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- PDB-8w1f: Crystal Structure of DPS-like protein PA4880 from Pseudomonas aer... -

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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: 8w1f
タイトルCrystal Structure of DPS-like protein PA4880 from Pseudomonas aeruginosa (dodecamer, Mg bound)
要素DPS-LIKE PROTEIN
キーワードMETAL BINDING PROTEIN / PA4880 / DPS protein / metal binding / DNA cleavage / dodecamer
機能・相同性
機能・相同性情報


ferroxidase activity / intracellular sequestering of iron ion / ferric iron binding / iron ion transport / iron ion binding / heme binding / cytosol
類似検索 - 分子機能
DNA-binding protein from starved cells-like / Bacterioferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
類似検索 - ドメイン・相同性
: / Bacterioferritin
類似検索 - 構成要素
生物種Pseudomonas aeruginosa PAO1 (緑膿菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3 Å
データ登録者Lovell, S. / Liu, L. / Seibold, S. / Battaile, K.P. / Rivera, M.
資金援助 米国, 1件
組織認可番号
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI169344 米国
引用ジャーナル: Front Mol Biosci / : 2024
タイトル: Pseudomonas aeruginosa gene PA4880 encodes a Dps-like protein with a Dps fold, bacterioferritin-type ferroxidase centers, and endonuclease activity.
著者: Rajapaksha, N. / Yao, H. / Cook, A. / Seibold, S. / Liu, L. / Battaile, K.P. / Fontenot, L. / Donnarumma, F. / Lovell, S. / Rivera, M.
履歴
登録2024年2月15日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年5月29日Provider: repository / タイプ: Initial release
改定 1.12024年6月19日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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: DPS-LIKE PROTEIN
B: DPS-LIKE PROTEIN
C: DPS-LIKE PROTEIN
D: DPS-LIKE PROTEIN
E: DPS-LIKE PROTEIN
F: DPS-LIKE PROTEIN
G: DPS-LIKE PROTEIN
H: DPS-LIKE PROTEIN
I: DPS-LIKE PROTEIN
J: DPS-LIKE PROTEIN
K: DPS-LIKE PROTEIN
L: DPS-LIKE PROTEIN
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)249,366117
ポリマ-242,90012
非ポリマー6,466105
41423
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: gel filtration, 12 mer
タイプ名称対称操作
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)215.790, 215.790, 277.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDモデル要素
11F-204-

MG

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要素

#1: タンパク質
DPS-LIKE PROTEIN


分子量: 20241.627 Da / 分子数: 12 / 由来タイプ: 組換発現
由来: (組換発現) Pseudomonas aeruginosa PAO1 (緑膿菌)
遺伝子: PA4880 / プラスミド: pET28a / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q9HUT3
#2: 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: 37 / 由来タイプ: 合成 / : Mg / タイプ: SUBJECT OF INVESTIGATION
#3: 化合物...
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 44 / 由来タイプ: 合成 / : SO4 / タイプ: SUBJECT OF INVESTIGATION
#4: 化合物...
ChemComp-FE2 / FE (II) ION


分子量: 55.845 Da / 分子数: 24 / 由来タイプ: 合成 / : Fe / タイプ: SUBJECT OF INVESTIGATION
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 23 / 由来タイプ: 天然 / : H2O
研究の焦点であるリガンドがあるかY

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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: 6.65 Å3/Da / 溶媒含有率: 81.51 %
結晶化温度: 291 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7
詳細: Salt Rx G2: 1 M magnesium sulfate, 100 mM Bis-Tris pH 7.0

