[日本語] English
万見
- PDB-9chl: P. vulgaris tetrameric HigBA- operator 2 DNA -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 9chl
タイトルP. vulgaris tetrameric HigBA- operator 2 DNA
要素
  • Antitoxin HigA
  • DNA (5'-D(*GP*TP*AP*TP*TP*AP*CP*AP*CP*AP*CP*CP*AP*TP*GP*TP*AP*AP*TP*AP*C)-3')
  • DNA (5'-D(*GP*TP*AP*TP*TP*AP*CP*AP*TP*GP*GP*TP*GP*TP*GP*TP*AP*AP*TP*AP*C)-3')
  • Endoribonuclease HigB
キーワードANTITOXIN/DNA BINDING PROTEIN/DNA / Toxin / antitoxin / promoter / DNA BINDING PROTEIN / ANTITOXIN-DNA BINDING PROTEIN-DNA complex
機能・相同性
機能・相同性情報


toxin sequestering activity / plasmid maintenance / RNA catabolic process / translation repressor activity / RNA endonuclease activity / negative regulation of cell growth / ribosome binding / 加水分解酵素; エステル加水分解酵素 / transcription cis-regulatory region binding / negative regulation of translation ...toxin sequestering activity / plasmid maintenance / RNA catabolic process / translation repressor activity / RNA endonuclease activity / negative regulation of cell growth / ribosome binding / 加水分解酵素; エステル加水分解酵素 / transcription cis-regulatory region binding / negative regulation of translation / DNA-binding transcription factor activity / protein heterodimerization activity / negative regulation of cell population proliferation / mRNA binding / regulation of DNA-templated transcription
類似検索 - 分子機能
Toxin HigB-1 / RelE-like toxin of type II toxin-antitoxin system HigB / Toxin-antitoxin system, antidote protein, HigA / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily
類似検索 - ドメイン・相同性
DNA / DNA (> 10) / Antitoxin HigA / Endoribonuclease HigB
類似検索 - 構成要素
生物種Proteus vulgaris (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: 2.4 Å
データ登録者Pavelich, I.J. / Schureck, M.A. / Hoffer, E.D. / Dunham, C.M.
資金援助 米国, 2件
組織認可番号国
Other government 米国
Other private 米国
引用ジャーナル: To Be Published
タイトル: P. vulgaris tetrameric HigBA- operator 2 DNA
著者: Pavelich, I.J. / Schureck, M.A. / Hoffer, E.D. / Dunham, C.M.
履歴
登録2024年7月1日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02025年7月2日Provider: repository / タイプ: Initial release

-
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

-
集合体

登録構造単位
A: Antitoxin HigA
B: Endoribonuclease HigB
C: Antitoxin HigA
D: Endoribonuclease HigB
I: DNA (5'-D(*GP*TP*AP*TP*TP*AP*CP*AP*CP*AP*CP*CP*AP*TP*GP*TP*AP*AP*TP*AP*C)-3')
J: DNA (5'-D(*GP*TP*AP*TP*TP*AP*CP*AP*TP*GP*GP*TP*GP*TP*GP*TP*AP*AP*TP*AP*C)-3')
E: Antitoxin HigA
F: Endoribonuclease HigB
G: Antitoxin HigA
H: Endoribonuclease HigB
K: DNA (5'-D(*GP*TP*AP*TP*TP*AP*CP*AP*CP*AP*CP*CP*AP*TP*GP*TP*AP*AP*TP*AP*C)-3')
L: DNA (5'-D(*GP*TP*AP*TP*TP*AP*CP*AP*TP*GP*GP*TP*GP*TP*GP*TP*AP*AP*TP*AP*C)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)116,97831
ポリマ－116,46012
非ポリマー51819
水5,747319
1
A: Antitoxin HigA
B: Endoribonuclease HigB
C: Antitoxin HigA
D: Endoribonuclease HigB
I: DNA (5'-D(*GP*TP*AP*TP*TP*AP*CP*AP*CP*AP*CP*CP*AP*TP*GP*TP*AP*AP*TP*AP*C)-3')
J: DNA (5'-D(*GP*TP*AP*TP*TP*AP*CP*AP*TP*GP*GP*TP*GP*TP*GP*TP*AP*AP*TP*AP*C)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)58,48215
ポリマ－58,2306
非ポリマー2529
水1086
タイプ名称対称操作数
identity operation1_555x,y,z1
2
E: Antitoxin HigA
F: Endoribonuclease HigB
G: Antitoxin HigA
H: Endoribonuclease HigB
K: DNA (5'-D(*GP*TP*AP*TP*TP*AP*CP*AP*CP*AP*CP*CP*AP*TP*GP*TP*AP*AP*TP*AP*C)-3')
L: DNA (5'-D(*GP*TP*AP*TP*TP*AP*CP*AP*TP*GP*GP*TP*GP*TP*GP*TP*AP*AP*TP*AP*C)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)58,49516
ポリマ－58,2306
非ポリマー26510
水1086
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)98.150, 98.130, 147.190
Angle α, β, γ (deg.)90.000, 109.490, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDモデル要素
11I-124-

