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- PDB-6txl: Crystal structure of thermotoga maritima E65Q Ferritin -

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基本情報

登録情報
データベース: PDB / ID: 6txl
タイトルCrystal structure of thermotoga maritima E65Q 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 / ferroxidase activity / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / cytosol / cytoplasm
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: 2.099 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)160,75962
ポリマ－155,2078
非ポリマー5,55254
水8,485471
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)482,277186
ポリマ－465,62124
非ポリマー16,656162
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 area96770 Å2
ΔGint-594 kcal/mol
Surface area146990 Å2
手法PISA
単位格子
Length a, b, c (Å)176.219, 176.219, 355.045
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...A0
141(chain A and (resid 2 through 6 or resid 8...A1 - 203
151(chain A and (resid 2 through 6 or resid 8...A59 - 65
161(chain A and (resid 2 through 6 or resid 8...A678
171(chain A and (resid 2 through 6 or resid 8...A7
181(chain A and (resid 2 through 6 or resid 8...A1 - 203
191(chain A and (resid 2 through 6 or resid 8...A79
1101(chain A and (resid 2 through 6 or resid 8...A1 - 203
1111(chain A and (resid 2 through 6 or resid 8...A124 - 130
1121(chain A and (resid 2 through 6 or resid 8...A1 - 203
1131(chain A and (resid 2 through 6 or resid 8...A135
1141(chain A and (resid 2 through 6 or resid 8...A159 - 157
1151(chain A and (resid 2 through 6 or resid 8...A159 - 161
1161(chain A and (resid 2 through 6 or resid 8...A163 - 200
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...B0
241(chain B and (resid 2 through 6 or resid 8...B1 - 205
251(chain B and (resid 2 through 6 or resid 8...B59 - 65
261(chain B and (resid 2 through 6 or resid 8...B678
271(chain B and (resid 2 through 6 or resid 8...B7
281(chain B and (resid 2 through 6 or resid 8...B1 - 205
291(chain B and (resid 2 through 6 or resid 8...B79
2101(chain B and (resid 2 through 6 or resid 8...B1 - 205
2111(chain B and (resid 2 through 6 or resid 8...B124 - 130
2121(chain B and (resid 2 through 6 or resid 8...B1 - 205
2131(chain B and (resid 2 through 6 or resid 8...B135
2141(chain B and (resid 2 through 6 or resid 8...B159 - 157
2151(chain B and (resid 2 through 6 or resid 8...B159 - 161
2161(chain B and (resid 2 through 6 or resid 8...B163 - 200
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...C0
351(chain C and (resid 2 through 6 or resid 8...C59 - 65
361(chain C and (resid 2 through 6 or resid 8...C1 - 200
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 - 79
391(chain C and (resid 2 through 6 or resid 8...C1 - 200
3101(chain C and (resid 2 through 6 or resid 8...C1 - 200
3111(chain C and (resid 2 through 6 or resid 8...C132 - 134
3121(chain C and (resid 2 through 6 or resid 8...C159 - 167
3131(chain C and (resid 2 through 6 or resid 8...C159 - 161
3141(chain C and (resid 2 through 6 or resid 8...C163 - 200
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...D1 - 201
451(chain D and (resid 2 through 6 or resid 8...D59 - 65
461(chain D and (resid 2 through 6 or resid 8...D678
471(chain D and (resid 2 through 6 or resid 8...D7
481(chain D and (resid 2 through 6 or resid 8...D1 - 201
491(chain D and (resid 2 through 6 or resid 8...D79