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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: NSLS-II / ビームライン: 19-ID / 波長: 0.9795 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2022年3月24日
放射モノクロメーター: Double Crystal Si 111 / 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: 0.9795 Å / 相対比: 1
反射解像度: 3→49.94 Å / Num. obs: 130805 / % possible obs: 100 % / 冗長度: 14.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.202 / Rpim(I) all: 0.055 / Rrim(I) all: 0.209 / Χ2: 1 / Net I/σ(I): 12.1 / Num. measured all: 1874799
反射 シェル解像度: 3→3.05 Å / % possible obs: 100 % / 冗長度: 15.1 % / Rmerge(I) obs: 1.798 / Num. measured all: 96579 / Num. unique obs: 6414 / CC1/2: 0.719 / Rpim(I) all: 0.476 / Rrim(I) all: 1.861 / Χ2: 0.99 / Net I/σ(I) obs: 1.8

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.21rc1_5156: ???)精密化
Aimlessデータスケーリング
XDSデータ削減
PHASER位相決定
精密化構造決定の手法: 分子置換 / 解像度: 3→31.27 Å / SU ML: 0.33 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 20.78 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2036 6576 5.04 %
Rwork0.1792 --
obs0.1804 130536 99.95 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 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→31.27 Å
タンパク質核酸リガンド溶媒全体
原子数16144 0 281 23 16448
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00816536
X-RAY DIFFRACTIONf_angle_d0.8722359
X-RAY DIFFRACTIONf_dihedral_angle_d12.2756179
X-RAY DIFFRACTIONf_chiral_restr0.0422465
X-RAY DIFFRACTIONf_plane_restr0.012982
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.030.3052160.29174098X-RAY DIFFRACTION100
3.03-3.070.32542270.29464030X-RAY DIFFRACTION100
3.07-3.110.33322190.2934109X-RAY DIFFRACTION100
3.11-3.150.32372150.30044097X-RAY DIFFRACTION100
3.15-3.190.32722040.29644090X-RAY DIFFRACTION100
3.19-3.230.30221970.27574093X-RAY DIFFRACTION100
3.23-3.280.27992100.24494098X-RAY DIFFRACTION100
3.28-3.330.25351920.23054120X-RAY DIFFRACTION100
3.33-3.380.26582350.23064072X-RAY DIFFRACTION100
3.38-3.430.2492320.2274049X-RAY DIFFRACTION100
3.43-3.490.26382040.22944142X-RAY DIFFRACTION100
3.49-3.560.2762150.21774095X-RAY DIFFRACTION100
3.56-3.620.20052050.19244114X-RAY DIFFRACTION100
3.62-3.70.20282490.18074042X-RAY DIFFRACTION100
3.7-3.780.22892030.18214143X-RAY DIFFRACTION100
3.78-3.870.22052170.17194122X-RAY DIFFRACTION100
3.87-3.960.18872040.1684105X-RAY DIFFRACTION100
3.96-4.070.18652330.15794138X-RAY DIFFRACTION100
4.07-4.190.15722070.13944103X-RAY DIFFRACTION100
4.19-4.320.15622330.13754119X-RAY DIFFRACTION100
4.32-4.480.16042280.13294115X-RAY DIFFRACTION100
4.48-4.660.16892150.12374130X-RAY DIFFRACTION100
4.66-4.870.15642390.13414128X-RAY DIFFRACTION100
4.87-5.120.18242260.15124155X-RAY DIFFRACTION100
5.12-5.440.16852130.15914169X-RAY DIFFRACTION100
5.44-5.860.20522230.18094191X-RAY DIFFRACTION100
5.86-6.450.22872070.19114203X-RAY DIFFRACTION100
6.45-7.370.16912300.1614226X-RAY DIFFRACTION100
7.37-9.240.16272580.13634242X-RAY DIFFRACTION100
9.24-31.270.20542200.1964422X-RAY DIFFRACTION99
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)
10.11520.23140.01680.46380.04030.081-0.0725-0.5769-0.3037-0.63760.204-0.60810.00350.4406-0.32590.9142-0.21320.48581.10610.14041.119345.6872-58.083-90.1228
