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- PDB-6io4: Silver-bound Glyceraldehyde-3-phosphate dehydrogenase A -

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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: 6io4
タイトルSilver-bound Glyceraldehyde-3-phosphate dehydrogenase A
要素Glyceraldehyde-3-phosphate dehydrogenase A
キーワードCYTOSOLIC PROTEIN / silver / dehydrogenase
機能・相同性
機能・相同性情報


glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / glucose metabolic process / NAD binding / NADP binding / identical protein binding / membrane / cytosol
類似検索 - 分子機能
Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 ...Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
SILVER ION / Glyceraldehyde-3-phosphate dehydrogenase A
類似検索 - 構成要素
生物種Escherichia coli (大腸菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.1 Å
データ登録者Wang, H. / Sun, H. / Wang, M.
資金援助 香港, 1件
組織認可番号
The University Grants Committee, Research Grants Council (RGC)17305415P 香港
引用ジャーナル: Chem Sci / : 2019
タイトル: Antimicrobial silver targets glyceraldehyde-3-phosphate dehydrogenase in glycolysis ofE. coli.
著者: Wang, H. / Wang, M. / Yang, X. / Xu, X. / Hao, Q. / Yan, A. / Hu, M. / Lobinski, R. / Li, H. / Sun, H.
履歴
登録2018年10月29日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02019年7月3日Provider: repository / タイプ: Initial release
改定 1.12019年8月14日Group: Data collection / Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.22019年11月20日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed ..._citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
改定 1.32023年11月22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: Glyceraldehyde-3-phosphate dehydrogenase A
B: Glyceraldehyde-3-phosphate dehydrogenase A
C: Glyceraldehyde-3-phosphate dehydrogenase A
D: Glyceraldehyde-3-phosphate dehydrogenase A
E: Glyceraldehyde-3-phosphate dehydrogenase A
F: Glyceraldehyde-3-phosphate dehydrogenase A
G: Glyceraldehyde-3-phosphate dehydrogenase A
H: Glyceraldehyde-3-phosphate dehydrogenase A
I: Glyceraldehyde-3-phosphate dehydrogenase A
J: Glyceraldehyde-3-phosphate dehydrogenase A
K: Glyceraldehyde-3-phosphate dehydrogenase A
L: Glyceraldehyde-3-phosphate dehydrogenase A
M: Glyceraldehyde-3-phosphate dehydrogenase A
N: Glyceraldehyde-3-phosphate dehydrogenase A
O: Glyceraldehyde-3-phosphate dehydrogenase A
P: Glyceraldehyde-3-phosphate dehydrogenase A
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)566,32032
ポリマ-564,59416
非ポリマー1,72616
00
1
A: Glyceraldehyde-3-phosphate dehydrogenase A
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)35,3952
ポリマ-35,2871
非ポリマー1081
0
タイプ名称対称操作
identity operation1_555x,y,z1
2
B: Glyceraldehyde-3-phosphate dehydrogenase A
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)35,3952
ポリマ-35,2871
非ポリマー1081
0
タイプ名称対称操作
identity operation1_555x,y,z1
3
C: Glyceraldehyde-3-phosphate dehydrogenase A
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)35,3952
ポリマ-35,2871
非ポリマー1081
0
タイプ名称対称操作
identity operation1_555x,y,z1
4
D: Glyceraldehyde-3-phosphate dehydrogenase A
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)35,3952
ポリマ-35,2871
非ポリマー1081
0
タイプ名称対称操作
identity operation1_555x,y,z1
5
E: Glyceraldehyde-3-phosphate dehydrogenase A
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)35,3952
ポリマ-35,2871
非ポリマー1081
0
タイプ名称対称操作
identity operation1_555x,y,z1
6
F: Glyceraldehyde-3-phosphate dehydrogenase A
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)35,3952
ポリマ-35,2871
非ポリマー1081
0
タイプ名称対称操作
identity operation1_555x,y,z1
7
