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- PDB-6txj: Crystal structure of thermotoga maritima A42V E65D Ferritin -

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基本情報

登録情報
データベース: PDB / ID: 6txj
タイトルCrystal structure of thermotoga maritima A42V E65D 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: 2.17 Å
データ登録者Wilk, P. / Grudnik, P. / Kumar, M. / Heddle, J. / Chakraborti, S. / Biela, A.P.
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2月9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)160,91162
ポリマ－155,3278
非ポリマー5,58454
水2,630146
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)482,732186
ポリマ－465,98124
非ポリマー16,751162
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 area90210 Å2
ΔGint-602 kcal/mol
Surface area144640 Å2
手法PISA
単位格子
Length a, b, c (Å)176.203, 176.203, 352.794
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 38 or resid 40...
21(chain B and (resid 2 through 38 or resid 40...
31(chain C and (resid 2 through 38 or resid 40...
41(chain D and (resid 2 through 38 or resid 40...
51(chain E and (resid 2 through 38 or resid 40...
61(chain F and (resid 2 through 38 or resid 40...
71(chain G and (resid 2 through 38 or resid 40...
81(chain H and (resid 2 through 38 or resid 40...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 2 through 38 or resid 40...A2 - 38
121(chain A and (resid 2 through 38 or resid 40...A40 - 49
131(chain A and (resid 2 through 38 or resid 40...A51 - 57
141(chain A and (resid 2 through 38 or resid 40...A59 - 68
151(chain A and (resid 2 through 38 or resid 40...A86 - 111
161(chain A and (resid 2 through 38 or resid 40...A2 - 164
171(chain A and (resid 2 through 38 or resid 40...A132 - 134
181(chain A and (resid 2 through 38 or resid 40...A136 - 137
191(chain A and (resid 2 through 38 or resid 40...A139 - 1403
1101(chain A and (resid 2 through 38 or resid 40...A145 - 13
1111(chain A and (resid 2 through 38 or resid 40...A145 - 148
1121(chain A and (resid 2 through 38 or resid 40...A150 - 154
1131(chain A and (resid 2 through 38 or resid 40...A156 - 157
1141(chain A and (resid 2 through 38 or resid 40...A159 - 164
211(chain B and (resid 2 through 38 or resid 40...B2 - 38
221(chain B and (resid 2 through 38 or resid 40...B40 - 49
231(chain B and (resid 2 through 38 or resid 40...B51 - 57
241(chain B and (resid 2 through 38 or resid 40...B59 - 68
251(chain B and (resid 2 through 38 or resid 40...B86 - 111
261(chain B and (resid 2 through 38 or resid 40...B1 - 164
271(chain B and (resid 2 through 38 or resid 40...B132 - 134
281(chain B and (resid 2 through 38 or resid 40...B136 - 137
291(chain B and (resid 2 through 38 or resid 40...B139 - 1403
2101(chain B and (resid 2 through 38 or resid 40...B145 - 13
2111(chain B and (resid 2 through 38 or resid 40...B145 - 148
2121(chain B and (resid 2 through 38 or resid 40...B150 - 154
2131(chain B and (resid 2 through 38 or resid 40...B156 - 157
2141(chain B and (resid 2 through 38 or resid 40...B159 - 164
311(chain C and (resid 2 through 38 or resid 40...C2 - 38
321(chain C and (resid 2 through 38 or resid 40...C40 - 49
331(chain C and (resid 2 through 38 or resid 40...C1 - 164
341(chain C and (resid 2 through 38 or resid 40...C0
