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- PDB-6txk: Crystal structure of thermotoga maritima E65K Ferritin -

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基本情報

登録情報
データベース: PDB / ID: 6txk
タイトルCrystal structure of thermotoga maritima E65K 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 (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: 2.359 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)160,97164
ポリマ－155,2158
非ポリマー5,75656
水7,963442
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)482,914192
ポリマ－465,64624
非ポリマー17,268168
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 area93910 Å2
ΔGint-597 kcal/mol
Surface area147320 Å2
手法PISA
単位格子
Length a, b, c (Å)175.811, 175.811, 354.136
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 2 through 6 or resid 8...
21(chain B and (resid 2 through 6 or resid 8...
31(chain C and (resid 2 through 6 or resid 8...
41(chain D and (resid 2 through 6 or resid 8...
51(chain E and (resid 2 through 6 or resid 8...
61(chain F and (resid 2 through 6 or resid 8...
71(chain G and (resid 2 through 6 or resid 8...
81(chain H and (resid 2 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 2 through 6 or resid 8...A2 - 6
121(chain A and (resid 2 through 6 or resid 8...A8 - 9
131(chain A and (resid 2 through 6 or resid 8...A11 - 17
141(chain A and (resid 2 through 6 or resid 8...A19 - 49
151(chain A and (resid 2 through 6 or resid 8...A0
161(chain A and (resid 2 through 6 or resid 8...A59 - 60
171(chain A and (resid 2 through 6 or resid 8...A1 - 203
181(chain A and (resid 2 through 6 or resid 8...A70 - 75
191(chain A and (resid 2 through 6 or resid 8...A77 - 80
1101(chain A and (resid 2 through 6 or resid 8...A1 - 203
1111(chain A and (resid 2 through 6 or resid 8...A81 - 111
1121(chain A and (resid 2 through 6 or resid 8...A0
1131(chain A and (resid 2 through 6 or resid 8...A1 - 203
1141(chain A and (resid 2 through 6 or resid 8...A1 - 203
1151(chain A and (resid 2 through 6 or resid 8...A156 - 157
1161(chain A and (resid 2 through 6 or resid 8...A159 - 164
211(chain B and (resid 2 through 6 or resid 8...B2 - 6
221(chain B and (resid 2 through 6 or resid 8...B8 - 9
231(chain B and (resid 2 through 6 or resid 8...B11 - 17
241(chain B and (resid 2 through 6 or resid 8...B19 - 49
251(chain B and (resid 2 through 6 or resid 8...B59 - 60
261(chain B and (resid 2 through 6 or resid 8...B2 - 68
271(chain B and (resid 2 through 6 or resid 8...B70 - 75
281(chain B and (resid 2 through 6 or resid 8...B77 - 80
291(chain B and (resid 2 through 6 or resid 8...B82
2101(chain B and (resid 2 through 6 or resid 8...B1 - 205
2111(chain B and (resid 2 through 6 or resid 8...B1 - 205
2121(chain B and (resid 2 through 6 or resid 8...B1 - 205
2131(chain B and (resid 2 through 6 or resid 8...B1 - 205
2141(chain B and (resid 2 through 6 or resid 8...B136 - 154
2151(chain B and (resid 2 through 6 or resid 8...B156 - 157
2161(chain B and (resid 2 through 6 or resid 8...B159 - 164
311(chain C and (resid 2 through 6 or resid 8...C2 - 6
321(chain C and (resid 2 through 6 or resid 8...C8 - 9
331(chain C and (resid 2 through 6 or resid 8...C11 - 17
341(chain C and (resid 2 through 6 or resid 8...C19 - 49
351(chain C and (resid 2 through 6 or resid 8...C59 - 60
361(chain C and (resid 2 through 6 or resid 8...C2 - 68
371(chain C and (resid 2 through 6 or resid 8...C70 - 75
381(chain C and (resid 2 through 6 or resid 8...C77 - 80
391(chain C and (resid 2 through 6 or resid 8...C82
3101(chain C and (resid 2 through 6 or resid 8...C1 - 200
