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- PDB-6txi: Crystal structure of thermotoga maritima E65A Ferritin -

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基本情報

登録情報
データベース: PDB / ID: 6txi
タイトルCrystal structure of thermotoga maritima E65A Ferritin
要素Ferritin
キーワードMETAL BINDING PROTEIN / Metal binding / engineered protein
機能・相同性
機能・相同性情報


bacterial non-heme ferritin / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / cytoplasm / cytosol
類似検索 - 分子機能
Ferritin, prokaryotic-type / Ferritin / 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
: / EICOSANE / Ferritin
類似検索 - 構成要素
生物種Thermotoga maritima MSB8 (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: 1.759 Å
データ登録者Wilk, P. / Grudnik, P. / Kumar, M. / Heddle, J. / Chakraborti, S.
資金援助 ポーランド, 1件
組織認可番号国
Foundation for Polish ScienceHoming/2017-3/22 ポーランド
引用ジャーナル: Nanoscale / 年: 2021
タイトル: A single residue can modulate nanocage assembly in salt dependent ferritin.
著者: Kumar, M. / Markiewicz-Mizera, J. / Janna Olmos, J.D. / Wilk, P. / Grudnik, P. / Biela, A.P. / Jemiola-Rzeminska, M. / Gorecki, A. / Chakraborti, S. / Heddle, J.G.
履歴
登録2020年1月14日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02021年7月28日Provider: repository / タイプ: Initial release
改定 1.12022年8月10日Group: Database references / カテゴリ: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.22024年1月24日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.country

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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: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
H: Ferritin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)158,87747
ポリマ－154,7508
非ポリマー4,12739
水21,6361201
1
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
H: Ferritin
ヘテロ分子

A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
H: Ferritin
ヘテロ分子

A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
H: Ferritin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)476,632141
ポリマ－464,25124
非ポリマー12,381117
水43224
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area100790 Å2
ΔGint-1229 kcal/mol
Surface area147040 Å2
手法PISA
単位格子
Length a, b, c (Å)175.700, 175.700, 353.568
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDモデル要素
11E-449-