351(chain C and (resid 2 through 38 or resid 40...C86 - 3
361(chain C and (resid 2 through 38 or resid 40...C113 - 122
371(chain C and (resid 2 through 38 or resid 40...C12422
381(chain C and (resid 2 through 38 or resid 40...C124 - 130
391(chain C and (resid 2 through 38 or resid 40...C132 - 134
3101(chain C and (resid 2 through 38 or resid 40...C139 - 1403
3111(chain C and (resid 2 through 38 or resid 40...C145 - 1
3121(chain C and (resid 2 through 38 or resid 40...C145 - 13
3131(chain C and (resid 2 through 38 or resid 40...C145 - 148
3141(chain C and (resid 2 through 38 or resid 40...C150 - 154
3151(chain C and (resid 2 through 38 or resid 40...C156 - 157
3161(chain C and (resid 2 through 38 or resid 40...C159 - 164
411(chain D and (resid 2 through 38 or resid 40...D2 - 38
421(chain D and (resid 2 through 38 or resid 40...D40 - 49
431(chain D and (resid 2 through 38 or resid 40...D51 - 57
441(chain D and (resid 2 through 38 or resid 40...D86 - 111
451(chain D and (resid 2 through 38 or resid 40...D113 - 122
461(chain D and (resid 2 through 38 or resid 40...D2 - 164
471(chain D and (resid 2 through 38 or resid 40...D124 - 130
481(chain D and (resid 2 through 38 or resid 40...D132 - 134
491(chain D and (resid 2 through 38 or resid 40...D139 - 1403
4101(chain D and (resid 2 through 38 or resid 40...D145 - 1
4111(chain D and (resid 2 through 38 or resid 40...D145 - 13
4121(chain D and (resid 2 through 38 or resid 40...D145 - 148
4131(chain D and (resid 2 through 38 or resid 40...D150 - 154
4141(chain D and (resid 2 through 38 or resid 40...D156 - 157
4151(chain D and (resid 2 through 38 or resid 40...D159 - 164
511(chain E and (resid 2 through 38 or resid 40...E2 - 38
521(chain E and (resid 2 through 38 or resid 40...E40 - 49
531(chain E and (resid 2 through 38 or resid 40...E51 - 57
541(chain E and (resid 2 through 38 or resid 40...E86 - 111
551(chain E and (resid 2 through 38 or resid 40...E113 - 122
561(chain E and (resid 2 through 38 or resid 40...E1 - 164
571(chain E and (resid 2 through 38 or resid 40...E124 - 130
581(chain E and (resid 2 through 38 or resid 40...E132 - 134
591(chain E and (resid 2 through 38 or resid 40...E139 - 1403
5101(chain E and (resid 2 through 38 or resid 40...E145 - 1
5111(chain E and (resid 2 through 38 or resid 40...E145 - 13
5121(chain E and (resid 2 through 38 or resid 40...E145 - 148
5131(chain E and (resid 2 through 38 or resid 40...E150 - 154
5141(chain E and (resid 2 through 38 or resid 40...E156 - 157
5151(chain E and (resid 2 through 38 or resid 40...E159 - 164
611(chain F and (resid 2 through 38 or resid 40...F2 - 38
621(chain F and (resid 2 through 38 or resid 40...F40 - 49
631(chain F and (resid 2 through 38 or resid 40...F51 - 57
641(chain F and (resid 2 through 38 or resid 40...F86 - 111
651(chain F and (resid 2 through 38 or resid 40...F113 - 122
661(chain F and (resid 2 through 38 or resid 40...F1 - 164
671(chain F and (resid 2 through 38 or resid 40...F124 - 130
681(chain F and (resid 2 through 38 or resid 40...F132 - 134
691(chain F and (resid 2 through 38 or resid 40...F139 - 1403
6101(chain F and (resid 2 through 38 or resid 40...F145 - 1