20.43280.00960.3510.09310.1020.37150.61941.3419-0.1990.12360.0414-0.3679-0.49060.50350.06640.6306-0.16580.0610.7023-0.04120.725138.2013-48.5381-85.741
31.6531-0.4237-0.61240.22470.36621.1169-0.08110.068-0.079-0.06640.00790.0449-0.3141-0.05090.00010.6309-0.0541-0.03650.45290.03350.602914.2521-39.4685-72.7381
40.2648-0.13510.00890.36-0.32890.6471-0.41560.7316-0.55590.07110.05350.17160.1508-0.1858-0.00040.6483-0.0217-0.01370.5579-0.02350.67328.3013-44.7814-79.9291
50.044-0.01760.01350.0298-0.02090.01510.0807-0.00970.6037-0.20210.1997-0.3336-0.94310.29270.00060.8813-0.1634-0.00841.04670.06050.72770.3581-66.7522-108.8801
60.015-0.01690.03280.18030.02360.1213-0.12970.7376-0.5062-0.7516-0.50670.096-0.5928-0.0127-00.7415-0.0738-0.00781.0066-0.070.781913.2546-68.4883-105.7105
70.6589-0.12431.040.97350.02051.8169-0.10350.00780.0774-0.0392-0.0211-0.13590.02640.089500.5179-0.07070.06350.6054-0.03180.551633.7198-67.4543-85.2545
80.47160.1098-0.4030.4178-0.07070.3632-0.1754-0.59140.3406-0.0634-0.00970.1418-0.4256-0.4556-0.00040.5876-0.06430.00050.6329-0.04070.621230.3187-57.7278-82.1771
90.06940.0112-0.05330.10130.0020.0545-0.6363-0.4684-0.34930.48670.7254-0.22350.71080.7530.00130.90030.3649-0.10651.0348-0.07710.996551.5075-83.0896-45.0468
100.03460.0086-0.03150.0018-0.00910.04680.02190.7298-0.51680.121-0.2896-1.16450.1069-0.42860.00010.64690.0673-0.04981.1538-0.19540.903852.2814-79.9104-55.7181
110.27330.3863-0.0040.5409-0.00440.00020.1754-0.58810.18350.4726-0.2376-0.5316-0.13020.6395-0.01720.67590.2951-0.10820.87320.00050.827548.2314-89.2437-58.4451
120.14470.1456-0.32650.8177-0.27840.65880.07670.3042-0.1661-0.294-0.08330.00590.21220.13590.00020.61040.04080.06970.5585-0.10050.652833.4127-85.381-81.1633
130.16410.01920.18290.6269-0.50180.5816-0.269-1.2807-0.2311-0.02410.03230.07320.0449-0.86510.00070.56710.04340.05950.6354-0.05590.692426.4695-84.2676-76.8892
140.2244-0.02650.05040.0016-0.0260.1802-0.39920.46530.53470.0523-0.6039-0.66620.0390.4535-0.00160.46370.07430.03880.9071-0.0560.738743.8744-79.4578-77.7402
150.27670.3153-0.21790.3457-0.24830.1715-0.31260.1520.1942-0.47550.1272-0.13520.4556-0.10830.00750.52410.1012-0.02140.7089-0.17050.739534.422-87.9097-89.4227
160.8750.9749-0.1071.0513-0.10680.0830.0519-0.2480.3334-0.1777-0.2438-0.11231.0489-0.42380.00050.72290.0830.04930.5745-0.14260.636532.2881-96.5268-78.8717
170.8779-0.0595-0.72930.02520.04770.6003-0.094-0.7841-0.20890.12480.03670.02630.3008-0.90510.00020.69490.014-0.00440.6546-0.03710.682426.111-94.6647-74.9167
180.01080.0525-0.04140.2197-0.17870.1418-0.29540.2886-0.2302-0.29960.2278-0.30190.35670.4260.00011.08480.1350.12750.6989-0.02140.823132.1894-102.3979-87.1261
190.0411-0.00040.0840.0256-0.00610.17-0.1510.1525-0.6833-0.27490.6142-0.2143-0.36640.94830.00090.87970.15450.10040.6599-0.11850.761828.3505-107.1356-75.5912
201.18040.52520.43320.7842-0.16150.3447-0.2244-0.1433-0.34880.00840.10370.44110.4293-0.146300.7207-0.0101-0.00990.38670.06440.62397.668-104.014-58.1936
210.514-0.1097-0.39080.1037-0.14720.8978-0.00110.0493-0.32990.0547-0.03340.0760.21120.11760.00030.74140.00730.00020.4676-0.04960.69478.9177-99.2086-60.2161