G: Glyceraldehyde-3-phosphate dehydrogenase A
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)35,3952
ポリマ-35,2871
非ポリマー1081
0
タイプ名称対称操作
identity operation1_555x,y,z1
8
H: Glyceraldehyde-3-phosphate dehydrogenase A
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)35,3952
ポリマ-35,2871
非ポリマー1081
0
タイプ名称対称操作
identity operation1_555x,y,z1
9
I: Glyceraldehyde-3-phosphate dehydrogenase A
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)35,3952
ポリマ-35,2871
非ポリマー1081
0
タイプ名称対称操作
identity operation1_555x,y,z1
10
J: Glyceraldehyde-3-phosphate dehydrogenase A
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)35,3952
ポリマ-35,2871
非ポリマー1081
0
タイプ名称対称操作
identity operation1_555x,y,z1
11
K: Glyceraldehyde-3-phosphate dehydrogenase A
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)35,3952
ポリマ-35,2871
非ポリマー1081
0
タイプ名称対称操作
identity operation1_555x,y,z1
12
L: Glyceraldehyde-3-phosphate dehydrogenase A
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)35,3952
ポリマ-35,2871
非ポリマー1081
0
タイプ名称対称操作
identity operation1_555x,y,z1
13
M: Glyceraldehyde-3-phosphate dehydrogenase A
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)35,3952
ポリマ-35,2871
非ポリマー1081
0
タイプ名称対称操作
identity operation1_555x,y,z1
14
N: Glyceraldehyde-3-phosphate dehydrogenase A
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)35,3952
ポリマ-35,2871
非ポリマー1081
0
タイプ名称対称操作
identity operation1_555x,y,z1
15
O: Glyceraldehyde-3-phosphate dehydrogenase A
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)35,3952
ポリマ-35,2871
非ポリマー1081
0
タイプ名称対称操作
identity operation1_555x,y,z1
16
P: Glyceraldehyde-3-phosphate dehydrogenase A
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)35,3952
ポリマ-35,2871
非ポリマー1081
0
タイプ名称対称操作
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)87.991, 110.019, 139.712
Angle α, β, γ (deg.)87.660, 86.940, 87.260
Int Tables number1
Space group name H-MP1

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要素

#1: タンパク質
Glyceraldehyde-3-phosphate dehydrogenase A / GAPDH-A / NAD-dependent glyceraldehyde-3-phosphate dehydrogenase


分子量: 35287.102 Da / 分子数: 16 / 変異: D78G / 由来タイプ: 組換発現
由来: (組換発現) Escherichia coli (strain K12) (大腸菌)
: K12 / 遺伝子: gapA, b1779, JW1768 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
参照: UniProt: P0A9B2, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: 化合物
ChemComp-AG / SILVER ION


分子量: 107.868 Da / 分子数: 16 / 由来タイプ: 合成 / : Ag

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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: 48.48 %
結晶化温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7 / 詳細: 0.1M Malic acid, PEG3350 20%

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データ収集

回折平均測定温度: 100 K / Ambient temp details: nitrogen flow / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: SSRF / ビームライン: BL17U1 / 波長: 0.97914 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2017年11月22日
放射モノクロメーター: graphite / 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: 0.97914 Å / 相対比: 1
反射解像度: 3.1→139.41 Å / Num. obs: 85684 / % possible obs: 90.4 % / 冗長度: 3.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.055 / Rrim(I) all: 0.105 / Net I/σ(I): 8.5 / Num. measured all: 306417
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.1-3.183.60.562397065700.8180.3380.6552.193.1
13.86-139.413.40.05232529670.9940.0320.06118.291.2

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.14_3260:001)精密化
Aimless0.5.32データスケーリング
PDB_EXTRACT3.24データ抽出
xia2データ削減
PHASER2.7.2位相決定
精密化構造決定の手法: 分子置換
開始モデル: 1GAD
