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- PDB-6txm: Crystal structure of thermotoga maritima E65R Ferritin -

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基本情報

登録情報
データベース: PDB / ID: 6txm
タイトルCrystal structure of thermotoga maritima E65R Ferritin
要素Ferritinフェリチン
キーワードMETAL BINDING PROTEIN / Metal binding (金属) / engineered protein (タンパク質工学)
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 / 細胞質基質 / 細胞質
類似検索 - 分子機能
Ferritin, prokaryotic-type / フェリチン / 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
エイコサン / フェリチン
類似検索 - 構成要素
生物種Thermotoga maritima (テルモトガ・マリティマ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.198 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)160,07249
ポリマ－155,4398
非ポリマー4,63341
水5,549308
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)480,217147
ポリマ－466,31824
非ポリマー13,899123
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 area106310 Å2
ΔGint-1263 kcal/mol
Surface area147050 Å2
手法PISA
単位格子
Length a, b, c (Å)176.262, 176.262, 353.783
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 9 or resid 11...
21(chain B and (resid 2 through 9 or resid 11...
31(chain C and (resid 2 through 9 or resid 11...
41(chain D and (resid 2 through 9 or resid 11...
51(chain E and (resid 2 through 9 or resid 11...
61(chain F and (resid 2 through 9 or resid 11...
71(chain G and (resid 2 through 9 or resid 11...
81(chain H and (resid 2 through 9 or resid 11...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 2 through 9 or resid 11...A2 - 9
121(chain A and (resid 2 through 9 or resid 11...A11 - 17
131(chain A and (resid 2 through 9 or resid 11...A1 - 203
141(chain A and (resid 2 through 9 or resid 11...A1 - 203
151(chain A and (resid 2 through 9 or resid 11...A67 - 68
161(chain A and (resid 2 through 9 or resid 11...A70 - 75
171(chain A and (resid 2 through 9 or resid 11...A7
181(chain A and (resid 2 through 9 or resid 11...A85
191(chain A and (resid 2 through 9 or resid 11...A95 - 110
1101(chain A and (resid 2 through 9 or resid 11...A1 - 203
1111(chain A and (resid 2 through 9 or resid 11...A113 - 122
1121(chain A and (resid 2 through 9 or resid 11...A1 - 203
1131(chain A and (resid 2 through 9 or resid 11...A133 - 134
1141(chain A and (resid 2 through 9 or resid 11...A1 - 203
1151(chain A and (resid 2 through 9 or resid 11...A156 - 157
1161(chain A and (resid 2 through 9 or resid 11...A1 - 203
1171(chain A and (resid 2 through 9 or resid 11...A159 - 164
211(chain B and (resid 2 through 9 or resid 11...B2 - 9
221(chain B and (resid 2 through 9 or resid 11...B11 - 17
231(chain B and (resid 2 through 9 or resid 11...B19 - 57
241(chain B and (resid 2 through 9 or resid 11...B62 - 65
251(chain B and (resid 2 through 9 or resid 11...B67 - 68
261(chain B and (resid 2 through 9 or resid 11...B70 - 75
271(chain B and (resid 2 through 9 or resid 11...B77 - 80
281(chain B and (resid 2 through 9 or resid 11...B82 - 85
291(chain B and (resid 2 through 9 or resid 11...B87 - 93
2101(chain B and (resid 2 through 9 or resid 11...B95 - 110
2111(chain B and (resid 2 through 9 or resid 11...B113 - 122
2121(chain B and (resid 2 through 9 or resid 11...B124 - 130
2131(chain B and (resid 2 through 9 or resid 11...B133 - 134
2141(chain B and (resid 2 through 9 or resid 11...B136 - 143
2151(chain B and (resid 2 through 9 or resid 11...B145 - 154
2161(chain B and (resid 2 through 9 or resid 11...B156 - 157
2171(chain B and (resid 2 through 9 or resid 11...B159 - 164
311(chain C and (resid 2 through 9 or resid 11...C2 - 9
321(chain C and (resid 2 through 9 or resid 11...C11 - 17
331(chain C and (resid 2 through 9 or resid 11...C19 - 57
341(chain C and (resid 2 through 9 or resid 11...C65
351(chain C and (resid 2 through 9 or resid 11...C67 - 68
361(chain C and (resid 2 through 9 or resid 11...C70 - 75
371(chain C and (resid 2 through 9 or resid 11...C77 - 80
381(chain C and (resid 2 through 9 or resid 11...C82 - 85
391(chain C and (resid 2 through 9 or resid 11...C87 - 93
3101(chain C and (resid 2 through 9 or resid 11...C1 - 164
3111(chain C and (resid 2 through 9 or resid 11...C1 - 164
3121(chain C and (resid 2 through 9 or resid 11...C133 - 134
3131(chain C and (resid 2 through 9 or resid 11...C156 - 154
3141(chain C and (resid 2 through 9 or resid 11...C156 - 157
3151(chain C and (resid 2 through 9 or resid 11...C159 - 164
411(chain D and (resid 2 through 9 or resid 11...D2 - 9
421(chain D and (resid 2 through 9 or resid 11...D11 - 17