220.01980.01570.05990.02590.07720.15980.0158-0.4734-0.5346-0.0549-0.05040.04480.35310.09170.00120.82520.04340.09840.4736-0.01640.61123.5656-109.5158-53.5085
230.446-0.04420.56770.11210.07420.80350.1611-0.333-0.4453-0.0402-0.09350.0458-0.05140.2999-0.00020.89620.0256-0.030.55550.02310.755216.6214-106.4012-51.5081
240.4575-0.27570.16980.591-0.22270.22560.409-0.38060.2795-0.02620.1386-0.0918-0.61380.82540.00060.6940.00850.04970.575-0.01260.689617.7394-98.9391-50.9561
250.27310.1401-0.06660.156-0.02320.0568-0.8308-0.1643-0.5140.8269-0.21990.5133-0.4252-0.3528-0.0071.0877-0.0555-0.03130.7639-0.1450.599832.5944-33.3425-45.1181
260.03180.0328-0.04280.0313-0.03440.07540.32-0.10241.30630.6471-0.34860.1674-0.55360.9947-0.00020.8349-0.1207-0.06810.79270.04270.717233.33-44.53-37.8046
270.1978-0.27070.19440.383-0.08950.70770.0242-0.1658-0.20410.57310.1028-0.39740.26580.17980.00030.64180.07810.02190.57040.03080.507924.9286-71.9095-32.7651
280.1532-0.23690.01180.5142-0.09390.0034-0.37710.20370.3292-0.46470.39140.48480.0461-0.05700.6916-0.0001-0.01910.6325-0.03420.577319.0163-71.5896-38.491
290.14210.0626-0.05640.027-0.02710.026-0.12930.34920.2078-0.32040.9012-0.95660.0290.29480.03690.6026-0.0446-0.09820.5441-0.07160.631636.0033-66.4889-35.0227
300.2265-0.11030.08180.14580.07930.177-0.052-0.2174-0.02480.97010.2981-0.0675-0.11330.23270.00050.7597-0.07160.00180.5730.01330.598526.115-77.6298-26.2975
311.23190.1924-0.01160.150.23050.415-0.31490.13560.05090.76690.83490.31220.0166-0.0424-0.00020.67920.01930.07130.55950.01080.60617.4622-66.7854-25.7728
320.25990.0640.17340.21740.13270.727-0.15020.0120.6345-0.31850.36731.03230.0023-0.0847-00.69040.04560.05150.61610.00950.614512.6831-66.7091-31.5983
330.0790.0244-0.00480.12180.10660.09790.4769-0.78081.02630.459-0.03740.3032-0.89540.5490.00070.86390.14860.09480.7673-0.05280.8832-13.0982-39.4204-37.8715
340.1523-0.0733-0.00740.0454-0.02770.08730.4148-0.4927-0.10690.51340.14530.5879-0.67540.1698-0.0010.80860.15880.1110.649-0.14970.7814-0.1149-37.0244-38.2638
350.3360.2445-0.00020.747-0.82481.11590.0791-0.01760.0219-0.0931-0.0838-0.0134-0.63060.288900.6167-0.0805-0.04440.4583-0.04170.561320.7829-40.0378-55.4989
360.3366-0.1877-0.14670.2906-0.30740.6112-0.526-0.0509-0.93690.57230.05940.3740.07780.05950.00010.723-0.0057-0.02910.4637-0.03930.675419.9964-48.2649-55.5311
370.1245-0.0030.02660.05390.04790.0414-0.46180.29180.0271-0.36580.03310.2592-0.6789-0.938800.97530.11290.01090.57120.0040.770810.6423-32.9143-57.0038
380.1655-0.21230.05070.2361-0.06920.0994-0.0262-0.7054-0.301-0.16530.07620.0255-0.37060.60650.00020.78180.02-0.00120.4896-0.12350.729527.7257-35.1083-57.3009
390.6423-0.31960.60790.5405-0.31190.55630.1008-0.2974-0.6806-0.1834-0.32210.2059-0.80740.29330.00010.6302-0.0463-0.03360.4706-0.02450.522325.3961-41.227-45.1218
400.38560.27990.17420.6894-0.00690.3539-0.7867-0.3736-0.80760.25280.24040.24410.1050.2707-00.6284-0.05090.02560.61650.03190.576424.1372-48.6819-45.8259
410.039-0.02660.05150.1387-0.05930.0877-0.47050.3054-0.3347-0.6790.3330.1848-0.7345-0.4874-0.00061.04530.0357-0.13320.81120.13160.94044.4004-29.7129-82.219