解像度: 3.1→87.773 Å / SU ML: 0.43 / 交差検証法: THROUGHOUT / σ(F): 1.96 / 位相誤差: 28.83 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2397 4129 4.83 %
Rwork0.1747 81440 -
obs0.1779 85569 90.25 %
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
原子変位パラメータBiso max: 219.97 Å2 / Biso mean: 94.9022 Å2 / Biso min: 42.11 Å2
精密化ステップサイクル: final / 解像度: 3.1→87.773 Å
タンパク質核酸リガンド溶媒全体
原子数38625 0 16 0 38641
Biso mean--111.54 --
残基数----5264
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.13650.33941610.28462944310593
3.1365-3.17470.33981550.25862854300992
3.1747-3.21490.35271370.2492885302293
3.2149-3.25720.32691240.25292925304992
3.2572-3.30190.38391300.24662834296492
3.3019-3.3490.35061550.24022845300090
3.349-3.3990.31051340.23142796293091
3.399-3.45210.33691310.21972756288789
3.4521-3.50870.28661200.21632799291987
3.5087-3.56920.34671270.20772592271985
3.5692-3.63410.2997990.2252393249276
3.6341-3.7040.28291230.21422643276684
3.704-3.77960.27891460.20742957310396
3.7796-3.86180.29351490.19762971312096
3.8618-3.95170.25231450.19452996314196
3.9517-4.05050.24521780.17162913309195
4.0505-4.160.22771630.16512938310194
4.16-4.28240.28041490.15512891304094
4.2824-4.42060.21391780.14552942312094
4.4206-4.57860.18111640.14052856302093
4.5786-4.76190.21521390.14022865300492
4.7619-4.97860.19771270.14552838296591
4.9786-5.24110.19531800.14442799297992
5.2411-5.56940.25311560.1622835299191
5.5694-5.99930.23441130.17712726283987
5.9993-6.60290.27511220.17652631275385
6.6029-7.55790.22061110.16222372248376
7.5579-9.52030.15921730.142863303693
9.5203-87.80850.19541400.1482781292189
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)
12.66150.23381.1690.9887-1.4053.07650.0706-0.13370.1730.03560.3403-0.11670.27720.9244-0.49661.09660.0980.22881.0169-0.2430.730798.7637-22.015-64.6188
28.9337-2.06811.20912.29540.54612.09580.21051.2681.0863-0.7901-0.0814-0.4594-0.3360.7363-0.26741.16080.12940.48490.8847-0.06190.759897.2695-14.3725-74.8918
35.0225-0.88194.07074.36670.27273.52890.1024-0.18670.9148-0.0621-0.2134-0.066-0.04780.70370.19161.34390.00420.34610.65620.01470.836685.273-9.4933-74.5654
43.10121.2862-2.13732.8918-0.64834.6450.35550.6992-0.0746-0.5027-0.17660.0853-0.2163-0.5125-0.1931.08150.19370.0560.8033-0.15130.561175.6034-23.7998-72.3141
51.6142-1.0387-1.72140.7551.02962.08870.10780.43090.1207-0.68160.2432-0.0618-0.4322-0.1135-0.28180.8810.0964-0.01180.5836-0.06520.49274.0861-17.3701-52.3177
61.5594-0.2525-0.43141.16961.14922.41020.11590.299-0.2967-0.0684-0.15120.13830.4862-0.30410.04680.90360.06340.00580.6592-0.1520.5172.9969-31.2383-58.881
73.9074-0.4754-2.07640.51790.89722.3292-0.39690.05480.09050.39010.3111-0.18810.63090.0360.03290.95330.08250.03510.3251-0.0690.702172.4451-25.9971-15.4434
84.2211-0.146-2.22123.28782.53543.57880.4296-0.20370.5088-0.10170.0157-0.35760.08130.1708-0.38711.14190.14670.03380.35-0.16020.672777.677-21.9734-11.407
90.778-0.2819-0.96490.7570.14862.8463-0.12560.1611-0.24850.2247-0.05380.25610.7481-0.33180.18020.9921-0.13120.11020.4867-0.17210.681662.8495-34.017-29.7145
104.16660.82020.27233.12970.96674.47820.02080.22810.1846-0.1076-0.23310.235-0.1941-0.57190.17510.6610.10030.06560.4749-0.12290.479361.466-18.736-42.7254
113.89422.6581.64076.2635-2.50093.72330.21620.2660.13030.3262-0.29850.7405-0.6096-0.37690.09050.9990.09310.12620.4114-0.1910.716258.9937-24.7587-21.6385
125.3228-1.1640.69427.2454-0.57114.66120.35510.9447-0.368-0.6842-0.3610.5442-0.10390.70940.16490.73640.04-0.12040.6293-0.0640.49376.6238-37.76774.1783