HOH

非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 1 through 6 or resid 8...
21(chain B and (resid 1 through 6 or resid 8...
31(chain C and (resid 1 through 6 or resid 8...
41(chain D and (resid 1 through 6 or resid 8...
51(chain E and (resid 1 through 6 or resid 8...
61(chain F and (resid 1 through 6 or resid 8...
71(chain G and (resid 1 through 6 or resid 8...
81(chain H and (resid 1 through 6 or resid 8...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 6 or resid 8...A1 - 6
121(chain A and (resid 1 through 6 or resid 8...A8 - 9
131(chain A and (resid 1 through 6 or resid 8...A11 - 49
141(chain A and (resid 1 through 6 or resid 8...A82 - 111
151(chain A and (resid 1 through 6 or resid 8...A0
161(chain A and (resid 1 through 6 or resid 8...A113 - 122
171(chain A and (resid 1 through 6 or resid 8...A1 - 203
181(chain A and (resid 1 through 6 or resid 8...A156 - 157
191(chain A and (resid 1 through 6 or resid 8...A159 - 164
211(chain B and (resid 1 through 6 or resid 8...B1 - 6
221(chain B and (resid 1 through 6 or resid 8...B8 - 9
231(chain B and (resid 1 through 6 or resid 8...B11 - 49
241(chain B and (resid 1 through 6 or resid 8...B51 - 57
251(chain B and (resid 1 through 6 or resid 8...B59 - 80
261(chain B and (resid 1 through 6 or resid 8...B82 - 111
271(chain B and (resid 1 through 6 or resid 8...B113 - 122
281(chain B and (resid 1 through 6 or resid 8...B124 - 154
291(chain B and (resid 1 through 6 or resid 8...B156 - 157
2101(chain B and (resid 1 through 6 or resid 8...B159 - 164
311(chain C and (resid 1 through 6 or resid 8...C1 - 6
321(chain C and (resid 1 through 6 or resid 8...C8 - 9
331(chain C and (resid 1 through 6 or resid 8...C11 - 49
341(chain C and (resid 1 through 6 or resid 8...C0
351(chain C and (resid 1 through 6 or resid 8...C113 - 122
361(chain C and (resid 1 through 6 or resid 8...C1 - 200
371(chain C and (resid 1 through 6 or resid 8...C124 - 154
381(chain C and (resid 1 through 6 or resid 8...C156 - 157
391(chain C and (resid 1 through 6 or resid 8...C159 - 164
411(chain D and (resid 1 through 6 or resid 8...D1 - 6
421(chain D and (resid 1 through 6 or resid 8...D8 - 9
431(chain D and (resid 1 through 6 or resid 8...D11 - 49
441(chain D and (resid 1 through 6 or resid 8...D51 - 57
451(chain D and (resid 1 through 6 or resid 8...D59 - 80
461(chain D and (resid 1 through 6 or resid 8...D82 - 111
471(chain D and (resid 1 through 6 or resid 8...D113 - 122
481(chain D and (resid 1 through 6 or resid 8...D124 - 154
491(chain D and (resid 1 through 6 or resid 8...D156 - 157
4101(chain D and (resid 1 through 6 or resid 8...D159 - 164
511(chain E and (resid 1 through 6 or resid 8...E1 - 6
521(chain E and (resid 1 through 6 or resid 8...E8 - 9
531(chain E and (resid 1 through 6 or resid 8...E11 - 49
541(chain E and (resid 1 through 6 or resid 8...E0
551(chain E and (resid 1 through 6 or resid 8...E113 - 122
561(chain E and (resid 1 through 6 or resid 8...E1 - 202
571(chain E and (resid 1 through 6 or resid 8...E124 - 154
581(chain E and (resid 1 through 6 or resid 8...E156 - 157
591(chain E and (resid 1 through 6 or resid 8...E159 - 164
611(chain F and (resid 1 through 6 or resid 8...F1 - 6
621(chain F and (resid 1 through 6 or resid 8...F8 - 9
631(chain F and (resid 1 through 6 or resid 8...F11 - 49
641(chain F and (resid 1 through 6 or resid 8...F51 - 57
651(chain F and (resid 1 through 6 or resid 8...F59 - 80
661(chain F and (resid 1 through 6 or resid 8...F82 - 111
671(chain F and (resid 1 through 6 or resid 8...F113 - 122
681(chain F and (resid 1 through 6 or resid 8...F124 - 154
691(chain F and (resid 1 through 6 or resid 8...F156 - 157
6101(chain F and (resid 1 through 6 or resid 8...F159 - 164
711(chain G and (resid 1 through 6 or resid 8...G1 - 6
721(chain G and (resid 1 through 6 or resid 8...G8 - 9
731(chain G and (resid 1 through 6 or resid 8...G11 - 49
741(chain G and (resid 1 through 6 or resid 8...G0
751(chain G and (resid 1 through 6 or resid 8...G113 - 122
761(chain G and (resid 1 through 6 or resid 8...G1 - 201
771(chain G and (resid 1 through 6 or resid 8...G124 - 154
781(chain G and (resid 1 through 6 or resid 8...G156 - 157
791(chain G and (resid 1 through 6 or resid 8...G159 - 164
811(chain H and (resid 1 through 6 or resid 8...H1 - 6
821(chain H and (resid 1 through 6 or resid 8...H8 - 9
831(chain H and (resid 1 through 6 or resid 8...H11 - 49
841(chain H and (resid 1 through 6 or resid 8...H51 - 57
851(chain H and (resid 1 through 6 or resid 8...H59 - 80
861(chain H and (resid 1 through 6 or resid 8...H82 - 111
871(chain H and (resid 1 through 6 or resid 8...H113 - 122
881(chain H and (resid 1 through 6 or resid 8...H124 - 154
891(chain H and (resid 1 through 6 or resid 8...H156 - 157
8101(chain H and (resid 1 through 6 or resid 8...H159 - 164

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要素

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タンパク質 , 1種, 8分子 ABCDEFGH

#1: タンパク質
Ferritin


分子量: 19343.805 Da / 分子数: 8 / 変異: E65A / 由来タイプ: 組換発現
由来: (組換発現) Thermotoga maritima MSB8 (バクテリア)
遺伝子: TM_1128 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9X0L2, bacterial non-heme ferritin

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非ポリマー , 5種, 1240分子

#2: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 16 / 由来タイプ: 合成 / 式: SO4
#3: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 11 / 由来タイプ: 合成 / 式: C3H8O3
#4: 化合物
ChemComp-FE / FE (III) ION


分子量: 55.845 Da / 分子数: 8 / 由来タイプ: 合成 / 式: Fe
#5: 化合物
ChemComp-LFA / EICOSANE / LIPID FRAGMENT / イコサン


分子量: 282.547 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C20H42
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1201 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかN

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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: 3.39 Å3/Da / 溶媒含有率: 63.75 %
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 / pH: 6 / 詳細: 2.4 M (NH4)2 SO4, 0.1M MES. pH 6.0.