420.4514-0.3273-0.35780.24030.25970.2832-0.2544-0.00471.1598-0.07870.6649-0.0170.08650.05020.03751.0731-0.0355-0.11150.66890.10190.71484.6231-38.9426-90.6895
431.11420.1955-0.21970.20250.18780.3158-0.27760.4186-0.0337-0.7620.3030.56110.252-0.30030.00010.5448-0.0907-0.08860.70490.00280.4789-4.2048-64.6981-92.52
440.6550.451-0.37160.4696-0.09450.26960.09830.14110.09350.7607-0.2237-0.58650.0508-0.16250.00040.7121-0.0216-0.03520.6630.00810.59541.047-67.3101-86.7578
450.0661-0.06020.06940.0525-0.06050.056-0.4226-0.00720.38360.40520.66860.4811-0.6639-0.63420.00020.7277-0.0076-0.06530.72010.12780.6879-10.9928-54.3267-90.4301
460.3963-0.1182-0.18090.12870.03020.0774-0.25690.4893-0.2366-0.80570.5817-0.0749-0.19720.12630.00110.7979-0.04280.02380.57410.05950.6007-8.1263-69.1655-98.8467
470.5705-0.2829-0.56550.2990.16480.6047-0.47860.566-0.1182-0.27970.8334-0.4057-0.121-0.1102-0.00020.6485-0.1167-0.05320.7221-0.04210.64274.8439-64.2355-99.5553
480.57930.26010.07590.2894-0.32480.7318-0.10130.08390.03920.51360.2762-0.95730.0647-0.05520.00010.6124-0.1113-0.07670.649-0.01540.58498.9999-66.4504-93.6931
490.5239-0.45680.29540.448-0.24140.1301-0.0985-0.3990.07860.75150.2081-0.150.0176-0.4800.83930.0146-0.00120.6110.12850.748818.8466-109.9017-43.5884
500.50560.5105-0.16321.17780.04861.0214-0.06560.00020.01450.02660.1707-0.14490.1150.22-00.59170.1005-0.02020.60320.03260.604335.6853-81.166-44.6171
510.19430.02020.09570.3109-0.41250.5574-0.48150.53480.0233-0.87620.63330.22270.51050.0387-0.00020.64670.0308-0.03020.6259-0.02640.64837.5103-83.0548-54.9483
520.02540.0018-0.00250.0528-0.03460.10760.39350.0780.65050.1869-0.2548-0.20470.0090.0292-0.00140.92570.09860.09590.7081-0.08150.655519.7678-71.2025-16.5863
530.2974-0.0417-0.12950.1636-0.03880.0722-0.2488-0.8822-0.33260.9089-0.33760.0442-0.19460.4769-0.00060.79560.15130.08550.7889-0.00990.63958.1202-66.0879-19.6747
540.69610.13540.1050.46230.02540.54510.0666-0.00260.10160.0397-0.10740.11970.04840.0812-00.61060.05110.10740.6-0.05920.6189-8.1848-57.7396-42.786
550.85470.5436-0.09510.8103-0.05390.46730.0566-0.18970.29960.1708-0.19370.04720.005-0.12580.00020.67690.09880.08070.6086-0.03140.6028-10.203-52.2916-36.8829
560.85640.3377-0.4460.5081-0.00190.3064-0.11070.44610.4190.1369-0.3388-0.2386-0.18660.7117-0.00020.59870.11440.02930.6092-0.00540.6712-1.3528-48.6385-43.387
570.3115-0.12620.14440.0823-0.04090.044-0.2350.6279-0.2626-0.29050.46520.4770.7223-0.0666-0.00030.778-0.1583-0.09330.7006-0.07060.7922-18.0174-100.6101-80.754
580.78220.37220.05841.3759-0.31650.4567-0.09270.16440.0812-0.0420.1599-0.0581-0.0259-0.2327-0.00010.5051-0.0465-0.04560.7375-0.02320.5821-14.5727-68.0789-81.3687
590.0625-0.2023-0.33030.84421.06781.3639-0.13380.1020.00890.26580.1934-0.04170.004-0.4019-0.00010.44920.0021-0.08140.7411-0.03520.7069-24.1834-65.2024-79.1962
600.7113-0.0788-0.3790.2564-0.15070.33550.0395-0.1662-0.07551.0206-0.04940.13880.2541-0.20760.00020.5863-0.0097-0.0610.70050.01390.6697-20.6378-67.4854-70.1524
610.1429-0.0223-0.12850.0317-0.00070.11520.3160.261-0.57010.3077-0.73460.16320.5606-1.41760.00170.927-0.17310.16390.9632-0.05450.7918-25.7036-85.9662-37.4291
620.0357-0.0213-0.02750.0451-0.03830.1019-0.21210.9089-0.43480.250.37460.7383-0.8572-0.40810.00110.7719-0.17230.12780.9237-0.02390.7352-24.7854-92.389-48.9727