6111(chain F and (resid 2 through 38 or resid 40...F145 - 13
6121(chain F and (resid 2 through 38 or resid 40...F145 - 148
6131(chain F and (resid 2 through 38 or resid 40...F150 - 154
6141(chain F and (resid 2 through 38 or resid 40...F156 - 157
6151(chain F and (resid 2 through 38 or resid 40...F159 - 164
711(chain G and (resid 2 through 38 or resid 40...G2 - 38
721(chain G and (resid 2 through 38 or resid 40...G40 - 49
731(chain G and (resid 2 through 38 or resid 40...G51 - 57
741(chain G and (resid 2 through 38 or resid 40...G59 - 68
751(chain G and (resid 2 through 38 or resid 40...G86 - 111
761(chain G and (resid 2 through 38 or resid 40...G2 - 164
771(chain G and (resid 2 through 38 or resid 40...G132 - 134
781(chain G and (resid 2 through 38 or resid 40...G136 - 137
791(chain G and (resid 2 through 38 or resid 40...G139 - 1403
7101(chain G and (resid 2 through 38 or resid 40...G145 - 13
7111(chain G and (resid 2 through 38 or resid 40...G145 - 148
7121(chain G and (resid 2 through 38 or resid 40...G150 - 154
7131(chain G and (resid 2 through 38 or resid 40...G156 - 157
7141(chain G and (resid 2 through 38 or resid 40...G159 - 164
811(chain H and (resid 2 through 38 or resid 40...H2 - 38
821(chain H and (resid 2 through 38 or resid 40...H40 - 49
831(chain H and (resid 2 through 38 or resid 40...H51 - 57
841(chain H and (resid 2 through 38 or resid 40...H59 - 68
851(chain H and (resid 2 through 38 or resid 40...H86 - 111
861(chain H and (resid 2 through 38 or resid 40...H1 - 164
871(chain H and (resid 2 through 38 or resid 40...H132 - 134
881(chain H and (resid 2 through 38 or resid 40...H136 - 137
891(chain H and (resid 2 through 38 or resid 40...H139 - 1403
8101(chain H and (resid 2 through 38 or resid 40...H145 - 13
8111(chain H and (resid 2 through 38 or resid 40...H145 - 148
8121(chain H and (resid 2 through 38 or resid 40...H150 - 154
8131(chain H and (resid 2 through 38 or resid 40...H156 - 157
8141(chain H and (resid 2 through 38 or resid 40...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: 19415.867 Da / 分子数: 8 / 変異: A42V, E65D / 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)
株: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / 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, 200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: 35 / 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: 7 / 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: 146 / 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: 63.76 %
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: 2.4 M (NH4)2 SO4, 0.1M MES. pH 6.0 / PH範囲: 6

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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: 14.2 / 波長: 0.9184 Å
検出器タイプ: DECTRIS PILATUS3 S 2M / 検出器: PIXEL / 日付: 2019年4月13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: 2.167→24.863 Å / Num. obs: 111200 / % possible obs: 99.7 % / 冗長度: 10.147 % / Biso Wilson estimate: 63.455 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.129 / Rrim(I) all: 0.136 / Χ2: 1.298 / Net I/σ(I): 12.99
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
2.17-2.310.3064.0470.5318174117855176340.3244.25898.8
2.3-2.4610.0532.5040.8616891416812168020.5392.63999.9