134.2844-0.2238-1.71113.5227-2.74375.6570.16380.3709-0.2614-0.71220.1942-0.15780.455-0.567-0.32711.24130.2352-0.10560.8198-0.03190.71921.3344-40.81166.2118
147.583-0.10285.32060.16290.60766.6861-0.20270.0868-0.7146-0.03870.34160.0937-0.02080.1041-0.210.92260.23560.01960.79860.05370.7186-2.1086-35.71510.7664
152.3066-1.3820.98941.9248-1.23193.0226-0.24730.5217-0.6928-0.9510.1670.8281-0.2281-0.39750.07951.12540.2809-0.16040.9278-0.18450.78682.0701-46.8574-2.5475
160.0943-0.0312-0.21081.8722-0.19084.8280.6190.6487-0.7266-1.3461-0.0013-0.52032.00870.8547-0.71771.83080.3388-0.10180.8461-0.23690.853413.9823-51.9171-3.1602
174.39690.34910.69072.4073-0.01743.98520.41881.2356-0.3187-1.01250.1454-0.44011.54870.6619-0.18341.21120.5953-0.00511.0843-0.13460.602820.9695-41.1817-6.6087
184.96351.55542.10835.88880.6780.8896-0.00660.84880.1254-0.52410.0639-0.1768-0.22890.106-0.25341.12230.23460.16840.824-0.00050.628.4115-32.4630.6539
191.5392-0.87540.95020.5559-0.50782.52390.25150.3215-0.0121-0.80620.0211-0.26910.60160.5136-0.18581.02170.26920.16180.6423-0.02020.6227.9912-42.075816.5682
203.3024-0.28730.04331.4291-2.08663.0920.32020.67350.5261-0.2122-0.1724-0.0761-0.2380.0377-0.18760.91710.22380.19030.62410.08030.612732.4606-32.23459.9722
214.51421.4915-1.1462.5413-1.1243.86280.22160.55660.9519-0.7945-0.1108-0.2314-1.15410.30140.17881.060.18810.04240.65380.27470.802124.5219-19.38826.9639
225.24990.52641.48631.7091.47093.84680.14730.61490.1435-0.8411-0.3247-0.2221-0.56230.34170.20020.96370.1940.15280.61280.1510.564224.341-27.86847.3067
234.78191.10572.08081.3953-0.83542.4241-0.0222-0.18590.01090.20660.1239-0.134-0.4223-0.0375-0.07080.7960.1458-0.01040.545-0.130.556932.7452-31.837951.315
242.78830.8531-0.47833.901-1.4935.45420.1185-0.39450.83550.6856-0.0534-0.1984-1.27540.2313-0.0650.8165-0.0586-0.0920.5595-0.16270.762242.9568-22.190350.0293
252.25340.03230.40381.0185-0.612.74610.09720.22960.373-0.1427-0.1677-0.1925-0.24560.39040.05250.66290.00870.10950.45380.03810.6340.0646-30.102725.0972
263.4061-1.1911-0.61323.53460.11345.41430.13030.1828-0.2695-0.3745-0.1806-0.27710.65430.55570.0740.66060.13550.10660.5091-0.02130.63141.5544-43.79626.8024
271.1427-0.37080.95243.00641.9235.7308-0.02470.54370.2474-0.1192-0.17410.00450.25070.67330.04630.64570.06810.10490.57250.07710.609843.3471-34.262235.941
280.82430.4491-0.99972.884-1.32483.5567-0.08360.00260.40790.16950.25380.7518-0.5345-0.726-0.13981.07390.26770.19340.7173-0.06651.080339.233836.70677.009
290.23610.40280.44932.42180.00841.0694-0.0650.03170.2087-0.22180.09910.0501-0.542-0.36170.08221.68360.33080.4198-0.0483-0.12970.954861.69643.476-0.2336
306.3622.05460.88836.4658-0.55227.74670.00770.3301-0.32390.07210.2592-0.335-0.78810.5872-0.05690.7261-0.15410.03620.4825-0.13480.671791.56414.9971-4.4581
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624.52430.2493-0.83340.3389-0.08220.1586-0.4750.0994-0.20140.19870.7561-0.60070.58911.5622-0.2120.90170.29940.09891.5896-0.37580.7012109.6548-28.892-46.0463
630.19740.20630.3080.98370.02221.12510.1378-0.2136-0.18140.08660.1088-0.15080.72011.2609-0.24611.08580.5353-0.03631.7164-0.52090.7322110.4378-31.759-38.468
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670.90760.60371.15051.6431.46634.85140.14480.08210.02980.18980.3846-0.50770.01391.2617-0.42690.72060.02040.02341.012-0.29820.659999.306-12.9042-21.1655
682.4772-0.2945-0.0382.4652-2.0211.6982-0.2921-0.26020.33510.53640.9485-0.1797-0.03471.0061-0.11990.85110.06320.10020.9999-0.42940.49798.3844-7.1395-23.8161