3111(chain C and (resid 2 through 6 or resid 8...C1 - 200
3121(chain C and (resid 2 through 6 or resid 8...C1 - 200
3131(chain C and (resid 2 through 6 or resid 8...C1 - 200
3141(chain C and (resid 2 through 6 or resid 8...C136 - 154
3151(chain C and (resid 2 through 6 or resid 8...C156 - 157
3161(chain C and (resid 2 through 6 or resid 8...C159 - 164
411(chain D and (resid 2 through 6 or resid 8...D2 - 6
421(chain D and (resid 2 through 6 or resid 8...D8 - 9
431(chain D and (resid 2 through 6 or resid 8...D0
441(chain D and (resid 2 through 6 or resid 8...D52
451(chain D and (resid 2 through 6 or resid 8...D52 - 68
461(chain D and (resid 2 through 6 or resid 8...D70 - 75
471(chain D and (resid 2 through 6 or resid 8...D70 - 75
481(chain D and (resid 2 through 6 or resid 8...D77 - 80
491(chain D and (resid 2 through 6 or resid 8...D1 - 201
4101(chain D and (resid 2 through 6 or resid 8...D1 - 201
4111(chain D and (resid 2 through 6 or resid 8...D1 - 201
4121(chain D and (resid 2 through 6 or resid 8...D1 - 201
4131(chain D and (resid 2 through 6 or resid 8...D136 - 154
4141(chain D and (resid 2 through 6 or resid 8...D156 - 157
4151(chain D and (resid 2 through 6 or resid 8...D159 - 164
511(chain E and (resid 2 through 6 or resid 8...E2 - 6
521(chain E and (resid 2 through 6 or resid 8...E8 - 9
531(chain E and (resid 2 through 6 or resid 8...E0
541(chain E and (resid 2 through 6 or resid 8...E52
551(chain E and (resid 2 through 6 or resid 8...E59 - 6068
561(chain E and (resid 2 through 6 or resid 8...E84
571(chain E and (resid 2 through 6 or resid 8...E82
581(chain E and (resid 2 through 6 or resid 8...E0
591(chain E and (resid 2 through 6 or resid 8...E113 - 122
5101(chain E and (resid 2 through 6 or resid 8...E1 - 202
5111(chain E and (resid 2 through 6 or resid 8...E132 - 134
5121(chain E and (resid 2 through 6 or resid 8...E156 - 157
5131(chain E and (resid 2 through 6 or resid 8...E159 - 164
611(chain F and (resid 2 through 6 or resid 8...F2 - 6
621(chain F and (resid 2 through 6 or resid 8...F8 - 9
631(chain F and (resid 2 through 6 or resid 8...F0
641(chain F and (resid 2 through 6 or resid 8...F52
651(chain F and (resid 2 through 6 or resid 8...F52 - 68
661(chain F and (resid 2 through 6 or resid 8...F70 - 75
671(chain F and (resid 2 through 6 or resid 8...F70 - 75
681(chain F and (resid 2 through 6 or resid 8...F77 - 80
691(chain F and (resid 2 through 6 or resid 8...F1 - 201
6101(chain F and (resid 2 through 6 or resid 8...F1 - 201
6111(chain F and (resid 2 through 6 or resid 8...F1 - 201
6121(chain F and (resid 2 through 6 or resid 8...F1 - 201
6131(chain F and (resid 2 through 6 or resid 8...F136 - 154
6141(chain F and (resid 2 through 6 or resid 8...F156 - 157
6151(chain F and (resid 2 through 6 or resid 8...F159 - 164
711(chain G and (resid 2 through 6 or resid 8...G2 - 6
721(chain G and (resid 2 through 6 or resid 8...G8 - 9
731(chain G and (resid 2 through 6 or resid 8...G11 - 17
741(chain G and (resid 2 through 6 or resid 8...G19 - 49
751(chain G and (resid 2 through 6 or resid 8...G0
761(chain G and (resid 2 through 6 or resid 8...G59 - 60
771(chain G and (resid 2 through 6 or resid 8...G1 - 200
781(chain G and (resid 2 through 6 or resid 8...G70 - 75
791(chain G and (resid 2 through 6 or resid 8...G77 - 80
7101(chain G and (resid 2 through 6 or resid 8...G1 - 200
7111(chain G and (resid 2 through 6 or resid 8...G81 - 111
7121(chain G and (resid 2 through 6 or resid 8...G0
7131(chain G and (resid 2 through 6 or resid 8...G1 - 200