2.46-2.6510.061.4351.5415755415681156610.7121.51299.9
2.65-2.910.7560.7363.2715542614480144500.9150.77399.8
2.9-3.2510.510.3157.7313730613097130640.9790.33199.7
3.25-3.749.3470.12818.6210813111591115680.9950.13599.8
3.74-4.5810.3770.06138.03102517988798790.9990.06599.9
4.58-6.459.7810.04747.8475183769276870.9990.0599.9
6.45-24.8639.340.02864.94416084478445510.02999.5

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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
Rotation7.59 Å48.27 Å
Translation7.59 Å48.27 Å

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解析

ソフトウェア
名称バージョン分類
PHENIX1.15.1-3469精密化
XSCALEデータスケーリング
PHASER2.8.2位相決定
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: 2.17→24.863 Å / SU ML: 0.48 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 36.32 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2462 2097 1.89 %
Rwork0.2098 108863 -
obs0.2105 110960 99.54 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso max: 171.16 Å2 / Biso mean: 85.1996 Å2 / Biso min: 45.38 Å2
精密化ステップサイクル: final / 解像度: 2.17→24.863 Å
タンパク質核酸リガンド溶媒全体
原子数10920 0 305 146 11371
Biso mean--106.55 76.64 -
残基数----1309
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A3216X-RAY DIFFRACTION5.487TORSIONAL
12B3216X-RAY DIFFRACTION5.487TORSIONAL
13C3216X-RAY DIFFRACTION5.487TORSIONAL
14D3216X-RAY DIFFRACTION5.487TORSIONAL
15E3216X-RAY DIFFRACTION5.487TORSIONAL
16F3216X-RAY DIFFRACTION5.487TORSIONAL
17G3216X-RAY DIFFRACTION5.487TORSIONAL
18H3216X-RAY DIFFRACTION5.487TORSIONAL
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 (%)
2.17-2.21690.40391350.3989700597
2.2169-2.27230.40221380.37737183100
2.2723-2.33370.37391400.36147253100
2.3337-2.40230.36041390.34457216100
2.4023-2.47980.33191400.3419722399
2.4798-2.56830.39391390.34327189100
2.5683-2.6710.3781400.32757283100
2.671-2.79240.35351390.31317215100
2.7924-2.93940.31191400.28927281100
2.9394-3.12330.33511390.27917244100
3.1233-3.36390.27471400.24677268100
3.3639-3.70140.24461410.2127295100
3.7014-4.23480.21661400.17877314100
4.2348-5.32670.18371420.15257383100
5.3267-24.8630.20121450.1571751199
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)
10.2814-0.66210.18081.0914-0.00790.52270.04010.10250.06230.0319-0.04780.05490.32930.17020.00030.67370.0750.01860.57990.04980.690827.735976.3867108.0766
20.46821.10260.76510.68250.0811-0.08190.1459-0.1738-0.25570.2145-0.0658-0.08650.26040.08880.00010.73640.0590.01130.69360.00760.738125.170780.3718112.3557
31.21560.09930.43060.3067-0.09640.20.0474-0.1335-0.09930.1524-0.0510.03060.43110.07280.00010.83990.0546-0.00440.58760.06350.684720.891267.5144115.634
40.1168-0.27660.22410.2363-0.64370.98540.14490.02550.06140.0873-0.0934-0.03050.23760.1326-0.00070.59590.0414-0.00610.58660.02030.736919.573987.932798.5071
50.09050.3723-0.13990.8989-0.3608-0.2049-0.0592-0.0535-0.01020.0370.04660.1240.04660.051-0.00050.6030.00270.03450.5698-0.01420.675816.774388.6655104.514
60.01560.0014-0.07790.1003-0.00230.2409-0.2341-0.5390.4581-0.61570.2017-0.06950.83070.8069-0.00060.60460.00430.03240.78620.00510.739134.980691.988199.2388
70.89960.23450.63640.05640.03461.1533-0.1153-0.1457-0.0795-0.2454-0.0051-0.0929-0.10140.0851-00.4514-0.008-0.01680.52440.01870.638616.6908100.469296.9796