HOH

-
要素

-
タンパク質 , 2種, 8分子 ACEGBDFH

#1: タンパク質
Antitoxin HigA / Antidote protein / Host inhibition of growth protein A


分子量: 11690.636 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Proteus vulgaris (バクテリア) / 遺伝子: higA / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q7A224
#2: タンパク質
Endoribonuclease HigB / Host inhibition of growth protein B / Killer protein / Toxin HigB / mRNA interferase HigB


分子量: 10983.193 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Proteus vulgaris (バクテリア) / 遺伝子: higB / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: Q7A225, 加水分解酵素; エステル加水分解酵素

-
DNA鎖 , 2種, 4分子 IKJL

#3: DNA鎖 DNA (5'-D(*GP*TP*AP*TP*TP*AP*CP*AP*CP*AP*CP*CP*AP*TP*GP*TP*AP*AP*TP*AP*C)-3')


分子量: 6390.175 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) Proteus vulgaris (バクテリア)
#4: DNA鎖 DNA (5'-D(*GP*TP*AP*TP*TP*AP*CP*AP*TP*GP*GP*TP*GP*TP*GP*TP*AP*AP*TP*AP*C)-3')


分子量: 6492.219 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) Proteus vulgaris (バクテリア)

-
非ポリマー , 3種, 338分子

#5: 化合物
ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 14 / 由来タイプ: 合成 / 式: Mg
#6: 化合物
ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 5 / 由来タイプ: 合成 / 式: Cl
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 319 / 由来タイプ: 天然 / 式: H2O

-
詳細

研究の焦点であるリガンドがあるかN
Has protein modificationY

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 2.87 Å3/Da / 溶媒含有率: 57.13 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: Tris-HCl, KCl, MgCl2, 2-mercaptoethanol, NaCl, EDTA, CaCl2, PEG 3350
PH範囲: 7.5-8

-
データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 24-ID-C / 波長: 0.9792 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2015年8月15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: 0.9792 Å / 相対比: 1
反射解像度: 2.4→67.3 Å / Num. obs: 98818 / % possible obs: 97.5 % / 冗長度: 2.777 % / Biso Wilson estimate: 53.629 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.081 / Χ2: 1.182 / Net I/σ(I): 9.13
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.4-2.52.0560.4651.76111510.7980.6295
2.5-2.62.40.3292.6192270.8990.41893.5
2.6-32.960.1974.88275940.9670.2498.9
3-42.9150.0711.56292820.9930.08598
4-52.9010.05117.33105470.9940.06298.1
5-62.8670.04517.6246330.9950.05598.5
6-82.8750.04117.9636910.9960.0598.4
8-102.9810.03520.2713230.9970.04297.6
10-202.7690.0320.2412020.9970.03797.6
20-353.090.03722.271440.9960.04597.3
35-67.32.9580.09421.8240.9830.11792.3

-
解析

ソフトウェア
名称バージョン分類
XDSデータ削減
XSCALEデータスケーリング
PHASER位相決定
PHENIX1.17.1精密化
Cootモデル構築
精密化構造決定の手法: 分子置換
開始モデル: 4MCX