692.87020.3164-2.57514.105-1.50862.9263-0.0168-0.56540.12560.09690.70860.53630.4458-2.0653-0.78470.9751-0.1455-0.05981.78650.41120.816337.196316.5561-38.5742
703.61230.6251.08322.06620.20580.81140.0711-0.99560.0070.488-0.66430.39870.8404-0.7030.07441.0937-0.2365-0.07811.80780.33550.832127.930216.9193-30.7989
711.67070.8299-0.06630.93350.74641.16790.4548-0.54320.18550.8986-0.76650.20620.4517-1.16520.20751.10220.09150.04912.3140.04610.929928.555427.8973-27.411
721.4441.5933-0.55482.22430.15181.3827-0.2507-1.0724-0.06550.3295-0.0128-0.0601-0.7739-0.6450.10161.23190.2602-0.09042.00390.10740.719241.662839.6278-31.0779
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761.8495-1.0061.18412.3897-0.79452.5396-0.1929-0.931-0.16590.51260.4097-0.6958-0.6027-0.0247-0.08731.0204-0.2408-0.19811.1714-0.04920.74456.397438.563-46.1647
771.2925-0.72930.2861.3624-0.92592.9363-0.1986-0.7689-0.15390.50180.60310.163-0.6391-0.9123-0.271.0717-0.0167-0.27571.46670.1680.619846.587334.8782-38.2499
782.59830.42081.54775.32530.42793.8180.2180.1884-0.2543-0.3886-0.0485-0.89120.12950.4761-0.15880.64550.0080.11150.5321-0.03320.745250.408345.3318-87.0288
791.45780.44820.63081.8437-0.96123.26020.0258-0.37950.07410.2454-0.1536-0.4657-0.66230.16420.12290.7424-0.1805-0.08040.8241-0.03780.545450.002248.8458-61.8045
804.20640.9033-0.10387.22760.71655.59440.1065-0.55190.23330.764-0.03150.4677-1.2102-1.6723-0.19490.8470.22720.03190.8738-0.08320.535633.12258.3431-63.68
815.1902-0.0262-1.95484.42430.7166.3956-0.3293-0.64490.27010.91740.5004-0.1497-0.3798-0.6297-0.16290.70370.1407-0.07610.646-0.02320.562340.733752.6004-67.9974
821.7472-0.2357-1.08050.45990.52280.9980.05810.24560.30050.05730.1058-0.77670.6047-0.2942-0.23390.9243-0.1662-0.19390.95710.24731.298163.91513.8093-59.6935
834.12071.7557-3.23171.98790.00574.13490.5223-0.1026-0.7839-0.12160.4775-0.13140.8810.5668-0.87730.88650.1871-0.34951.03790.00421.166967.606218.9893-58.8347
845.3002-0.5519-1.0274.48860.0363.37670.0519-1.1277-1.0153-0.25140.467-0.1530.33850.2268-0.53810.77920.0082-0.18510.81160.17651.134269.222120.3317-57.2023
853.69982.66970.96932.70951.97182.4099-0.04540.6843-0.7363-0.07640.2796-2.23941.34811.2415-0.42811.28650.31320.04260.825-0.14021.638871.869.342-71.4807
860.88382.63650.24688.8711-0.77125.92750.4442-0.0089-0.259-1.89130.28970.16151.94690.6138-0.61881.41390.175-0.41710.81460.04271.188461.38640.7992-71.2237
870.47360.8168-0.20461.8861-0.39530.08510.3238-0.1921-0.7811-1.00550.12230.3641.3487-0.1365-0.2111.6051-0.2175-0.51490.70380.3231.319842.2576.2993-69.5388
884.44795.21090.35788.00222.11191.53870.5279-1.0882-1.3858-0.4206-0.32840.1581.6078-0.8787-0.25651.264-0.4932-0.42961.25170.76111.751937.92054.4189-60.8279
891.72940.7604-0.43920.3711-0.49622.46010.64130.1598-1.0245-0.29410.05420.37551.93540.0469-0.61131.69890.0382-0.55640.79260.29561.40851.70284.5944-63.3605
901.13911.56640.92512.15191.27180.75050.2404-1.4223-1.26330.34990.52060.65630.2093-1.769-0.81250.6141-0.3488-0.16531.53910.49341.128414.152734.8646-70.512
916.8121.09150.0144.52820.45911.0336-0.3349-0.8759-0.15860.36720.70971.27030.1901-1.1146-0.33420.884-0.03280.00281.58120.56591.001514.785542.5241-67.2094
926.1625-0.91562.63983.99390.20111.29130.0615-1.4688-0.33260.96840.49051.47540.5606-0.9863-0.39551.1301-0.14560.15382.08280.84081.65154.161830.7216-62.3265
930.69480.2861-0.61660.1919-0.29660.57040.1421-0.3901-0.11840.4282-0.48550.32510.1736-0.0021-0.38780.8822-0.5488-0.04862.00940.82721.73050.735324.7677-64.9734