4101(chain D and (resid 2 through 6 or resid 8...D1 - 201
4111(chain D and (resid 2 through 6 or resid 8...D124 - 130
4121(chain D and (resid 2 through 6 or resid 8...D1 - 201
4131(chain D and (resid 2 through 6 or resid 8...D135
4141(chain D and (resid 2 through 6 or resid 8...D159 - 157
4151(chain D and (resid 2 through 6 or resid 8...D159 - 161
4161(chain D and (resid 2 through 6 or resid 8...D163 - 200
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...E11 - 17
541(chain E and (resid 2 through 6 or resid 8...E19 - 49
551(chain E and (resid 2 through 6 or resid 8...E59 - 65
561(chain E and (resid 2 through 6 or resid 8...E7 - 68
571(chain E and (resid 2 through 6 or resid 8...E70 - 75
581(chain E and (resid 2 through 6 or resid 8...E77 - 79
591(chain E and (resid 2 through 6 or resid 8...E82 - 110
5101(chain E and (resid 2 through 6 or resid 8...E132 - 134
5111(chain E and (resid 2 through 6 or resid 8...E136 - 154
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 - 161
5141(chain E and (resid 2 through 6 or resid 8...E163 - 200
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...F11 - 17
641(chain F and (resid 2 through 6 or resid 8...F19 - 49
651(chain F and (resid 2 through 6 or resid 8...F52 - 57
661(chain F and (resid 2 through 6 or resid 8...F59 - 65
671(chain F and (resid 2 through 6 or resid 8...F67 - 68
681(chain F and (resid 2 through 6 or resid 8...F70 - 75
691(chain F and (resid 2 through 6 or resid 8...F77 - 79
6101(chain F and (resid 2 through 6 or resid 8...F82 - 110
6111(chain F and (resid 2 through 6 or resid 8...F113 - 122
6121(chain F and (resid 2 through 6 or resid 8...F124 - 130
6131(chain F and (resid 2 through 6 or resid 8...F132 - 134
6141(chain F and (resid 2 through 6 or resid 8...F136 - 154
6151(chain F and (resid 2 through 6 or resid 8...F156 - 157
6161(chain F and (resid 2 through 6 or resid 8...F159 - 161
6171(chain F and (resid 2 through 6 or resid 8...F163 - 200
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...G0
751(chain G and (resid 2 through 6 or resid 8...G59 - 65
761(chain G and (resid 2 through 6 or resid 8...G1 - 201
771(chain G and (resid 2 through 6 or resid 8...G70 - 75
781(chain G and (resid 2 through 6 or resid 8...G77 - 79
791(chain G and (resid 2 through 6 or resid 8...G1 - 201
7101(chain G and (resid 2 through 6 or resid 8...G1 - 201
7111(chain G and (resid 2 through 6 or resid 8...G132 - 134
7121(chain G and (resid 2 through 6 or resid 8...G159 - 167
7131(chain G and (resid 2 through 6 or resid 8...G159 - 161
7141(chain G and (resid 2 through 6 or resid 8...G163 - 200
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...H0
841(chain H and (resid 2 through 6 or resid 8...H52
851(chain H and (resid 2 through 6 or resid 8...H59 - 6568
861(chain H and (resid 2 through 6 or resid 8...H1 - 202
871(chain H and (resid 2 through 6 or resid 8...H77 - 79
881(chain H and (resid 2 through 6 or resid 8...H82 - 110
891(chain H and (resid 2 through 6 or resid 8...H1 - 202
8101(chain H and (resid 2 through 6 or resid 8...H124
8111(chain H and (resid 2 through 6 or resid 8...H136 - 154
8121(chain H and (resid 2 through 6 or resid 8...H159 - 167
8131(chain H and (resid 2 through 6 or resid 8...H159 - 161
8141(chain H and (resid 2 through 6 or resid 8...H163 - 200