4mcx


解像度: 2.4→67.3 Å / 交差検証法: FREE R-VALUE
Rfactor反射数%反射
Rfree0.2211 2537 -
Rwork0.1747 --
obs-95528 94.34 %
原子変位パラメータBiso max: 169.53 Å2 / Biso mean: 57.3775 Å2 / Biso min: 27.16 Å2
精密化ステップサイクル: LAST / 解像度: 2.4→67.3 Å
タンパク質核酸リガンド溶媒全体
原子数6095 1710 19 319 8143
LS精密化 シェル解像度: 2.4→2.486 Å
Rfactor反射数%反射
Rfree0.3414 --
Rwork0.2964 --
obs-4965 97.27 %
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)
16.9679-1.29571.80113.2027-3.02343.46-0.25920.45930.4551-1.2620.5963-0.0496-0.1995-0.7735-0.16330.6741-0.04690.06280.59110.02510.457343.824984.8763-27.397
28.20930.7427-4.16648.24431.41749.93750.2427-0.33151.05660.291-0.31340.2727-1.0599-0.80660.07330.5492-0.0691-0.05730.4609-0.04440.480639.964774.0163-14.8398
32.90992.89343.84326.79041.33736.65590.525-0.9657-0.46520.6912-0.46510.10591.0884-0.9649-0.20210.5798-0.1342-0.00380.41070.00130.344237.811662.0101-11.5669
41.9256-0.75981.42730.3557-0.00872.50930.15840.1807-0.0682-0.0534-0.0604-0.11130.17940.0435-0.06910.3978-0.11930.01020.2930.00350.293340.114364.6488-21.7143
58.88514.2371-6.23939.2309-3.10564.40540.27690.6820.4597-0.16290.29410.00840.0701-0.095-0.65310.4168-0.0516-0.01070.45220.0020.30839.830374.1949-29.9559
60.8009-1.5205-1.77362.90573.39654.00580.7774-0.37721.42740.61470.34580.3664-1.34781.4891-0.73620.6114-0.10520.05290.58510.03140.684752.271179.2424-38.2395
70.8154-0.7613-0.15371.9647-0.57490.907-0.19430.00950.6689-0.0912-0.0980.0103-0.2944-0.06890.25970.6147-0.2831-0.0560.72190.03130.542344.723987.2724-56.0199
88.7021.23871.43374.38183.69387.4467-0.20231.13920.3-1.42120.3030.2635-0.9596-0.39860.08150.6817-0.0082-0.01060.72640.06720.735631.95792.1479-26.8162
95.6371.8262-0.40216.30931.80634.15060.0877-0.00230.59350.3155-0.18490.1233-0.08060.18130.05370.459-0.04890.02240.46120.01120.512241.855693.9952-20.9853
108.41164.28313.51879.17644.6412.5780.2874-0.5122-0.46460.5988-0.17640.23080.2531-0.2927-0.10840.4471-0.11230.05180.40550.0520.433138.441983.8868-18.5928
115.5739-3.59-0.28463.64380.15030.679-0.1765-0.2332-0.00410.19350.06841.19670.1285-0.41910.08370.5044-0.10590.11090.4953-0.06520.77824.388180.76-20.1592
120.7766-1.4718-0.4648.19390.32590.28150.2343-1.0475-0.14670.48230.50431.1861-0.9368-0.2498-0.44130.7074-0.05660.27230.5218-0.04730.58727.768586.1802-14.3617
134.5794-3.76411.24395.9405-3.87663.0930.1980.13680.37770.4777-0.02961.2615-1.1951-0.6412-0.63790.6371-0.1010.0180.5212-0.03810.804426.918489.6599-19.6302
142.6443-1.9440.49243.3139-2.13781.76722.10290.7951-0.29750.09880.19970.60391.1711-0.3828-1.27130.7457-0.1647-0.23280.79520.16030.655125.901590.5559-30.9652
157.93681.96452.15620.4990.56620.6356-0.6593-0.2183-0.01740.34380.14571.0642-0.877-0.41870.23370.6274-0.06390.18120.5025-0.10730.806829.465292.7697-14.4251
169.5021-0.9179-0.66412.78790.83986.03410.2945-0.5425-0.00370.1635-0.37050.356-0.0925-0.14170.18120.518-0.06630.070.4870.03850.451224.493465.6574-41.9455
178.2637-0.3770.15437.6787-6.40359.2484-0.1037-0.28210.6223-0.3458-0.00670.7656-0.0018-0.7074-0.0230.3905-0.0927-0.04270.5059-0.02260.499935.372469.4566-54.521
