58chain 'J' and (resid 112 through 132 )
59X-RAY DIFFRACTION59chain 'J' and (resid 133 through 146 )
60X-RAY DIFFRACTION60chain 'J' and (resid 147 through 159 )
61X-RAY DIFFRACTION61chain 'J' and (resid 160 through 208 )
62X-RAY DIFFRACTION62chain 'J' and (resid 209 through 285 )
63X-RAY DIFFRACTION63chain 'J' and (resid 286 through 317 )

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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