630.4577-0.22620.16230.56990.02740.0624-0.04060.309-0.6379-0.1188-0.0917-0.02210.1057-0.1422-0.00040.6579-0.1611-0.02590.483-0.0350.6875-5.4585-100.5377-66.3115
640.3532-0.2626-0.22840.19910.0820.18490.3602-0.0390.6418-0.12420.39320.2446-0.3188-0.22070.00010.5993-0.13880.00830.61490.00820.6093-3.011-92.7851-67.7653
650.3744-0.0595-0.00780.4133-0.20310.1258-0.05-0.0027-0.52630.0774-0.04170.07380.08930.14050.00010.6911-0.20810.0880.70520.03620.6686-5.8548-106.1515-63.8052
660.44520.21090.30270.1812-0.12270.81730.31030.211-0.3567-0.2768-0.13310.0777-0.4304-0.4296-0.00020.7223-0.1289-0.02250.6973-0.01920.678-14.7206-97.9734-72.4486
670.47930.03320.37380.32410.06150.33450.69220.22430.5063-0.12470.14780.0103-0.6826-0.57790.00060.6787-0.13030.01780.646-0.01850.6502-11.2679-91.2493-74.3112
680.2013-0.0760.0340.05060.01190.0249-0.0584-0.33090.36070.46680.55330.2201-0.2514-0.54010.00030.65560.078-0.02681.13590.14320.9024-32.4315-59.686-76.7246
690.01280.0402-0.01780.2366-0.05210.02050.32070.13220.793-0.5021-0.770.3876-0.0925-0.5403-0.00310.47690.0718-0.02031.12340.02590.8372-32.8228-67.0599-66.3862
700.65670.3049-0.47190.69140.37310.89390.2866-0.1734-0.35110.1914-0.13390.13910.4758-0.36550.00040.5606-0.0470.13610.6447-0.02180.6821-18.0291-70.9089-43.8185
710.3540.260.35090.21130.19080.43420.48640.8885-0.4273-0.2141-0.47590.40350.43060.57640.00030.4395-0.00420.1240.60750.0070.6674-11.5132-73.5711-48.1062
720.19130.17320.21730.63350.3950.3128-0.0842-0.10380.09110.0527-0.1797-0.03780.1326-0.60360.00010.32880.05460.03890.71570.02730.7473-21.9368-67.199-40.8807
730.3383-0.27550.01960.94350.046-0.00260.27510.13590.0901-0.0086-0.29390.21030.84980.102900.6637-0.09680.11340.75110.02260.7142-22.725-81.1576-45.9006
740.17480.10630.11630.08630.09250.16540.20540.59-0.2496-0.2149-0.17010.1540.54960.4329-0.00030.69230.00580.07550.79230.01170.6906-16.4996-82.7734-49.8814
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 32 )
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 147 )
4X-RAY DIFFRACTION4chain 'A' and (resid 148 through 177 )
5X-RAY DIFFRACTION5chain 'B' and (resid 8 through 17 )
6X-RAY DIFFRACTION6chain 'B' and (resid 18 through 32 )
7X-RAY DIFFRACTION7chain 'B' and (resid 33 through 147 )
8X-RAY DIFFRACTION8chain 'B' and (resid 148 through 177 )
9X-RAY DIFFRACTION9chain 'C' and (resid 10 through 17 )
10X-RAY DIFFRACTION10chain 'C' and (resid 18 through 22 )
11X-RAY DIFFRACTION11chain 'C' and (resid 23 through 32 )
12X-RAY DIFFRACTION12chain 'C' and (resid 33 through 63 )
13X-RAY DIFFRACTION13chain 'C' and (resid 64 through 93 )
14X-RAY DIFFRACTION14chain 'C' and (resid 94 through 104 )
15X-RAY DIFFRACTION15chain 'C' and (resid 105 through 118 )
16X-RAY DIFFRACTION16chain 'C' and (resid 119 through 147 )
17X-RAY DIFFRACTION17chain 'C' and (resid 148 through 177 )
18X-RAY DIFFRACTION18chain 'D' and (resid 8 through 22 )
19X-RAY DIFFRACTION19chain 'D' and (resid 23 through 32 )
20X-RAY DIFFRACTION20chain 'D' and (resid 33 through 63 )
21X-RAY DIFFRACTION21chain 'D' and (resid 64 through 104 )
22X-RAY DIFFRACTION22chain 'D' and (resid 105 through 118 )