185.52993.32982.94323.29014.60917.7475-0.10531.2222-0.0891-0.82370.6257-0.8432-0.68671.1553-0.55580.5132-0.160.02170.6304-0.01180.437147.424971.5667-57.8493
190.2211-0.5743-0.53371.08221.00562.8195-0.17010.0437-0.066-0.04060.17730.08-0.15550.4467-0.00350.3088-0.12280.02430.4005-0.00530.366244.784869.33-47.6579
208.58134.2358-2.60379.304-4.62727.91140.30920.1237-0.01330.92370.07930.2692-0.11540.3083-0.37830.3243-0.04090.030.3152-0.04810.282135.098269.0442-39.0516
211.9498-1.3347-0.87953.99850.63766.50820.03860.20080.03040.2192-0.37030.32531.1164-0.44740.39130.4696-0.17420.08260.45690.0080.558827.892260.9549-20.2151
221.44710.1982-1.92130.413-1.26275.29610.1661-0.22760.6250.4548-1.09070.33620.18680.2812-0.09450.9162-0.374-0.05680.6226-0.11460.884915.060468.4642-9.8754
237.90471.02885.72797.87042.99975.05460.4083-1.52070.17250.6672-0.22650.1603-0.016-1.2888-0.04950.53820.00320.09240.61340.02240.699917.273377.5328-42.5548
244.5-0.17220.75143.86931.50816.88050.0019-0.00940.32990.34350.13030.22420.4835-0.3028-0.11410.4897-0.09940.01680.480.00640.475715.434367.6044-48.3701
256.95193.2745.68777.04565.01145.7503-0.08060.16990.0516-0.5940.0448-0.5019-0.51320.1133-0.04220.4158-0.15490.05580.45950.01780.456225.617671.0437-50.8019
260.2769-0.6483-0.47445.06094.03363.28820.1476-0.01421.14451.1392-0.2161-0.2312-1.26380.9704-0.00720.5832-0.0887-0.03180.4439-0.05020.572730.883682.8846-42.0706
274.5259-5.94720.99478.092-1.25260.9912-0.05920.48770.8278-0.79780.0380.2672-0.06540.18370.08370.4965-0.049-0.09990.49840.18810.815327.770286.0573-52.6305
286.8968-2.691-4.42586.30630.88247.81140.14120.64531.4628-0.0284-0.01280.2305-0.6993-0.6866-0.21990.3815-0.1105-0.07330.59960.02630.695621.039982.373-49.6551
290.53031.4882-0.91953.8336-2.42831.6298-0.50260.78321.7819-0.4354-0.4234-0.5074-0.8329-0.70850.36560.5736-0.0089-0.1070.71380.1050.866416.619179.9824-54.9265
303.5689-0.6919-1.39243.2526-1.36675.3751-0.02610.2386-0.21140.00430.0020.18130.9485-0.06420.05370.6472-0.0542-0.0670.5247-0.01260.381249.102161.2273-8.9244
312.6687-0.02471.16353.3522-2.8172.83850.3431-0.0989-0.3519-0.42320.2623-0.14321.43410.6333-0.57220.66130.0915-0.07090.6284-0.10340.456252.820856.0144-33.2456
326.07620.05810.67567.75660.80412.20490.15280.1018-1.0969-1.70780.3512-0.6982-0.55431.3681-0.46660.6130.04410.050.8039-0.1930.454656.238155.36-58.0929
335.72576.25921.4156.9070.65769.09380.95431.0518-0.32270.665-0.49420.73370.79410.182-0.38090.85850.02660.011.0003-0.23830.479248.45354.4243-68.1829
346.72940.10440.9334.8978-0.5952.01980.0022-0.3798-0.2312-0.23650.4259-0.41160.95750.3914-0.36530.56250.05960.04390.6186-0.17870.420652.486457.0937-52.2914
353.10970.40622.22955.1404-1.13513.91060.2677-0.1542-0.2674-0.04770.1483-0.40031.21950.4904-0.37890.61570.079-0.08980.5575-0.05810.396652.394456.6583-18.2144
362.15020.581.75914.8014-1.1555.70240.551-0.07730.1001-0.3561-0.1654-0.39610.29610.4362-0.20880.5633-0.07010.00970.5583-0.0280.512473.6356104.0852-41.9294
375.2722-1.0698-2.31567.6455.28424.2475-0.19940.2294-0.2851-0.05180.1688-0.84610.66170.86950.0580.4309-0.05540.03160.52830.05610.461762.719100.3284-54.5211