431(chain D and (resid 2 through 9 or resid 11...D19 - 57
441(chain D and (resid 2 through 9 or resid 11...D59 - 60
451(chain D and (resid 2 through 9 or resid 11...D65
461(chain D and (resid 2 through 9 or resid 11...D67 - 68
471(chain D and (resid 2 through 9 or resid 11...D70 - 75
481(chain D and (resid 2 through 9 or resid 11...D77 - 80
491(chain D and (resid 2 through 9 or resid 11...D82 - 85
4101(chain D and (resid 2 through 9 or resid 11...D87 - 93
4111(chain D and (resid 2 through 9 or resid 11...D1 - 201
4121(chain D and (resid 2 through 9 or resid 11...D1 - 201
4131(chain D and (resid 2 through 9 or resid 11...D133 - 134
4141(chain D and (resid 2 through 9 or resid 11...D156 - 154
4151(chain D and (resid 2 through 9 or resid 11...D156 - 157
4161(chain D and (resid 2 through 9 or resid 11...D159 - 164
511(chain E and (resid 2 through 9 or resid 11...E2 - 9
521(chain E and (resid 2 through 9 or resid 11...E11 - 17
531(chain E and (resid 2 through 9 or resid 11...E19 - 57
541(chain E and (resid 2 through 9 or resid 11...E59 - 60
551(chain E and (resid 2 through 9 or resid 11...E65
561(chain E and (resid 2 through 9 or resid 11...E67 - 68
571(chain E and (resid 2 through 9 or resid 11...E70 - 75
581(chain E and (resid 2 through 9 or resid 11...E77 - 80
591(chain E and (resid 2 through 9 or resid 11...E82 - 85
5101(chain E and (resid 2 through 9 or resid 11...E87 - 93
5111(chain E and (resid 2 through 9 or resid 11...E1 - 202
5121(chain E and (resid 2 through 9 or resid 11...E1 - 202
5131(chain E and (resid 2 through 9 or resid 11...E133 - 134
5141(chain E and (resid 2 through 9 or resid 11...E156 - 154
5151(chain E and (resid 2 through 9 or resid 11...E156 - 157
5161(chain E and (resid 2 through 9 or resid 11...E159 - 164
611(chain F and (resid 2 through 9 or resid 11...F2 - 9
621(chain F and (resid 2 through 9 or resid 11...F11 - 17
631(chain F and (resid 2 through 9 or resid 11...F19 - 57
641(chain F and (resid 2 through 9 or resid 11...F59 - 60
651(chain F and (resid 2 through 9 or resid 11...F65
661(chain F and (resid 2 through 9 or resid 11...F67 - 68
671(chain F and (resid 2 through 9 or resid 11...F70 - 75
681(chain F and (resid 2 through 9 or resid 11...F77 - 80
691(chain F and (resid 2 through 9 or resid 11...F82 - 85
6101(chain F and (resid 2 through 9 or resid 11...F87 - 93
6111(chain F and (resid 2 through 9 or resid 11...F1 - 201
6121(chain F and (resid 2 through 9 or resid 11...F1 - 201
6131(chain F and (resid 2 through 9 or resid 11...F133 - 134
6141(chain F and (resid 2 through 9 or resid 11...F156 - 154
6151(chain F and (resid 2 through 9 or resid 11...F156 - 157
6161(chain F and (resid 2 through 9 or resid 11...F159 - 164
711(chain G and (resid 2 through 9 or resid 11...G2 - 9
721(chain G and (resid 2 through 9 or resid 11...G11 - 17
731(chain G and (resid 2 through 9 or resid 11...G19 - 57
741(chain G and (resid 2 through 9 or resid 11...G65
751(chain G and (resid 2 through 9 or resid 11...G67 - 68
761(chain G and (resid 2 through 9 or resid 11...G70 - 75
771(chain G and (resid 2 through 9 or resid 11...G77 - 80
781(chain G and (resid 2 through 9 or resid 11...G82 - 85
791(chain G and (resid 2 through 9 or resid 11...G87 - 93
7101(chain G and (resid 2 through 9 or resid 11...G1 - 201
7111(chain G and (resid 2 through 9 or resid 11...G1 - 201
7121(chain G and (resid 2 through 9 or resid 11...G133 - 134
7131(chain G and (resid 2 through 9 or resid 11...G156 - 154
7141(chain G and (resid 2 through 9 or resid 11...G156 - 157
7151(chain G and (resid 2 through 9 or resid 11...G159 - 164
811(chain H and (resid 2 through 9 or resid 11...H2 - 9
821(chain H and (resid 2 through 9 or resid 11...H11 - 17
831(chain H and (resid 2 through 9 or resid 11...H1 - 201
841(chain H and (resid 2 through 9 or resid 11...H0
851(chain H and (resid 2 through 9 or resid 11...H67 - 68
861(chain H and (resid 2 through 9 or resid 11...H70 - 75
871(chain H and (resid 2 through 9 or resid 11...H1 - 201
881(chain H and (resid 2 through 9 or resid 11...H0
891(chain H and (resid 2 through 9 or resid 11...H87 - 93
8101(chain H and (resid 2 through 9 or resid 11...H1 - 201
8111(chain H and (resid 2 through 9 or resid 11...H1133 - 134
8121(chain H and (resid 2 through 9 or resid 11...H133 - 134
8131(chain H and (resid 2 through 9 or resid 11...H145 - 154
8141(chain H and (resid 2 through 9 or resid 11...H156 - 157
8151(chain H and (resid 2 through 9 or resid 11...H159 - 164