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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: 19400.855 Da / 分子数: 8 / 変異: E65Q / 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, 525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: 27 / 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: 15 / 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: 471 / 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: 3.42 Å3/Da / 溶媒含有率: 64.01 %
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. 10mg/ml protein in 20mM HEPES, 150mM NaCl. Mixed 1:1 ratio

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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: 2.099→26.884 Å / Num. obs: 123375 / % possible obs: 99.6 % / 冗長度: 10.043 % / Biso Wilson estimate: 51.253 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.152 / Rrim(I) all: 0.16 / Χ2: 1.351 / Net I/σ(I): 10.27
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
2.1-2.229.9742.570.719404519849194550.3312.70898
2.22-2.3810.3341.5041.319281718666186580.6121.582100
2.38-2.579.6160.9012.1316724517395173920.7960.952100
2.57-2.8110.790.534.0917309816048160420.9320.557100
2.81-3.1410.5620.2648.3515373814568145560.9820.27799.9
3.14-3.629.5740.13816.1512327612881128760.9930.146100
3.62-4.439.7950.08227.6310706410932109300.9970.087100
4.43-6.249.6190.06534.1982302856185560.9980.06999.9
6.24-26.8849.2620.04341.2545468493249090.9990.04599.5

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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 Å27.48 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
PHASER2.8.2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: 2.099→26.884 Å / SU ML: 0.36 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 28.19
Rfactor反射数%反射
Rfree0.2218 2094 1.7 %
Rwork0.1925 --
obs0.193 123101 99.84 %
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: 152.38 Å2 / Biso mean: 66.7762 Å2 / Biso min: 40.37 Å2
精密化ステップサイクル: final / 解像度: 2.099→26.884 Å
タンパク質核酸リガンド溶媒全体
原子数10936 0 313 471 11720
Biso mean--88.41 67.5 -
残基数----1312
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A3079X-RAY DIFFRACTION5.245TORSIONAL
12B3079X-RAY DIFFRACTION5.245TORSIONAL
13C3079X-RAY DIFFRACTION5.245TORSIONAL
14D3079X-RAY DIFFRACTION5.245TORSIONAL
15E3079X-RAY DIFFRACTION5.245TORSIONAL
16F3079X-RAY DIFFRACTION5.245TORSIONAL
17G3079X-RAY DIFFRACTION5.245TORSIONAL
18H3079X-RAY DIFFRACTION5.245TORSIONAL
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 (%)
2.099-2.14780.40071350.3916791399
2.1478-2.20150.35661390.34748033100
2.2015-2.2610.3151390.33738034100
2.261-2.32750.34251390.30447995100
2.3275-2.40250.34991390.28398009100
2.4025-2.48840.32371380.27638013100
2.4884-2.58790.28911400.25588063100
2.5879-2.70560.27661390.24828034100
2.7056-2.84810.24551390.22318034100
2.8481-3.02630.24811400.2128074100
3.0263-3.25960.20491400.21238096100
3.2596-3.58690.22361400.18468088100
3.5869-4.10440.18661410.16858120100
4.1044-5.16510.18361410.14278176100
5.1651-26.8840.18641450.1568832599
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.091-5.6177-1.58625.28471.58952.16130.27710.02540.0097-0.53170.5592-1.4279-0.98480.4386-0.85270.69230.05870.02280.89210.03050.943547.88784.9006116.2382
20.75120.04880.63790.88790.06320.86520.0859-0.0184-0.04110.0624-0.084-0.03150.14090.0832-0.00930.52490.01510.00670.4347-0.01350.561725.848473.525113.4084
35.31173.1727-0.46726.1641-2.27812.74130.2871-0.66770.57430.6669-0.33581.02930.0048-0.03970.06280.6978-0.04730.09040.6154-0.00050.65743.535168.3441116.8796