7141(chain G and (resid 2 through 6 or resid 8...G1 - 200
7151(chain G and (resid 2 through 6 or resid 8...G156 - 157
7161(chain G and (resid 2 through 6 or resid 8...G159 - 164
811(chain H and (resid 2 through 6 or resid 8...H2 - 6
821(chain H and (resid 2 through 6 or resid 8...H8 - 9
831(chain H and (resid 2 through 6 or resid 8...H11 - 17
841(chain H and (resid 2 through 6 or resid 8...H19 - 49
851(chain H and (resid 2 through 6 or resid 8...H0
861(chain H and (resid 2 through 6 or resid 8...H59 - 60
871(chain H and (resid 2 through 6 or resid 8...H1 - 201
881(chain H and (resid 2 through 6 or resid 8...H70 - 75
891(chain H and (resid 2 through 6 or resid 8...H77 - 80
8101(chain H and (resid 2 through 6 or resid 8...H1 - 201
8111(chain H and (resid 2 through 6 or resid 8...H81 - 111
8121(chain H and (resid 2 through 6 or resid 8...H0
8131(chain H and (resid 2 through 6 or resid 8...H1 - 201
8141(chain H and (resid 2 through 6 or resid 8...H1 - 201
8151(chain H and (resid 2 through 6 or resid 8...H156 - 157
8161(chain H and (resid 2 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: 19401.906 Da / 分子数: 8 / 変異: E65K / 由来タイプ: 組換発現
由来: (組換発現) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (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, 498分子

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


分子量: 96.063 Da / 分子数: 32 / 由来タイプ: 合成 / 式: SO4
#4: 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: 12 / 由来タイプ: 合成 / 式: C3H8O3
#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: 442 / 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: 14.3 / 波長: 0.895 Å
検出器タイプ: RAYONIX MX-225 / 検出器: CCD / 日付: 2019年5月18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: 0.895 Å / 相対比: 1
反射解像度: 2.359→20.44 Å / Num. obs: 86438 / % possible obs: 99.8 % / 冗長度: 7.516 % / Biso Wilson estimate: 40.582 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.23 / Rrim(I) all: 0.248 / Χ2: 1.049 / Net I/σ(I): 8.72
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
2.36-2.57.6481.5311.3310561413863138090.4641.64599.6
2.5-2.677.6831.061.9510013913034130330.6651.138100
2.67-2.897.6670.6753.159321912160121590.8290.725100
2.89-3.167.6360.4075.258552711202112000.9330.438100
3.16-3.537.5150.2069.787644710176101730.9810.222100
3.53-4.087.4930.12415.3567501901290090.9920.133100
4.08-4.987.4090.0822.256686765376510.9960.086100
4.98-7.017.2730.09618.343568599559900.9950.10499.9
7.01-20.446.1450.0528.0420980350234140.9980.05597.5

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位相決定

位相決定手法: 分子置換
Phasing MR
最高解像度最低解像度
Rotation7.82 Å48.25 Å
Translation7.82 Å48.25 Å

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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
PHASER2.8.3位相決定
PHENIX1.15.1_3469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: 2.359→20.44 Å / SU ML: 0.31 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 25.61
Rfactor反射数%反射
Rfree0.2365 2092 2.43 %
Rwork0.2011 --
obs0.2019 86126 99.65 %
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: 144.23 Å2 / Biso mean: 51.2991 Å2 / Biso min: 28.16 Å2
精密化ステップサイクル: final / 解像度: 2.359→20.44 Å
タンパク質核酸リガンド溶媒全体
原子数10936 0 320 442 11698
Biso mean--75.88 54.02 -
残基数----1312
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A3088X-RAY DIFFRACTION4.943TORSIONAL
12B3088X-RAY DIFFRACTION4.943TORSIONAL
13C3088X-RAY DIFFRACTION4.943TORSIONAL
14D3088X-RAY DIFFRACTION4.943TORSIONAL
15E3088X-RAY DIFFRACTION4.943TORSIONAL
16F3088X-RAY DIFFRACTION4.943TORSIONAL