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要素

#1: タンパク質
Ferritin / フェリチン


分子量: 19429.920 Da / 分子数: 8 / 変異: E65R / 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) (テルモトガ・マリティマ)
遺伝子: TM_1128 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9X0L2, bacterial non-heme ferritin
#2: 化合物...
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン / 硫酸塩


分子量: 96.063 Da / 分子数: 24 / 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 / グリセリン


分子量: 92.094 Da / 分子数: 13 / 由来タイプ: 合成 / 式: C3H8O3
#4: 化合物
ChemComp-LFA / EICOSANE / LIPID FRAGMENT / イコサン / エイコサン


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


分子量: 18.015 Da / 分子数: 308 / 由来タイプ: 天然 / 式: H2O
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: 3.4 Å3/Da / 溶媒含有率: 63.85 %
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 in 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: 14.1 / 波長: 0.9184 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 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: 0.9184 Å / 相対比: 1
反射解像度: 2.198→47.979 Å / Num. obs: 107042 / % possible obs: 99.8 % / 冗長度: 10.24 % / Biso Wilson estimate: 47.179 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.216 / Rrim(I) all: 0.228 / Χ2: 1.048 / Net I/σ(I): 7.52
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
2.2-2.339.8582.1510.8316810117179170520.4032.26999.3
2.33-2.4910.6151.4011.4517151016158161580.6281.472100
2.49-2.6910.280.912.2915482715061150610.810.958100
2.69-2.9510.110.5214.0614030913890138780.9220.54999.9
2.95-3.2910.5570.37.1713300712599125990.9750.315100
3.29-3.810.0290.15712.9511171211157111390.9910.16599.8
3.8-4.6510.6230.10519.49100666947794760.9950.111100
4.65-6.549.9720.10219.4973839741074050.9960.10799.9
6.54-47.9799.8640.07626.3142148429442730.9970.0899.5