942.01340.5030.43021.2098-0.46010.83710.3670.0211-0.3728-0.35260.52160.76860.7619-1.3063-0.24281.3056-0.7935-0.54211.58070.69551.725312.410615.3411-76.3883
952.16450.67750.97351.08870.72060.9010.5522-0.5248-0.5626-0.14990.61020.52680.8748-0.57420.07061.3381-0.6627-0.44171.31770.80651.521428.051115.1431-63.1528
961.74160.506-0.66720.6547-0.2860.2715-0.16860.09920.0238-0.62130.41831.40770.2404-0.6551-0.24961.3287-0.587-0.34911.20560.59191.744723.902411.593-68.1645
970.68180.147-0.03560.09070.09110.13210.3311-0.2776-0.6541-0.13480.1240.07540.2688-0.0113-0.11111.3822-0.5814-0.59090.85370.34781.179629.560711.1297-75.0589
982.2324.26652.43128.17174.80024.46430.19860.3494-0.1853-0.35120.56320.04161.2301-0.81-0.75581.2365-0.403-0.41890.66080.17760.998328.616917.4453-89.1863
991.07230.5068-0.79660.2528-0.22032.1330.2358-0.1098-0.686-0.65080.10.26041.165-0.3933-0.28341.1798-0.3836-0.5830.80690.19921.182231.626916.9319-82.7004
1005.1342-1.3475-1.16150.44590.60051.18040.8752-0.5532-0.6829-0.52460.09780.44131.0169-0.8514-0.76111.1015-0.4972-0.49641.2980.56631.26419.51421.7867-77.5445
1011.60240.16590.19471.4578-1.6371.94460.1977-0.17430.15480.5812-0.1062-0.2218-0.7320.0466-0.08461.3584-0.03480.09580.5621-0.29480.844274.261835.324929.9304
1022.47071.97451.11674.0852-0.41221.20060.2959-0.2684-0.16221.7315-0.3595-0.5596-0.26550.61440.08951.379-0.0609-0.25780.6762-0.14970.819482.598724.879139.2899
1035.57680.2489-0.37514.9512-0.08994.471-0.57-1.04940.33931.27880.0220.0130.0383-0.16320.46381.4840.08990.01060.6562-0.16590.617873.717215.786640.9224
1040.8746-0.4317-0.63050.655-0.03081.874-0.0847-0.21870.00390.42060.19150.06050.238-0.0592-0.08441.16150.00150.15380.4681-0.11330.655562.19659.880225.5615
1052.98811.5715-1.22064.83551.40483.962-0.0174-0.02590.21430.24450.26580.3661-0.2311-0.1275-0.18820.99040.06050.07380.3743-0.00210.712258.27646.6485-17.1029
1061.61482.1558-0.99623.8479-0.30151.63560.18820.43690.30530.01730.15160.3101-0.4497-0.346-0.31660.82380.1450.06030.40850.02570.720352.61695.5885-18.934
1074.02310.59750.14180.72171.46424.00680.17230.0385-0.04240.6432-0.35930.4230.9556-0.32780.1040.9183-0.14950.07660.3915-0.02070.687850.134-8.617-6.5879
1082.42352.6305-0.7915.5982-1.40430.9653-0.37020.217-0.12240.24150.68750.33240.6399-0.1497-0.20331.2915-0.03910.09090.3154-0.03540.675661.0872-7.740810.2271
1091.5815-0.3058-0.96030.1237-0.30333.9540.1394-0.10370.14810.37150.09310.27750.0388-0.4373-0.19940.913-0.03580.14780.4445-0.08750.757352.43917.77657.9428
1102.2712-0.4107-0.85342.06740.71013.33610.124-0.1306-0.01190.21110.0406-0.01840.38480.1932-0.16821.02940.0151-0.00750.2976-0.1020.650169.0331-3.99629.6638
1112.9435-0.40072.04931.2086-1.54132.8031-0.09440.1092-0.00760.7422-0.32110.32110.2778-0.02080.2740.9091-0.03480.11320.3163-0.08570.685662.0115-3.6855-1.7746
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 66 )A1 - 66
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 94 )A67 - 94
3X-RAY DIFFRACTION3chain 'A' and (resid 95 through 111 )A95 - 111
4X-RAY DIFFRACTION4chain 'A' and (resid 112 through 164 )A112 - 164
5X-RAY DIFFRACTION5chain 'A' and (resid 165 through 196 )A165 - 196
6X-RAY DIFFRACTION6chain 'A' and (resid 197 through 330 )A197 - 330
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 45 )B1 - 45
8X-RAY DIFFRACTION8chain 'B' and (resid 46 through 74 )B46 - 74
9X-RAY DIFFRACTION9chain 'B' and (resid 75 through 224 )B75 - 224
10X-RAY DIFFRACTION10chain 'B' and (resid 225 through 314 )B225 - 314
11X-RAY DIFFRACTION11chain 'B' and (resid 315 through 330 )B315 - 330