385.32681.8174-1.05173.8441-5.47398.25610.09030.9180.0887-0.71960.46990.87431.0902-1.0271-0.63090.4547-0.1268-0.01170.5621-0.01680.40550.74498.2321-57.8391
390.36270.02410.5512.5738-1.37171.931-0.0896-0.06530.09820.12350.2093-0.0640.0125-0.3491-0.12120.2963-0.11590.01570.43820.01870.341253.3831100.4666-47.6548
408.85034.87442.52428.04355.84638.9560.28060.2364-0.07310.87480.1426-0.36470.07220.1686-0.40150.3667-0.08570.02370.42280.05020.33462.9315100.2079-39.4096
414.0851-0.52552.21784.5911-1.06045.1004-0.0262-0.0380.14060.5456-0.1627-0.3955-0.98390.29350.1620.4906-0.19010.0130.3731-0.00010.398170.0224109.1034-21.1086
420.0562-0.0736-0.02930.01320.01420.0117-0.31780.4376-0.6696-0.0005-0.1444-1.17890.29970.0608-0.05410.9747-0.2384-0.00090.78960.03661.029683.1736101.312-9.841
439.33152.861-6.44044.8315-3.15844.95140.7831-1.4193-0.53590.8343-0.5495-0.2939-0.52330.7386-0.00790.633-0.069-0.05580.68490.00160.663480.898992.2555-42.58
445.16011.7595-2.46854.65090.43884.37880.15710.2222-0.25910.25150.0967-0.3445-0.32290.1198-0.22130.3731-0.07950.01580.4199-0.04860.448982.7169102.1728-48.4
459.08814.6748-7.79216.9165-5.37797.7127-0.39090.2525-0.0305-0.57760.16730.43490.6352-0.63450.1640.3933-0.0825-0.03720.4189-0.02280.462572.583198.773-50.7926
462.8576-3.8046-0.30697.0483-0.0782.6186-0.08970.069-0.8953-0.16010.1803-0.32540.1574-0.241-0.0870.4559-0.08090.0520.4923-0.08220.73569.393784.7475-49.2623
478.3477-2.3934.11358.7196-2.89175.95350.2370.4825-1.2264-0.0448-0.1922-0.40530.59260.856-0.09110.4226-0.05110.09530.5111-0.01020.660877.145787.404-49.6417
482.19792.13251.31513.6880.90990.91330.7530.3622-1.4016-0.48950.2356-0.06380.17060.0859-0.82080.4868-0.15610.08590.6448-0.17720.85281.173990.0202-54.869
492.87160.3971-1.8522.12461.31045.6093-0.13940.0514-0.5785-0.14170.53240.2980.35590.4068-0.31030.5787-0.0361-0.08210.57570.00040.463154.340484.9322-27.4274
506.6591-0.03112.5657.5327-1.26813.72130.358-0.2704-0.95740.6036-0.101-0.23380.9560.1972-0.19850.557-0.10670.05130.46990.03950.405258.183695.7073-14.8815
519.72112.0086-3.94916.742-0.30184.24570.3849-0.73980.75290.84530.30620.0467-1.01030.4176-0.68160.585-0.14380.00810.4148-0.02360.321960.3025107.8182-11.5687
520.7498-0.104-1.06350.4674-0.06842.22830.1505-0.0413-0.04280.1056-0.17010.1468-0.28090.03250.01390.4313-0.13070.02440.323-0.02570.361158.0469105.1297-21.7073
535.11076.08273.53838.73711.89624.977-0.07840.9691-0.16920.04710.3799-0.148-0.0112-0.0416-0.23770.4652-0.06180.04480.42930.01640.311858.313895.5695-29.9572
544.0676-1.524-0.79364.03732.27574.7394-0.02120.3965-0.293-0.08550.0925-0.05950.0887-0.8330.02180.4603-0.22070.00570.4545-0.00180.385149.377288.5398-48.2361
550.4211-0.10511.07475.1783.7096.4928-0.56240.3784-0.9550.0195-0.1484-0.44-0.6668-0.2486-0.2290.7643-0.39890.0930.88240.14870.877357.186975.3397-59.4097
568.41221.9178-3.27925.5303-0.42147.4477-0.61040.795-0.6259-1.56860.6076-0.36560.59190.37740.16020.5568-0.0488-0.00710.6553-0.06930.581666.245577.5824-26.7963
573.38611.6651-0.98285.6794-1.53272.06210.1007-0.29140.04610.3335-0.0738-0.13620.209-0.08750.00830.4111-0.108-0.01290.3424-0.02940.387658.116481.1313-19.7176