80.3894-0.29660.39610.4458-0.05210.6920.0609-0.04730.05870.372-0.05170.2863-0.07920.06460.00350.6134-0.0531-0.04480.79310.0030.855231.6136107.6272114.2206
90.42380.0690.06780.15650.25390.2914-0.1429-0.276-0.2510.1990.084-0.59570.03310.5023-0.00020.71310.0306-0.10261.14540.03770.807353.362799.3613152.9995
10-0.41350.25090.0970.35790.28640.97970.0998-0.08930.07480.0146-0.08350.3646-0.10.32650.00070.61450.0239-0.10541.08390.030.859147.265699.5108151.4032
11-0.18860.21990.05361.9476-0.25020.6296-0.0084-0.19560.10460.17950.04760.1650.00250.38690.00030.70170.0376-0.10741.1404-0.01120.764146.937297.123164.8128
12-0.29750.13950.32460.26330.1383-0.0932-0.0732-0.21790.1301-0.27740.05540.24920.13780.5972-0.00020.67590.1905-0.04461.02840.09440.778751.860188.1011140.1623
13-0.34731.00930.17510.7248-0.40371.38720.1711-0.1889-0.005-0.096-0.16840.05760.29960.2489-0.0010.67290.1282-0.04380.91950.08750.87445.795689.1701142.0274
140.3240.0735-0.36670.0810.2366-0.06-0.0817-0.0276-0.169-0.17840.1843-0.34980.16170.4492-0.00030.73970.1062-0.08231.01610.07180.885452.654886.7476130.9278
150.716-0.7544-0.49860.67260.45790.24840.0263-0.07870.0463-0.18510.27640.68250.19820.14530.00010.66890.0648-0.11730.91670.03390.790742.931787.5074127.5691
160.2992-0.05250.17690.89540.71910.57710.04150.3197-0.11450.08480.43360.0512-0.1309-0.78220.00430.6891-0.0781-0.10530.88170.08170.855740.727108.1903125.2137
17-0.1648-0.26830.14850.2741-0.62360.4073-0.05980.07140.05320.1215-0.1143-0.0739-0.42140.512-0.00070.7934-0.2402-0.07370.9306-0.04610.778639.5328138.1895150.5221
18-0.66190.06070.2089-0.46480.07140.2751-0.01-0.00620.13290.08360.23140.00070.08980.1288-0.00180.8132-0.2278-0.09270.9209-0.00390.756333.6464131.6872148.4237
190.0821-0.1320.04990.0439-0.01550.07630.2947-0.6525-0.041-0.21320.6132-0.34111.30162.04010.00130.9343-0.3019-0.09661.1637-0.19780.894236.8734144.8628157.0997
200.7255-0.5941-0.2220.0684-0.06350.06180.0274-0.0860.2136-0.0839-0.0578-0.1439-0.07270.41020.00040.6991-0.2609-0.08120.9245-0.03780.745347.3137133.0066147.7868
210.55820.3340.42120.3309-0.15310.5752-0.0336-0.1045-0.0920.15-0.122-0.0997-0.1325-0.14-0.00530.7471-0.1813-0.08590.95820.02810.77143.7423123.3557147.6312
220.3872-0.28230.26380.4817-0.1210.2376-0.38810.9803-0.5734-0.0062-0.0328-0.27350.5678-0.9329-0.00010.7627-0.24580.00650.895-0.04660.716336.6649122.2847128.0097
230.0290.0612-0.030.67480.13560.06920.3540.3386-0.8046-0.23010.08071.1911-1.0863-0.0512-0.00071.0519-0.2381-0.23980.8098-0.06330.913827.3023148.1605120.9314
241.1162-0.42140.3313-0.3884-0.22920.3262-0.0388-0.00380.17290.1669-0.0147-0.1207-0.42290.26770.00010.9289-0.2559-0.0780.7172-0.1050.796124.2279148.2464145.2329
25-0.1917-0.40850.18210.2071-0.27650.2904-0.19960.10070.12520.08760.0381-0.02930.0776-0.3933-0.00020.9916-0.1066-0.06350.7953-0.08260.808512.0935149.3087146.2484
260.78530.33970.17540.4348-0.32850.8833-0.33710.0310.2320.3709-0.11220.9366-0.30420.0241-0.0661.21-0.0851-0.0131.0241-0.140.883412.1181141.8648165.5296
270.05220.1454-0.4820.5370.2830.14650.1378-0.1304-0.0109-0.1138-0.08140.1162-0.24020.34340.00030.9145-0.0969-0.12381.055-0.03230.654630.8534116.8686182.9235