45.14520.2259-4.48444.9777-3.94576.73830.52670.8706-1.104-0.39120.56890.54681.0368-1.4738-0.88010.90070.0134-0.16980.7452-0.0220.86960.08480.700392.1357
51.2524-0.57770.13330.8434-0.14920.5924-0.07630.12410.13-0.03860.0113-0.056-0.01670.11380.06970.4559-0.01120.02710.45910.02090.540419.235694.1835100.743
63.71731.87431.20713.9704-0.02432.36020.4707-0.7840.81850.5646-0.5415-0.3558-0.46160.00360.03640.5870.0058-0.11530.6835-0.14540.985831.811107.3054115.403
71.84461.3748-0.3174.3450.33120.66260.1782-0.3885-0.05830.2136-0.2231-0.5631-0.03970.24360.04040.5382-0.0007-0.15060.6370.00180.56753.41999.9292153.7482
80.07680.4681-0.2012.6874-1.04592.18040.1059-0.17120.0080.1349-0.02130.0592-0.28520.096-0.04970.46360.0069-0.10040.65410.02160.606246.9186100.0957151.9072
90.89840.47040.26822.06390.37540.89330.1964-0.3167-0.25190.3433-0.2505-0.26820.0680.11510.05850.5660.0057-0.11450.7150.04710.617254.581100.222163.0653
100.09880.6913-0.41087.4515-1.38682.316-0.05140.04750.24990.50580.19170.5456-0.199-0.3595-0.0890.5256-0.0484-0.06470.6851-0.02780.630244.2639102.3184166.4419
114.29951.5821-0.72353.88471.70091.73610.525-0.48160.02850.44090.23441.77070.0522-0.7449-0.71280.7781-0.13220.0510.83580.03170.982435.826183.4379167.772
125.73360.1878-3.14465.26331.17283.0631-0.4006-0.3237-0.39220.1667-0.8119-1.06890.2397-0.0431.17720.88340.0946-0.18120.6389-0.01840.922148.603467.2359148.7544
130.68561.20830.30472.40860.03151.31820.0643-0.0516-0.17220.0394-0.0229-0.22440.05120.2475-0.06520.46140.0248-0.0440.59820.03510.584552.355790.1246140.5496
140.33010.97950.09635.994-2.2352.00590.0362-0.10520.0146-0.0820.16850.62380.13220.0055-0.20410.52120.0164-0.04260.57330.030.659143.77592.7105140.817
151.35980.39990.41192.0453-0.14661.30850.03320.0464-0.2366-0.4451-0.0257-0.38610.33120.2645-0.02230.44080.0195-0.01990.5630.02680.588652.684985.8218135.6604
160.59930.8455-0.69345.043-1.66711.05880.04070.08970.0732-0.1750.3910.69810.0851-0.1412-0.38050.5618-0.001-0.09930.61740.01390.671742.846387.9794128.5333
172.7808-1.62910.28153.6271.10122.18780.00450.5380.2738-0.64140.59781.0068-0.1857-0.9523-0.70050.6616-0.0719-0.14650.60380.1630.840140.3694108.5958126.7538
185.48240.07055.00380.8598-0.02564.57610.2234-0.61740.2621.83950.28690.078-0.3250.874-0.25140.9589-0.1036-0.05240.84040.01990.63238.9664138.5007173.5198
190.3022-0.5123-0.34520.89630.29323.66710.0131-0.09220.08320.14860.0608-0.050.18860.0187-0.02380.5314-0.13780.00180.655-0.02740.62336.2477136.787150.1997
200.72210.11860.67821.03190.2341.83470.0637-0.06650.02990.13330.0148-0.08770.3061-0.0229-0.07030.5527-0.1068-0.00240.57630.0260.612645.1973128.905148.5797
216.1262-2.3613-3.89731.13992.47786.7535-0.24310.8499-0.07760.1107-0.154-0.11551.005-0.89460.47260.7554-0.1490.05940.6437-0.01610.66536.0819122.9871128.6793
221.5618-0.44550.72791.2146-0.92792.7239-0.1973-0.19660.27590.25930.0234-0.0703-0.521-0.36350.12560.5853-0.0785-0.02370.6479-0.0930.74526.9818148.4703143.8832
231.3274-0.06940.49320.382-0.46541.2495-0.0171-0.25160.29690.11050.0133-0.0568-0.287-0.18310.02460.5786-0.0753-0.00470.6107-0.12850.699819.4333148.6416145.8796
242.27170.07280.23873.4646-1.94111.1223-0.3034-0.42740.05790.99860.03180.48711.0157-0.73540.12360.8254-0.10290.02971.2615-0.06020.685512.2039141.7611166.7494