584.247-0.8019-2.78222.90880.37851.8753-0.02960.977-0.7511-0.5942-0.2265-1.7053-0.67310.85510.27970.5145-0.11180.07370.59520.02470.591771.530191.2358-27.2999
597.2748-5.82740.1684.7564-0.43063.18440.2278-1.2493-0.58180.09760.0399-0.8466-0.3267-0.0696-0.06880.5648-0.0673-0.14470.43260.13110.913174.710388.1246-16.8189
605.4127-3.31260.10666.49834.82946.71010.1053-0.0023-0.25750.60990.2331-1.30.73160.4066-0.36590.5023-0.1139-0.04150.38090.01980.673671.089781.3674-19.7584
613.68660.5296-0.48290.1151-0.04140.1148-0.2401-0.1298-0.20370.15020.4956-1.17310.45140.6985-0.19050.6772-0.0945-0.11350.44390.0620.737868.671876.9953-14.3961
623.2230.1752-0.00424.19230.08455.05860.22590.07470.2513-0.07860.10030.3277-0.6926-0.6568-0.23460.59560.06820.1560.4933-0.00590.399645.8135112.8089-16.9658
637.55752.74173.83327.19546.39436.92110.1665-0.1654-0.1066-0.45050.313-0.3251-1.2247-0.8593-0.42990.59360.00180.07750.52090.09150.349648.0418110.5614-41.6066
643.1175-0.8137-0.99013.47681.0744.54780.31120.36090.5558-0.45020.21270.5646-0.558-1.3516-0.53690.70070.08690.00130.85510.19490.487243.1601114.5806-59.6849
650.75840.21541.48440.3793-0.01485.77510.1025-0.12390.10560.12580.22250.1527-0.536-0.9857-0.30580.58120.03820.04360.63770.1110.481446.4519111.9597-43.9087
664.24941.598-3.64022.7294-3.00139.2180.4141-0.56190.62150.16620.07860.5278-0.6242-0.0794-0.47130.82180.15090.25190.61730.00750.483943.9439115.3878-9.6884
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 8 )A1 - 8
2X-RAY DIFFRACTION2chain 'A' and (resid 9 through 20 )A9 - 20
3X-RAY DIFFRACTION3chain 'A' and (resid 21 through 31 )A21 - 31
4X-RAY DIFFRACTION4chain 'A' and (resid 32 through 63 )A32 - 63
5X-RAY DIFFRACTION5chain 'A' and (resid 64 through 78 )A64 - 78
6X-RAY DIFFRACTION6chain 'A' and (resid 79 through 83 )A79 - 83
7X-RAY DIFFRACTION7chain 'A' and (resid 84 through 101 )A84 - 101
8X-RAY DIFFRACTION8chain 'B' and (resid 0 through 7 )B0 - 7
9X-RAY DIFFRACTION9chain 'B' and (resid 8 through 23 )B8 - 23
10X-RAY DIFFRACTION10chain 'B' and (resid 24 through 39 )B24 - 39
11X-RAY DIFFRACTION11chain 'B' and (resid 40 through 62 )B40 - 62
12X-RAY DIFFRACTION12chain 'B' and (resid 63 through 71 )B63 - 71
13X-RAY DIFFRACTION13chain 'B' and (resid 72 through 79 )B72 - 79
14X-RAY DIFFRACTION14chain 'B' and (resid 80 through 84 )B80 - 84
15X-RAY DIFFRACTION15chain 'B' and (resid 85 through 91 )B85 - 91
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 8 )C1 - 8
17X-RAY DIFFRACTION17chain 'C' and (resid 9 through 20 )C9 - 20
18X-RAY DIFFRACTION18chain 'C' and (resid 21 through 31 )C21 - 31
19X-RAY DIFFRACTION19chain 'C' and (resid 32 through 63 )C32 - 63
20X-RAY DIFFRACTION20chain 'C' and (resid 64 through 79 )C64 - 79
21X-RAY DIFFRACTION21chain 'C' and (resid 80 through 94 )C80 - 94
22X-RAY DIFFRACTION22chain 'C' and (resid 95 through 102 )C95 - 102
23X-RAY DIFFRACTION23chain 'D' and (resid 0 through 7 )D0 - 7
24X-RAY DIFFRACTION24chain 'D' and (resid 8 through 23 )D8 - 23