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 21 )C1 - 21
13X-RAY DIFFRACTION13chain 'C' and (resid 22 through 45 )C22 - 45
14X-RAY DIFFRACTION14chain 'C' and (resid 46 through 66 )C46 - 66
15X-RAY DIFFRACTION15chain 'C' and (resid 67 through 94 )C67 - 94
16X-RAY DIFFRACTION16chain 'C' and (resid 95 through 111 )C95 - 111
17X-RAY DIFFRACTION17chain 'C' and (resid 112 through 142 )C112 - 142
18X-RAY DIFFRACTION18chain 'C' and (resid 143 through 164 )C143 - 164
19X-RAY DIFFRACTION19chain 'C' and (resid 165 through 196 )C165 - 196
20X-RAY DIFFRACTION20chain 'C' and (resid 197 through 263 )C197 - 263
21X-RAY DIFFRACTION21chain 'C' and (resid 264 through 279 )C264 - 279
22X-RAY DIFFRACTION22chain 'C' and (resid 280 through 330 )C280 - 330
23X-RAY DIFFRACTION23chain 'D' and (resid 1 through 56 )D1 - 56
24X-RAY DIFFRACTION24chain 'D' and (resid 57 through 142 )D57 - 142
25X-RAY DIFFRACTION25chain 'D' and (resid 143 through 263 )D143 - 263
26X-RAY DIFFRACTION26chain 'D' and (resid 264 through 303 )D264 - 303
27X-RAY DIFFRACTION27chain 'D' and (resid 304 through 330 )D304 - 330
28X-RAY DIFFRACTION28chain 'E' and (resid 1 through 142 )E1 - 142
29X-RAY DIFFRACTION29chain 'E' and (resid 143 through 330 )E143 - 330
30X-RAY DIFFRACTION30chain 'F' and (resid 1 through 21 )F1 - 21
31X-RAY DIFFRACTION31chain 'F' and (resid 22 through 45 )F22 - 45
32X-RAY DIFFRACTION32chain 'F' and (resid 46 through 63 )F46 - 63
33X-RAY DIFFRACTION33chain 'F' and (resid 64 through 90 )F64 - 90
34X-RAY DIFFRACTION34chain 'F' and (resid 91 through 128 )F91 - 128
35X-RAY DIFFRACTION35chain 'F' and (resid 129 through 150 )F129 - 150
36X-RAY DIFFRACTION36chain 'F' and (resid 151 through 176 )F151 - 176
37X-RAY DIFFRACTION37chain 'F' and (resid 177 through 263 )F177 - 263
38X-RAY DIFFRACTION38chain 'F' and (resid 264 through 279 )F264 - 279
39X-RAY DIFFRACTION39chain 'F' and (resid 280 through 330 )F280 - 330
40X-RAY DIFFRACTION40chain 'G' and (resid 1 through 56 )G1 - 56
41X-RAY DIFFRACTION41chain 'G' and (resid 57 through 83 )G57 - 83
42X-RAY DIFFRACTION42chain 'G' and (resid 84 through 142 )G84 - 142
43X-RAY DIFFRACTION43chain 'G' and (resid 143 through 164 )G143 - 164
44X-RAY DIFFRACTION44chain 'G' and (resid 165 through 196 )G165 - 196
45X-RAY DIFFRACTION45chain 'G' and (resid 197 through 237 )G197 - 237
46X-RAY DIFFRACTION46chain 'G' and (resid 238 through 279 )G238 - 279
47X-RAY DIFFRACTION47chain 'G' and (resid 280 through 330 )G280 - 330
48X-RAY DIFFRACTION48chain 'H' and (resid 1 through 45 )H1 - 45
49X-RAY DIFFRACTION49chain 'H' and (resid 46 through 74 )H46 - 74
50X-RAY DIFFRACTION50chain 'H' and (resid 75 through 128 )H75 - 128
51X-RAY DIFFRACTION51chain 'H' and (resid 129 through 150 )H129 - 150
52X-RAY DIFFRACTION52chain 'H' and (resid 151 through 176 )H151 - 176
53X-RAY DIFFRACTION53chain 'H' and (resid 177 through 237 )H177 - 237
54X-RAY DIFFRACTION54chain 'H' and (resid 238 through 263 )H238 - 263
55X-RAY DIFFRACTION55chain 'H' and (resid 264 through 303 )H264 - 303
56X-RAY DIFFRACTION56chain 'H' and (resid 304 through 330 )H304 - 330
57X-RAY DIFFRACTION57chain 'I' and (resid 1 through 74 )I1 - 74
58X-RAY DIFFRACTION58chain 'I' and (resid 75 through 94 )I75 - 94
59X-RAY DIFFRACTION59chain 'I' and (resid 95 through 164 )I95 - 164
60X-RAY DIFFRACTION60chain 'I' and (resid 165 through 237 )I165 - 237
61X-RAY DIFFRACTION61chain 'I' and (resid 238 through 263 )I238 - 263
62X-RAY DIFFRACTION62chain 'I' and (resid 264 through 293 )I264 - 293