17G3088X-RAY DIFFRACTION4.943TORSIONAL
18H3088X-RAY DIFFRACTION4.943TORSIONAL
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 (%)
2.359-2.41370.33271360.2993549199
2.4137-2.4740.36681390.3045608100
2.474-2.54080.32191380.28795539100
2.5408-2.61540.35071390.2825580100
2.6154-2.69960.29621400.26755583100
2.6996-2.79590.31231390.26365604100
2.7959-2.90750.28531390.23735566100
2.9075-3.03940.24941390.22435601100
3.0394-3.19910.25251400.22695603100
3.1991-3.39870.23481390.20245601100
3.3987-3.65970.23541400.17815626100
3.6597-4.02550.2041400.17355635100
4.0255-4.60220.17091410.14735664100
4.6022-5.77650.20061420.17395691100
5.7765-20.440.21571410.1809564296
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)
19.0432-5.9397-1.3479.25375.27573.8169-0.2649-0.0920.4052-0.36740.5126-1.1553-0.72130.3247-0.2920.37720.0883-0.08570.58340.02230.6148.024784.6062115.9064
20.870.38010.67670.41130.12350.80840.0915-0.1208-0.02380.1166-0.08870.01980.0971-0.0442-0.01120.3890.01530.02430.3153-0.02490.406823.320472.7795113.5054
31.4385-0.81260.62070.6381-0.30011.2946-0.04170.04190.1445-0.033-0.0180.0189-0.00190.05780.05640.33340.00250.03370.2998-0.01540.413919.340191.0399.5859
45.84774.13692.41054.15812.24411.7535-0.0037-0.3201-0.13970.0582-0.0074-0.241-0.0227-0.04570.07420.35090.0347-0.03190.36080.03150.410616.2474103.1533101.5379
54.72623.4280.84314.9257-0.21881.70660.6867-1.10450.77150.9053-0.77640.0239-0.13-0.06480.030.5614-0.0272-0.12550.6325-0.19260.907331.774107.1224115.0263
64.1248-3.18994.01368.88610.37735.7763-0.13270.0891.2832-0.1018-0.4618-0.9125-0.20890.5090.55930.588-0.1824-0.05510.5478-0.09660.676856.4335120.4302146.2028
70.4631.1121-0.29765.2472-0.49950.36210.2331-0.283-0.2290.3322-0.2736-0.30810.01840.17980.01760.33070.0178-0.0950.48330.00770.402952.974896.621154.5535
80.14791.5416-0.84555.8813-2.35881.7172-0.0006-0.03850.196-0.16680.26650.7672-0.0076-0.134-0.30820.34010.0101-0.07420.47170.01730.45244.099497.9457153.6045
90.54360.2217-0.41522.40710.28231.07920.0509-0.1049-0.02490.3982-0.12940.03840.0925-0.05690.07670.3726-0.0195-0.08730.4824-0.01050.427247.814298.1193163.1133
102.0395-1.6673-2.15362.20931.82832.2928-0.67020.0115-0.5830.4279-0.5782-0.43150.5840.36731.21090.59960.1013-0.10760.52620.01610.793448.647366.9476148.3783
110.87481.2170.16344.20130.10121.14770.10360.0093-0.0878-0.2384-0.1669-0.3213-0.04740.276-0.06250.28930.0061-0.02380.4085-0.00380.351152.314490.6965140.0028
120.47630.6750.28645.3061-2.59581.7994-0.0175-0.07380.0376-0.24130.22310.28830.0924-0.1758-0.27140.34150.0125-0.01670.42440.01950.450443.902189.6331141.9233
130.68260.59490.04372.1490.29460.85650.0326-0.0204-0.0784-0.2511-0.0505-0.08890.02530.09890.04270.3322-0.0008-0.0110.3990.00650.44148.910787.3232131.2828
142.89340.07730.31964.6021-1.95465.5817-0.2590.32220.3644-0.80130.79561.3896-0.0802-0.9031-0.40020.6895-0.0784-0.240.43720.13690.708940.1922108.5137126.6756
153.09752.35931.80954.2071-2.07756.03240.5079-0.8150.17631.1490.16850.4769-0.144-0.4789-0.46440.6341-0.0997-0.04230.63080.03710.519438.7403138.4228173.4337
160.5239-0.32-0.12850.3362-0.33571.7775-0.02220.00160.06870.0187-0.0062-0.03080.208-0.03990.05280.3755-0.08670.00860.3675-0.00260.440340.0791131.6237146.7638
171.1012-0.18120.72960.4681-1.36484.92020.0073-0.02540.17990.20580.1588-0.06-0.4537-0.29940.01020.4047-0.0387-0.01160.3686-0.04420.511626.952148.1573143.6112
180.6745-0.0367-1.2074-0.0939-0.22736.9382-0.04050.03050.04810.0478-0.06070.02330.0583-0.62630.10050.3793-0.09010.0110.4344-0.06390.472521.9429140.7518146.667