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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: BESSY / ビームライン: 14.1 / 波長: 0.9184 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2019年10月18日
放射モノクロメーター: DCM Si111 / 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: 0.9184 Å / 相対比: 1
反射解像度: 1.759→48.938 Å / Num. obs: 206460 / % possible obs: 99.9 % / 冗長度: 10.187 % / Biso Wilson estimate: 38.63 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.089 / Χ2: 1.087 / Net I/σ(I): 19.79
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.76-1.8710.1222.4030.9433454533184330520.3922.53299.6
1.87-1.9910.0311.231.8931335131243312380.7021.297100
1.99-2.1510.4480.5894.230357529061290550.9220.62100
2.15-2.369.8510.2938.2726386326786267850.9760.309100
2.36-2.6410.5840.16714.525728424309243090.9930.176100
2.64-3.049.9780.08726.2621416021465214640.9980.092100
3.04-3.7210.6680.04152.8819464618247182450.9990.043100
3.72-5.259.9650.02676.42141512142031420110.027100
5.25-48.9389.8890.02284.55802118129811110.02399.8

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解析

ソフトウェア
名称バージョン分類
XSCALEデータスケーリング
PHENIX1.15.1精密化
PDB_EXTRACT3.25データ抽出
XDSデータ削減
精密化構造決定の手法: 分子置換
開始モデル: 1vlg