25X-RAY DIFFRACTION25chain 'D' and (resid 24 through 39 )D24 - 39
26X-RAY DIFFRACTION26chain 'D' and (resid 40 through 46 )D40 - 46
27X-RAY DIFFRACTION27chain 'D' and (resid 47 through 62 )D47 - 62
28X-RAY DIFFRACTION28chain 'D' and (resid 63 through 84 )D63 - 84
29X-RAY DIFFRACTION29chain 'D' and (resid 85 through 91 )D85 - 91
30X-RAY DIFFRACTION30chain 'I' and (resid 1 through 5 )I1 - 5
31X-RAY DIFFRACTION31chain 'I' and (resid 6 through 15 )I6 - 15
32X-RAY DIFFRACTION32chain 'I' and (resid 16 through 20 )I16 - 20
33X-RAY DIFFRACTION33chain 'I' and (resid 21 through 21 )I21
34X-RAY DIFFRACTION34chain 'J' and (resid 1 through 10 )J1 - 10
35X-RAY DIFFRACTION35chain 'J' and (resid 11 through 21 )J11 - 21
36X-RAY DIFFRACTION36chain 'E' and (resid 1 through 8 )E1 - 8
37X-RAY DIFFRACTION37chain 'E' and (resid 9 through 20 )E9 - 20
38X-RAY DIFFRACTION38chain 'E' and (resid 21 through 31 )E21 - 31
39X-RAY DIFFRACTION39chain 'E' and (resid 32 through 63 )E32 - 63
40X-RAY DIFFRACTION40chain 'E' and (resid 64 through 78 )E64 - 78
41X-RAY DIFFRACTION41chain 'E' and (resid 79 through 94 )E79 - 94
42X-RAY DIFFRACTION42chain 'E' and (resid 95 through 102 )E95 - 102
43X-RAY DIFFRACTION43chain 'F' and (resid 0 through 7 )F0 - 7
44X-RAY DIFFRACTION44chain 'F' and (resid 8 through 23 )F8 - 23
45X-RAY DIFFRACTION45chain 'F' and (resid 24 through 39 )F24 - 39
46X-RAY DIFFRACTION46chain 'F' and (resid 40 through 62 )F40 - 62
47X-RAY DIFFRACTION47chain 'F' and (resid 63 through 84 )F63 - 84
48X-RAY DIFFRACTION48chain 'F' and (resid 85 through 91 )F85 - 91
49X-RAY DIFFRACTION49chain 'G' and (resid 1 through 8 )G1 - 8
50X-RAY DIFFRACTION50chain 'G' and (resid 9 through 20 )G9 - 20
51X-RAY DIFFRACTION51chain 'G' and (resid 21 through 31 )G21 - 31
52X-RAY DIFFRACTION52chain 'G' and (resid 32 through 63 )G32 - 63
53X-RAY DIFFRACTION53chain 'G' and (resid 64 through 78 )G64 - 78
54X-RAY DIFFRACTION54chain 'G' and (resid 79 through 94 )G79 - 94
55X-RAY DIFFRACTION55chain 'G' and (resid 95 through 102 )G95 - 102
56X-RAY DIFFRACTION56chain 'H' and (resid 0 through 7 )H0 - 7
57X-RAY DIFFRACTION57chain 'H' and (resid 8 through 39 )H8 - 39
58X-RAY DIFFRACTION58chain 'H' and (resid 40 through 46 )H40 - 46
59X-RAY DIFFRACTION59chain 'H' and (resid 47 through 62 )H47 - 62
60X-RAY DIFFRACTION60chain 'H' and (resid 63 through 84 )H63 - 84
61X-RAY DIFFRACTION61chain 'H' and (resid 85 through 91 )H85 - 91
62X-RAY DIFFRACTION62chain 'K' and (resid 1 through 10 )K1 - 10
63X-RAY DIFFRACTION63chain 'K' and (resid 11 through 15 )K11 - 15
64X-RAY DIFFRACTION64chain 'K' and (resid 16 through 21 )K16 - 21
65X-RAY DIFFRACTION65chain 'L' and (resid 1 through 15 )L1 - 15
66X-RAY DIFFRACTION66chain 'L' and (resid 16 through 21 )L16 - 21

+
万見について

-
お知らせ

-
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

-
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

+
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

+
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

+
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。

-
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