190.6014-0.00850.30970.2039-0.40490.9716-0.0273-0.0770.17350.1130.0663-0.1263-0.1997-0.0584-0.05310.3982-0.0285-0.01830.3566-0.06740.49918.35151.3451145.0884
202.7137-1.6401-1.87963.72391.94115.3034-0.0957-0.41650.10820.8034-0.04640.26930.5735-0.81820.14410.5754-0.06990.04690.8299-0.03410.49412.3397141.3451166.3383
219.69453.71161.72712.83221.94942.1957-0.2799-0.2547-1.25090.03310.4261-0.56670.7914-0.0123-0.13330.52270.0156-0.01150.6710.06510.611150.6599103.6357178.1784
221.506-0.4142-1.20040.32640.13130.99810.0904-0.1510.12660.0976-0.055-0.1104-0.12710.1165-0.06840.4969-0.0345-0.08940.4847-0.06080.383932.9968119.5014183.9536
232.8319-0.6361-1.42040.93760.92931.40430.19080.23450.3172-0.1428-0.12030.0208-0.2788-0.2177-0.04020.59750.0026-0.03970.5250.01620.401725.4176128.5831175.3975
244.5009-1.46082.03853.3866-2.72552.672-0.3658-0.35420.62010.4718-0.17790.4609-0.9889-0.46950.40080.68170.0096-0.01550.8141-0.07050.63616.2651121.832203.2856
252.5169-0.6578-1.00321.33270.39290.6064-0.1794-0.0594-0.2370.1586-0.00450.06090.11070.01180.14380.4734-0.0287-0.04920.47750.01090.299122.109108.2706192.2588
262.4938-0.5344-0.91341.7694-0.00861.5577-0.1817-0.2708-0.31460.1417-0.1061-0.04550.26090.20590.20970.521-0.0072-0.05880.58320.0730.392821.792100.4354200.2586
272.4733-2.7424-1.56823.96251.72851.07940.19330.2693-0.3993-0.7025-0.32070.2627-0.0061-0.06420.09870.5391-0.0210.01590.55720.05030.406415.118995.2578193.6983
282.0614-0.5391-1.22435.20530.40214.5126-0.16310.1675-0.5276-0.6541-0.4049-0.27310.71390.18410.53620.9137-0.08930.15760.6497-0.09660.816428.661686.3929180.1239
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 5 )A1 - 5
2X-RAY DIFFRACTION2chain 'A' and (resid 6 through 164 )A6 - 164
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 115 )B1 - 115
4X-RAY DIFFRACTION4chain 'B' and (resid 116 through 146 )B116 - 146
5X-RAY DIFFRACTION5chain 'B' and (resid 147 through 164 )B147 - 164
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 5 )C1 - 5
7X-RAY DIFFRACTION7chain 'C' and (resid 6 through 36 )C6 - 36
8X-RAY DIFFRACTION8chain 'C' and (resid 37 through 65 )C37 - 65
9X-RAY DIFFRACTION9chain 'C' and (resid 66 through 164 )C66 - 164
10X-RAY DIFFRACTION10chain 'D' and (resid 1 through 5 )D1 - 5
11X-RAY DIFFRACTION11chain 'D' and (resid 6 through 36 )D6 - 36
12X-RAY DIFFRACTION12chain 'D' and (resid 37 through 70 )D37 - 70
13X-RAY DIFFRACTION13chain 'D' and (resid 71 through 146 )D71 - 146
14X-RAY DIFFRACTION14chain 'D' and (resid 147 through 164 )D147 - 164
15X-RAY DIFFRACTION15chain 'E' and (resid 1 through 5 )E1 - 5
16X-RAY DIFFRACTION16chain 'E' and (resid 6 through 164 )E6 - 164
17X-RAY DIFFRACTION17chain 'F' and (resid 1 through 36 )F1 - 36
18X-RAY DIFFRACTION18chain 'F' and (resid 37 through 65 )F37 - 65
19X-RAY DIFFRACTION19chain 'F' and (resid 66 through 146 )F66 - 146
20X-RAY DIFFRACTION20chain 'F' and (resid 147 through 164 )F147 - 164
21X-RAY DIFFRACTION21chain 'G' and (resid 1 through 5 )G1 - 5
22X-RAY DIFFRACTION22chain 'G' and (resid 6 through 115 )G6 - 115
23X-RAY DIFFRACTION23chain 'G' and (resid 116 through 164 )G116 - 164
24X-RAY DIFFRACTION24chain 'H' and (resid 1 through 5 )H1 - 5
25X-RAY DIFFRACTION25chain 'H' and (resid 6 through 75 )H6 - 75
26X-RAY DIFFRACTION26chain 'H' and (resid 76 through 115 )H76 - 115
27X-RAY DIFFRACTION27chain 'H' and (resid 116 through 146 )H116 - 146
28X-RAY DIFFRACTION28chain '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://pdbjlc1.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