1vlg


解像度: 1.759→48.938 Å / SU ML: 0.25 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 24.46
Rfactor反射数%反射
Rfree0.2045 2167 1.05 %
Rwork0.1801 --
obs0.1803 206405 99.9 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 289.7 Å2 / Biso mean: 55.9934 Å2 / Biso min: 25.15 Å2
精密化ステップサイクル: final / 解像度: 1.759→48.938 Å
タンパク質核酸リガンド溶媒全体
原子数10904 0 435 1201 12540
Biso mean--80.58 58.62 -
残基数----1312
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A5968X-RAY DIFFRACTION9.56TORSIONAL
12B5968X-RAY DIFFRACTION9.56TORSIONAL
13C5968X-RAY DIFFRACTION9.56TORSIONAL
14D5968X-RAY DIFFRACTION9.56TORSIONAL
15E5968X-RAY DIFFRACTION9.56TORSIONAL
16F5968X-RAY DIFFRACTION9.56TORSIONAL
17G5968X-RAY DIFFRACTION9.56TORSIONAL
18H5968X-RAY DIFFRACTION9.56TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7592-1.80010.4071420.38391337699
1.8001-1.84510.391440.34413566100
1.8451-1.8950.35391430.311813501100
1.895-1.95080.3231440.304813559100
1.9508-2.01370.24531440.260813516100
2.0137-2.08570.27411430.224213552100
2.0857-2.16920.22961450.202813615100
2.1692-2.26790.20091430.183213540100
2.2679-2.38750.21181450.177313589100
2.3875-2.53710.23011440.180913616100
2.5371-2.7330.23881450.185113623100
2.733-3.0080.18981450.178113654100
3.008-3.44310.19621450.170213715100
3.4431-4.33760.14881460.148213759100
4.3376-48.9380.19631490.16114057100
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)
10.3082-0.42160.00590.3062-0.19610.11070.04070.04740.18350.0185-0.09390.04410.12240.12-00.28950.02850.00780.313-0.00010.355829.445777.1153108.7168
20.2173-0.32770.36790.4448-0.10740.17650.05-0.11340.04830.1145-0.09860.08230.05330.0028-00.3194-0.01020.01730.3357-0.02690.358621.124679.1459113.8611
30.3047-0.14890.33620.0390.11570.58430.0857-0.0189-0.10140.007-0.0599-0.06930.11980.017500.3282-0.0009-0.01130.26640.02080.353627.396369.7587114.3897
40.1758-0.03240.03020.162-0.28540.1930.189-0.38860.14360.2406-0.09290.29140.0732-0.011600.3914-0.10060.07110.4342-0.05520.42453.39268.1291116.5432
50.369-0.61220.20090.3577-0.0410.23040.08910.0551-0.0437-0.0343-0.0838-0.01490.04560.018500.3067-0.008-00.3002-0.00250.329319.633687.933698.6514
60.4815-0.2678-0.12410.1512-0.28760.05430.029-0.11480.27190.0977-0.06480.12410.0419-0.009100.2959-0.0004-0.00120.2815-0.03960.358318.722791.653107.224
70.1837-0.25650.1220.0937-0.06980.1193-0.08660.29890.1117-0.18810.0620.06640.0960.087-00.32030.01380.03890.3251-0.00920.389323.634785.377198.0441
80.3328-0.19170.04760.00670.0214-0.0859-0.01670.04090.0831-0.0546-0.0239-0.0749-0.0364-0.011500.288-0.0134-0.00910.29050.01620.409516.7172100.313897.1409
90.06330.20990.20530.57010.04110.15840.0432-0.32520.47880.4404-0.2976-0.03740.0356-0.1031-0.00880.4074-0.033-0.10310.422-0.16370.659631.7987107.2872114.7087
100.1674-0.0690.14370.22640.4120.25430.0576-0.20560.0344-0.0518-0.0824-0.1430.0010.1086-00.3245-0.0133-0.08340.43540.00140.390453.5172100.4386152.9275
11-0.25160.1442-0.02110.31770.02640.5520.0664-0.10340.0095-0.0444-0.0903-0.0372-0.03150.065-00.3007-0-0.07340.40520.01440.379246.980999.1473151.6838
120.19690.0426-0.18250.0129-0.01670.2213-0.0106-0.0888-0.3390.0548-0.3725-0.24950.35920.1792-0.01310.4109-0.0253-0.09610.4990.10020.458155.965185.0561159.1134
13-0.04740.06640.12030.22720.3980.47640.0368-0.17510.11040.04390.05650.03950.0859-0.11950.00020.3935-0.0537-0.10320.49930.00960.392954.0165104.3937163.5769
14-0.20620.0220.10610.40650.72860.96750.1184-0.07420.21930.3384-0.28030.15740.0125-0.3253-0.01720.3307-0.101-0.03790.4895-0.04670.297544.3631102.4079165.8841
15-0.02170.0336-0.0130.24070.11480.07190.3087-0.07280.3810.5704-0.32150.688-0.0091-0.2498-0.0010.502-0.15930.04880.5644-0.0580.521135.559683.1795167.0567