63X-RAY DIFFRACTION63chain 'I' and (resid 294 through 330 )I294 - 330
64X-RAY DIFFRACTION64chain 'J' and (resid 1 through 56 )J1 - 56
65X-RAY DIFFRACTION65chain 'J' and (resid 57 through 82 )J57 - 82
66X-RAY DIFFRACTION66chain 'J' and (resid 83 through 224 )J83 - 224
67X-RAY DIFFRACTION67chain 'J' and (resid 225 through 293 )J225 - 293
68X-RAY DIFFRACTION68chain 'J' and (resid 294 through 330 )J294 - 330
69X-RAY DIFFRACTION69chain 'K' and (resid 1 through 66 )K1 - 66
70X-RAY DIFFRACTION70chain 'K' and (resid 67 through 83 )K67 - 83
71X-RAY DIFFRACTION71chain 'K' and (resid 84 through 111 )K84 - 111
72X-RAY DIFFRACTION72chain 'K' and (resid 112 through 164 )K112 - 164
73X-RAY DIFFRACTION73chain 'K' and (resid 165 through 196 )K165 - 196
74X-RAY DIFFRACTION74chain 'K' and (resid 197 through 237 )K197 - 237
75X-RAY DIFFRACTION75chain 'K' and (resid 238 through 264 )K238 - 264
76X-RAY DIFFRACTION76chain 'K' and (resid 265 through 303 )K265 - 303
77X-RAY DIFFRACTION77chain 'K' and (resid 304 through 330 )K304 - 330
78X-RAY DIFFRACTION78chain 'L' and (resid 1 through 148 )L1 - 148
79X-RAY DIFFRACTION79chain 'L' and (resid 149 through 251 )L149 - 251
80X-RAY DIFFRACTION80chain 'L' and (resid 252 through 280 )L252 - 280
81X-RAY DIFFRACTION81chain 'L' and (resid 281 through 330 )L281 - 330
82X-RAY DIFFRACTION82chain 'M' and (resid 1 through 21 )M1 - 21
83X-RAY DIFFRACTION83chain 'M' and (resid 22 through 45 )M22 - 45
84X-RAY DIFFRACTION84chain 'M' and (resid 46 through 83 )M46 - 83
85X-RAY DIFFRACTION85chain 'M' and (resid 84 through 111 )M84 - 111
86X-RAY DIFFRACTION86chain 'M' and (resid 112 through 150 )M112 - 150
87X-RAY DIFFRACTION87chain 'M' and (resid 151 through 280 )M151 - 280
88X-RAY DIFFRACTION88chain 'M' and (resid 281 through 303 )M281 - 303
89X-RAY DIFFRACTION89chain 'M' and (resid 304 through 330 )M304 - 330
90X-RAY DIFFRACTION90chain 'N' and (resid 1 through 21 )N1 - 21
91X-RAY DIFFRACTION91chain 'N' and (resid 22 through 74 )N22 - 74
92X-RAY DIFFRACTION92chain 'N' and (resid 75 through 101 )N75 - 101
93X-RAY DIFFRACTION93chain 'N' and (resid 102 through 118 )N102 - 118
94X-RAY DIFFRACTION94chain 'N' and (resid 119 through 164 )N119 - 164
95X-RAY DIFFRACTION95chain 'N' and (resid 165 through 196 )N165 - 196
96X-RAY DIFFRACTION96chain 'N' and (resid 197 through 224 )N197 - 224
97X-RAY DIFFRACTION97chain 'N' and (resid 225 through 251 )N225 - 251
98X-RAY DIFFRACTION98chain 'N' and (resid 252 through 280 )N252 - 280
99X-RAY DIFFRACTION99chain 'N' and (resid 281 through 303 )N281 - 303
100X-RAY DIFFRACTION100chain 'N' and (resid 304 through 330 )N304 - 330
101X-RAY DIFFRACTION101chain 'O' and (resid 1 through 83 )O1 - 83
102X-RAY DIFFRACTION102chain 'O' and (resid 84 through 110 )O84 - 110
103X-RAY DIFFRACTION103chain 'O' and (resid 111 through 148 )O111 - 148
104X-RAY DIFFRACTION104chain 'O' and (resid 149 through 330 )O149 - 330
105X-RAY DIFFRACTION105chain 'P' and (resid 1 through 45 )P1 - 45
106X-RAY DIFFRACTION106chain 'P' and (resid 46 through 110 )P46 - 110
107X-RAY DIFFRACTION107chain 'P' and (resid 111 through 148 )P111 - 148
108X-RAY DIFFRACTION108chain 'P' and (resid 149 through 176 )P149 - 176
109X-RAY DIFFRACTION109chain 'P' and (resid 177 through 224 )P177 - 224
110X-RAY DIFFRACTION110chain 'P' and (resid 225 through 303 )P225 - 303
111X-RAY DIFFRACTION111chain 'P' and (resid 304 through 330 )P304 - 330

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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