23X-RAY DIFFRACTION23chain 'D' and (resid 119 through 147 )
24X-RAY DIFFRACTION24chain 'D' and (resid 148 through 177 )
25X-RAY DIFFRACTION25chain 'E' and (resid 8 through 17 )
26X-RAY DIFFRACTION26chain 'E' and (resid 18 through 32 )
27X-RAY DIFFRACTION27chain 'E' and (resid 33 through 63 )
28X-RAY DIFFRACTION28chain 'E' and (resid 64 through 93 )
29X-RAY DIFFRACTION29chain 'E' and (resid 94 through 104 )
30X-RAY DIFFRACTION30chain 'E' and (resid 105 through 118 )
31X-RAY DIFFRACTION31chain 'E' and (resid 119 through 147 )
32X-RAY DIFFRACTION32chain 'E' and (resid 148 through 177 )
33X-RAY DIFFRACTION33chain 'F' and (resid 8 through 22 )
34X-RAY DIFFRACTION34chain 'F' and (resid 23 through 32 )
35X-RAY DIFFRACTION35chain 'F' and (resid 33 through 63 )
36X-RAY DIFFRACTION36chain 'F' and (resid 64 through 93 )
37X-RAY DIFFRACTION37chain 'F' and (resid 94 through 104 )
38X-RAY DIFFRACTION38chain 'F' and (resid 105 through 118 )
39X-RAY DIFFRACTION39chain 'F' and (resid 119 through 147 )
40X-RAY DIFFRACTION40chain 'F' and (resid 148 through 177 )
41X-RAY DIFFRACTION41chain 'G' and (resid 9 through 22 )
42X-RAY DIFFRACTION42chain 'G' and (resid 23 through 32 )
43X-RAY DIFFRACTION43chain 'G' and (resid 33 through 63 )
44X-RAY DIFFRACTION44chain 'G' and (resid 64 through 93 )
45X-RAY DIFFRACTION45chain 'G' and (resid 94 through 104 )
46X-RAY DIFFRACTION46chain 'G' and (resid 105 through 118 )
47X-RAY DIFFRACTION47chain 'G' and (resid 119 through 147 )
48X-RAY DIFFRACTION48chain 'G' and (resid 148 through 177 )
49X-RAY DIFFRACTION49chain 'H' and (resid 9 through 32 )
50X-RAY DIFFRACTION50chain 'H' and (resid 33 through 147 )
51X-RAY DIFFRACTION51chain 'H' and (resid 148 through 177 )
52X-RAY DIFFRACTION52chain 'I' and (resid 9 through 17 )
53X-RAY DIFFRACTION53chain 'I' and (resid 18 through 32 )
54X-RAY DIFFRACTION54chain 'I' and (resid 33 through 93 )
55X-RAY DIFFRACTION55chain 'I' and (resid 94 through 147 )
56X-RAY DIFFRACTION56chain 'I' and (resid 148 through 177 )
57X-RAY DIFFRACTION57chain 'J' and (resid 9 through 32 )
58X-RAY DIFFRACTION58chain 'J' and (resid 33 through 104 )
59X-RAY DIFFRACTION59chain 'J' and (resid 105 through 147 )
60X-RAY DIFFRACTION60chain 'J' and (resid 148 through 177 )
61X-RAY DIFFRACTION61chain 'K' and (resid 8 through 22 )
62X-RAY DIFFRACTION62chain 'K' and (resid 23 through 32 )
63X-RAY DIFFRACTION63chain 'K' and (resid 33 through 63 )
64X-RAY DIFFRACTION64chain 'K' and (resid 64 through 93 )
65X-RAY DIFFRACTION65chain 'K' and (resid 94 through 118 )
66X-RAY DIFFRACTION66chain 'K' and (resid 119 through 148 )
67X-RAY DIFFRACTION67chain 'K' and (resid 149 through 177 )
68X-RAY DIFFRACTION68chain 'L' and (resid 9 through 22 )
69X-RAY DIFFRACTION69chain 'L' and (resid 23 through 32 )
70X-RAY DIFFRACTION70chain 'L' and (resid 33 through 63 )
71X-RAY DIFFRACTION71chain 'L' and (resid 64 through 93 )
72X-RAY DIFFRACTION72chain 'L' and (resid 94 through 118 )
73X-RAY DIFFRACTION73chain 'L' and (resid 119 through 147 )
74X-RAY DIFFRACTION74chain 'L' and (resid 148 through 177 )

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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