160.01460.0003-0.0113-0.0005-0.01790.0327-0.026-0.5899-0.08150.13460.1205-0.0558-0.0128-0.02080.00010.47020.0493-0.11690.44550.10440.601948.703367.2111148.4639
170.24560.28410.10680.14710.29940.44350.0006-0.0385-0.0689-0.05940.0605-0.0493-0.06340.1254-00.31130.0176-0.05690.370.03060.383952.264189.9126140.0146
180.30650.19270.08620.17760.20530.1663-0.0108-0.07350.0524-0.06840.11140.17060.0089-0.051300.34970.0062-0.0660.35840.0370.389244.396890.5594141.3412
190.47420.21530.12390.26860.4721-0.0557-0.02260.0238-0.1004-0.16960.0559-0.26170.01960.14100.35280.0013-0.02630.36260.03780.404153.433287.2757133.3524
200.22330.1891-0.12520.0499-0.16-0.0684-0.1027-0.00090.0071-0.18230.15460.10740.0451-0.057-00.3487-0.019-0.08330.29940.0290.334742.832487.3879127.982
210.03490.20620.21070.40910.45810.4134-0.1359-0.0946-0.0743-0.51820.27930.5269-0.1616-0.1580.11820.5485-0.0394-0.2050.36660.13960.581740.2264108.3355126.3054
220.1616-0.15650.03470.3291-0.03280.0475-0.0338-0.00630.11580.0319-0.0166-0.1146-0.0702-0.146100.2784-0.0642-0.03060.3447-0.03070.333639.1435138.27150.8828
230.2008-0.15570.01290.1518-0.25030.1617-0.0735-0.02490.06490.0751-0.0641-0.02940.3044-0.2234-00.343-0.0777-0.00550.3731-0.02350.328333.095131.8923147.6235
240.1411-0.076-0.06860.2088-0.21540.0829-0.0112-0.10910.1740.08770.0167-0.1547-0.06810.2457-00.3506-0.0668-0.02380.3778-0.03550.410339.125142.4746148.491
250.2536-0.19010.07660.242-0.09150.06290.022-0.02340.1346-0.05090.0164-0.1629-0.03570.0955-00.2862-0.0601-0.0220.3492-0.00810.315847.9524131.1909151.5582
260.2477-0.07320.04660.1741-0.14240.1584-0.0544-0.08210.0386-0.0084-0.0329-0.02310.2362-0.080100.3759-0.0408-0.0070.35620.02150.334843.2846123.3912147.8705
270.2179-0.25740.20990.1302-0.08580.13750.16740.2555-0.04780.0741-0.2536-0.10770.2657-0.2109-00.4926-0.10210.03260.3835-0.02870.341135.9982122.5694128.1863
280.5011-0.17010.13670.29-0.02820.0846-0.0602-0.01910.1960.04240.0081-0.0354-0.09080.044100.3494-0.0381-0.02340.3661-0.03650.392526.9108148.0316143.3942
290.2665-0.00020.30350.08210.15420.1379-0.0368-0.00660.04620.009-0.0418-0.03940.1084-0.196800.311-0.0378-0.00670.3699-0.05570.321221.9976140.8126146.6954
300.1390.10190.14480.277-0.08360.0968-0.01870.10320.1994-0.0381-0.0823-0.1338-0.4758-0.064300.355-0.0519-0.04150.3544-0.04710.400730.9799149.0083145.83
310.0831-0.1143-0.02030.05170.05620.0107-0.0609-0.03090.27620.01360.084-0.1029-0.08190.0733-00.4142-0.0021-0.04910.3745-0.09230.42418.1011155.194142.6296
320.1223-0.11430.09080.16940.13260.033-0.1399-0.12050.103-0.0259-0.0046-0.03330.0784-0.1064-00.32040.0119-0.01580.4007-0.07430.354811.6025148.8871146.4063
330.1209-0.15750.0330.1466-0.22870.1904-0.3586-0.2482-0.18140.0102-0.02640.35120.215-0.4893-0.00170.4625-0.04130.06170.7476-0.11040.387212.089141.3183165.9966
340.15710.01330.0075-0.14510.10310.02860.1616-0.0683-0.16670.0898-0.13380.098-0.03710.05450.00880.429-0.0162-0.07060.4454-0.02960.30235.0926116.2472185.4615
350.14190.0603-0.30940.08280.02130.00230.0715-0.1594-0.1298-0.1364-0.07180.1035-0.04890.022900.4592-0.0173-0.0610.4764-0.0380.327426.5426116.7748180.4994
360.72540.0561-0.4647-0.29440.08740.56390.0885-0.08680.1880.0874-0.0158-0.1611-0.08240.0994-00.442-0.04-0.05230.435-0.05310.340235.3162123.8466179.8563
370.11670.0001-0.12130.0547-0.12880.08620.40090.79290.1679-0.1032-0.30950.3155-0.1066-0.21170.00010.55580.1253-0.02080.6487-0.02450.503912.9204132.687178.0451
380.3970.66-0.37170.5375-0.22480.1022-0.1296-0.13180.03140.1652-0.0284-0.05860.23-0.0231-00.49540.0152-0.04360.5254-0.00820.25522.6049108.897195.898