259.71643.28151.60142.4261-0.67912.49990.034-0.9635-2.26710.06590.4744-0.67741.77290.0039-0.2630.8394-0.0033-0.07140.85480.16521.003950.4911103.8548178.624
261.529-0.3877-1.3651.05210.42481.22780.124-0.2450.0928-0.0013-0.14190.024-0.20670.090.020.7335-0.0608-0.13380.7141-0.04880.605632.9345119.717184.377
274.8853-3.4973-1.07753.44921.41440.99510.32620.0592-0.1862-0.1628-0.18630.2365-0.130.107-0.17540.7731-0.0405-0.0590.67160.01020.598932.393126.5823174.061
282.08420.50360.3930.2053-0.40033.04270.21760.4003-0.0023-0.6652-0.29971.1506-0.36090.0753-0.03511.04260.2203-0.17591.1119-0.10090.83812.6752132.2817178.6461
290.7944-2.2557-0.51736.44781.37880.5243-0.462-0.96691.18580.84030.28570.7829-0.9575-0.95250.44170.93650.02460.0381.1652-0.20111.07626.4743122.3411203.5183
301.63250.8282-0.97080.7035-0.20091.0081-0.1901-0.3915-0.35690.2314-0.039-0.0620.1790.19040.18690.72760.0282-0.09830.76420.05410.640522.1301105.8159195.5261
313.3354-2.8758-2.35254.94941.99391.98430.1088-0.0454-0.2782-0.4247-0.21510.1461-0.0804-0.03020.16830.71990.0252-0.02020.81150.1060.79915.157195.4905194.0657
323.3822-0.8145-1.9853.67781.06453.6719-0.0391-0.0456-1.1356-1.1834-0.2255-0.39080.7589-0.06250.34821.0245-0.02080.25950.6881-0.12051.32328.664186.5589180.6032
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 146 )A6 - 146
3X-RAY DIFFRACTION3chain 'A' and (resid 147 through 164 )A147 - 164
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 5 )B1 - 5
5X-RAY DIFFRACTION5chain 'B' and (resid 6 through 146 )B6 - 146
6X-RAY DIFFRACTION6chain 'B' and (resid 147 through 164 )B147 - 164
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 36 )C1 - 36
8X-RAY DIFFRACTION8chain 'C' and (resid 37 through 75 )C37 - 75
9X-RAY DIFFRACTION9chain 'C' and (resid 76 through 115 )C76 - 115
10X-RAY DIFFRACTION10chain 'C' and (resid 116 through 146 )C116 - 146
11X-RAY DIFFRACTION11chain 'C' and (resid 147 through 164 )C147 - 164
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 5 )D1 - 5
13X-RAY DIFFRACTION13chain 'D' and (resid 6 through 35 )D6 - 35
14X-RAY DIFFRACTION14chain 'D' and (resid 36 through 65 )D36 - 65
15X-RAY DIFFRACTION15chain 'D' and (resid 66 through 115 )D66 - 115
16X-RAY DIFFRACTION16chain 'D' and (resid 116 through 146 )D116 - 146
17X-RAY DIFFRACTION17chain 'D' and (resid 147 through 164 )D147 - 164
18X-RAY DIFFRACTION18chain 'E' and (resid 1 through 5 )E1 - 5
19X-RAY DIFFRACTION19chain 'E' and (resid 6 through 76 )E6 - 76
20X-RAY DIFFRACTION20chain 'E' and (resid 77 through 146 )E77 - 146
21X-RAY DIFFRACTION21chain 'E' and (resid 147 through 164 )E147 - 164
22X-RAY DIFFRACTION22chain 'F' and (resid 1 through 36 )F1 - 36
23X-RAY DIFFRACTION23chain 'F' and (resid 37 through 146 )F37 - 146
24X-RAY DIFFRACTION24chain 'F' and (resid 147 through 164 )F147 - 164
25X-RAY DIFFRACTION25chain 'G' and (resid 1 through 5 )G1 - 5
26X-RAY DIFFRACTION26chain 'G' and (resid 6 through 115 )G6 - 115
27X-RAY DIFFRACTION27chain 'G' and (resid 116 through 146 )G116 - 146
28X-RAY DIFFRACTION28chain 'G' and (resid 147 through 164 )G147 - 164
29X-RAY DIFFRACTION29chain 'H' and (resid 1 through 5 )H1 - 5
30X-RAY DIFFRACTION30chain 'H' and (resid 6 through 115 )H6 - 115
31X-RAY DIFFRACTION31chain 'H' and (resid 116 through 146 )H116 - 146
32X-RAY DIFFRACTION32chain '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://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