28-0.20390.11890.34190.5814-1.04331.24280.1231-0.11690.08440.2438-0.1881-0.0579-0.20770.46-0.00010.8043-0.1114-0.16981.018-0.10840.673337.5339121.4796183.8671
290.3404-0.1330.28510.18110.70.39960.2235-0.6537-0.0819-0.45570.14960.138-0.20960.52010.00330.9017-0.1263-0.02121.0568-0.04690.735932.624126.6177173.452
300.79920.1834-0.18990.2038-0.2080.19590.29250.15870.1436-0.6492-0.0655-0.6062-0.32690.19380.00610.9385-0.0283-0.06850.9102-0.06770.738913.4776133.1102177.5655
310.39150.582-0.30120.5302-0.39510.3999-0.0647-0.51090.06140.29410.1319-0.11230.16630.4166-0.00010.93580.0422-0.10381.0964-0.01520.594422.6977108.8113195.5355
320.20790.2305-0.32070.3812-0.42370.82530.2310.2815-0.3739-0.1942-0.4280.3301-0.1843-0.1661-0.00130.76810.0462-0.1010.934-0.05180.601120.4879105.5268187.0574
33-0.05370.19740.31210.9612-0.41740.6318-0.0803-0.2208-0.03960.1319-0.002-0.08560.07850.14340.00050.91960.0343-0.0751.00880.0250.668820.539997.8881193.7933
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 36 )A2 - 36
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 76 )A37 - 76
3X-RAY DIFFRACTION3chain 'A' and (resid 77 through 164 )A77 - 164
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 36 )B1 - 36
5X-RAY DIFFRACTION5chain 'B' and (resid 37 through 75 )B37 - 75
6X-RAY DIFFRACTION6chain 'B' and (resid 76 through 84 )B76 - 84
7X-RAY DIFFRACTION7chain 'B' and (resid 85 through 146 )B85 - 146
8X-RAY DIFFRACTION8chain 'B' and (resid 147 through 164 )B147 - 164
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 36 )C1 - 36
10X-RAY DIFFRACTION10chain 'C' and (resid 37 through 76 )C37 - 76
11X-RAY DIFFRACTION11chain 'C' and (resid 77 through 164 )C77 - 164
12X-RAY DIFFRACTION12chain 'D' and (resid 2 through 36 )D2 - 36
13X-RAY DIFFRACTION13chain 'D' and (resid 37 through 76 )D37 - 76
14X-RAY DIFFRACTION14chain 'D' and (resid 77 through 115 )D77 - 115
15X-RAY DIFFRACTION15chain 'D' and (resid 116 through 146 )D116 - 146
16X-RAY DIFFRACTION16chain 'D' and (resid 147 through 164 )D147 - 164
17X-RAY DIFFRACTION17chain 'E' and (resid 1 through 36 )E1 - 36
18X-RAY DIFFRACTION18chain 'E' and (resid 37 through 66 )E37 - 66
19X-RAY DIFFRACTION19chain 'E' and (resid 67 through 76 )E67 - 76
20X-RAY DIFFRACTION20chain 'E' and (resid 77 through 115 )E77 - 115
21X-RAY DIFFRACTION21chain 'E' and (resid 116 through 146 )E116 - 146
22X-RAY DIFFRACTION22chain 'E' and (resid 147 through 164 )E147 - 164
23X-RAY DIFFRACTION23chain 'F' and (resid 1 through 5 )F1 - 5
24X-RAY DIFFRACTION24chain 'F' and (resid 6 through 115 )F6 - 115
25X-RAY DIFFRACTION25chain 'F' and (resid 116 through 146 )F116 - 146
26X-RAY DIFFRACTION26chain 'F' and (resid 147 through 164 )F147 - 164
27X-RAY DIFFRACTION27chain 'G' and (resid 2 through 65 )G2 - 65
28X-RAY DIFFRACTION28chain 'G' and (resid 66 through 115 )G66 - 115
29X-RAY DIFFRACTION29chain 'G' and (resid 116 through 146 )G116 - 146
30X-RAY DIFFRACTION30chain 'G' and (resid 147 through 164 )G147 - 164
31X-RAY DIFFRACTION31chain 'H' and (resid 1 through 36 )H1 - 36
32X-RAY DIFFRACTION32chain 'H' and (resid 37 through 65 )H37 - 65
33X-RAY DIFFRACTION33chain 'H' and (resid 66 through 164 )H66 - 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