390.32140.2475-0.31130.1773-0.2485-0.05330.0028-0.0545-0.2325-0.2553-0.08950.1086-0.0526-0.1024-00.5252-0.0259-0.01020.4816-0.03080.347420.7416105.4513187.1908
400.33660.1573-0.25640.2892-0.35570.3929-0.3073-0.8205-0.32950.24930.23280.41040.02840.3601-0.00170.5360.0523-0.07180.64590.00170.357927.3293110.178196.2923
410.12060.1791-0.31370.29920.15360.0827-0.0085-0.1198-0.05490.0783-0.1005-0.10010.07410.0003-00.51250.02260.00930.51170.0490.34816.356597.7137197.3319
420.14780.2176-0.02330.26150.10830.029-0.16950.2326-0.3027-0.9752-0.2537-0.00410.6606-0.3581-0.03240.776-0.06290.28830.5047-0.0580.677628.893186.6063179.7697
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 35 )A1 - 35
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 65 )A36 - 65
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 146 )A66 - 146
4X-RAY DIFFRACTION4chain 'A' and (resid 147 through 164 )A147 - 164
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 36 )B1 - 36
6X-RAY DIFFRACTION6chain 'B' and (resid 37 through 65 )B37 - 65
7X-RAY DIFFRACTION7chain 'B' and (resid 66 through 84 )B66 - 84
8X-RAY DIFFRACTION8chain 'B' and (resid 85 through 146 )B85 - 146
9X-RAY DIFFRACTION9chain 'B' and (resid 147 through 164 )B147 - 164
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 35 )C1 - 35
11X-RAY DIFFRACTION11chain 'C' and (resid 36 through 75 )C36 - 75
12X-RAY DIFFRACTION12chain 'C' and (resid 76 through 84 )C76 - 84
13X-RAY DIFFRACTION13chain 'C' and (resid 85 through 115 )C85 - 115
14X-RAY DIFFRACTION14chain 'C' and (resid 116 through 146 )C116 - 146
15X-RAY DIFFRACTION15chain 'C' and (resid 147 through 164 )C147 - 164
16X-RAY DIFFRACTION16chain 'D' and (resid 1 through 5 )D1 - 5
17X-RAY DIFFRACTION17chain 'D' and (resid 6 through 35 )D6 - 35
18X-RAY DIFFRACTION18chain 'D' and (resid 36 through 70 )D36 - 70
19X-RAY DIFFRACTION19chain 'D' and (resid 71 through 115 )D71 - 115
20X-RAY DIFFRACTION20chain 'D' and (resid 116 through 146 )D116 - 146
21X-RAY DIFFRACTION21chain 'D' and (resid 147 through 164 )D147 - 164
22X-RAY DIFFRACTION22chain 'E' and (resid 1 through 36 )E1 - 36
23X-RAY DIFFRACTION23chain 'E' and (resid 37 through 65 )E37 - 65
24X-RAY DIFFRACTION24chain 'E' and (resid 66 through 84 )E66 - 84
25X-RAY DIFFRACTION25chain 'E' and (resid 85 through 115 )E85 - 115
26X-RAY DIFFRACTION26chain 'E' and (resid 116 through 146 )E116 - 146
27X-RAY DIFFRACTION27chain 'E' and (resid 147 through 164 )E147 - 164
28X-RAY DIFFRACTION28chain 'F' and (resid 1 through 36 )F1 - 36
29X-RAY DIFFRACTION29chain 'F' and (resid 37 through 65 )F37 - 65
30X-RAY DIFFRACTION30chain 'F' and (resid 66 through 84 )F66 - 84
31X-RAY DIFFRACTION31chain 'F' and (resid 85 through 115 )F85 - 115
32X-RAY DIFFRACTION32chain 'F' and (resid 116 through 146 )F116 - 146
33X-RAY DIFFRACTION33chain 'F' and (resid 147 through 164 )F147 - 164
34X-RAY DIFFRACTION34chain 'G' and (resid 1 through 35 )G1 - 35
35X-RAY DIFFRACTION35chain 'G' and (resid 36 through 65 )G36 - 65
36X-RAY DIFFRACTION36chain 'G' and (resid 66 through 146 )G66 - 146
37X-RAY DIFFRACTION37chain 'G' and (resid 147 through 164 )G147 - 164
38X-RAY DIFFRACTION38chain 'H' and (resid 1 through 36 )H1 - 36
39X-RAY DIFFRACTION39chain 'H' and (resid 37 through 65 )H37 - 65
40X-RAY DIFFRACTION40chain 'H' and (resid 66 through 84 )H66 - 84
41X-RAY DIFFRACTION41chain 'H' and (resid 85 through 146 )H85 - 146
42X-RAY DIFFRACTION42chain 'H' and (resid 147 through 164 )H147 - 164

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万見について

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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://pdbjlvh1.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