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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
Rotation7.83 Å49.01 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: 2.198→47.979 Å / SU ML: 0.37 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 27.94
Rfactor反射数%反射
Rfree0.2433 2100 1.96 %
Rwork0.2039 --
obs0.2047 106996 99.8 %
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: 180.15 Å2 / Biso mean: 62.7003 Å2 / Biso min: 35.38 Å2
精密化ステップサイクル: final / 解像度: 2.198→47.979 Å
タンパク質核酸リガンド溶媒全体
原子数10952 0 278 308 11538
Biso mean--97.09 63.87 -
残基数----1312
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A3064X-RAY DIFFRACTION5.367TORSIONAL
12B3064X-RAY DIFFRACTION5.367TORSIONAL
13C3064X-RAY DIFFRACTION5.367TORSIONAL
14D3064X-RAY DIFFRACTION5.367TORSIONAL
15E3064X-RAY DIFFRACTION5.367TORSIONAL
16F3064X-RAY DIFFRACTION5.367TORSIONAL
17G3064X-RAY DIFFRACTION5.367TORSIONAL
18H3064X-RAY DIFFRACTION5.367TORSIONAL
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 (%)
2.1982-2.24940.40251370.3713680998
2.2494-2.30560.42561380.33316918100
2.3056-2.3680.31551400.29866962100
2.368-2.43760.30421390.28386961100
2.4376-2.51630.33951390.29136954100
2.5163-2.60630.321400.27476957100
2.6063-2.71060.32291390.26446975100
2.7106-2.83390.30421400.24696969100
2.8339-2.98330.28411400.23356995100
2.9833-3.17020.24841390.23346966100
3.1702-3.41490.23841400.20317006100
3.4149-3.75850.23791410.18467008100
3.7585-4.3020.18161410.16727053100
4.302-5.41890.2081420.1567090100
5.4189-47.9790.21711450.17877273100
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)
15.7491-0.46391.99780.7189-0.02221.5214-0.11390.2448-0.0024-0.01980.0285-0.09420.05650.2320.01490.47360.03960.01930.4251-0.01980.507729.395577.2556108.6864
25.65781.97681.09112.3739-0.10080.38750.2016-0.34480.31220.1965-0.29420.20740.0699-0.06790.05790.4578-0.00260.02910.4246-0.05050.458722.485479.8765114.3773
31.1026-0.34430.30540.07040.1530.50920.099-0.0031-0.33410.0207-0.0557-0.15070.20810.0838-0.03940.5140.0341-0.01570.4281-0.0170.530929.221770.6596109.9632
47.00513.56942.33472.05031.66461.581300.00720.52780.1119-0.07740.27970.1269-0.01680.02640.5350.0066-0.02770.39590.01040.459824.083768.3392120.8183
54.49583.09170.91657.81161.2382.7650.6122-1.10750.28740.737-0.88890.3634-0.3373-0.63630.2110.6355-0.06820.09410.6856-0.01570.53693.34768.4274116.2776
63.95820.22052.44390.36810.00782.62580.06220.0451-0.1084-0.0562-0.04560.0279-0.0288-0.0468-0.01240.4550.00810.01250.4305-0.00130.532418.784287.73898.0376
75.21651.99622.10142.56010.53011.3840.1654-0.60010.62180.211-0.26710.32080.1446-0.20820.13040.42850.02540.09090.4144-0.05050.528518.276591.6792106.7988
81.774-0.4980.33180.5754-0.27460.7233-0.0674-0.04510.2441-0.0709-0.0339-0.1281-0.12420.16460.10080.39710.00090.02370.4090.00150.529521.248399.3368100.7415
91.72452.13350.07555.99930.38330.47440.1264-0.2706-0.0421-0.1464-0.2321-0.47940.00170.24890.01550.40650.0121-0.09330.5913-0.00010.46953.6754100.6072152.9794
100.40481.6259-0.37274.9401-1.13431.6572-0.0073-0.15670.044-0.2190.20950.56150.0556-0.111-0.23640.38170.0196-0.08810.59180.04220.527744.29997.4557153.696
110.84780.3266-0.03611.19110.6790.41330.0773-0.1309-0.11420.1876-0.0887-0.20530.06190.09140.01240.4810.0066-0.1060.6396-0.01130.567354.8697101.4898159.3612
120.20461.3648-0.455.5144-1.34952.03170.0699-0.01970.16630.16470.06760.56710.1072-0.3825-0.01240.5-0.0277-0.02980.6766-0.04460.552844.4052102.3929165.9233
133.6534-0.73250.10643.1187-4.10336.62750.2760.0388-0.12770.75520.28271.4824-0.2913-0.7766-0.68640.6904-0.13960.03090.6745-0.06330.789335.722683.3136167.1041
140.29870.4320.27624.7386-0.26181.31170.0568-0.0713-0.16480.18320.04420.12730.04510.1686-0.06940.39910.0492-0.04610.54820.03450.573351.83586.9629141.1062
150.73790.4979-0.03911.09180.15780.87930.0114-0.00430.0034-0.11690.022-0.06280.01690.1073-0.04520.44320.0215-0.05580.51470.03840.556247.302188.1909134.5444
162.52390.5241-0.9745.3329-2.25736.02220.2472-0.08370.3673-0.45430.47360.9624-0.1564-0.5275-0.61810.754-0.0029-0.18470.49610.14620.839440.396108.6522126.4362
170.327-0.05990.16180.2171-0.7863.79170.03760.0094-0.11720.04750.1398-0.0774-0.26710.1293-0.12610.4925-0.0822-0.00410.56350.00110.579739.4724138.721152.0195
180.1011-0.40.36070.62471.01427.92790.0004-0.01480.01840.0659-0.01420.03980.7721-0.8520.02340.4993-0.14060.02310.5157-0.00810.579333.4384132.2952148.2188
190.2293-0.28810.37020.4748-0.6080.810.001-0.04570.0568-0.02050.0116-0.08060.10260.13310.00610.4743-0.1073-0.00280.52220.02890.51544.2272130.9442149.4151
207.5691-1.4876-4.32213.26661.0252.8429-0.07480.4433-0.33180.2528-0.16980.02961.5323-0.58970.19950.7855-0.1251-0.04310.57590.00920.562635.9012122.8315128.3296
211.2584-0.34260.77790.987-0.85754.21470.0941-0.05980.18790.18620.12990.0354-0.0969-0.0298-0.23210.4828-0.0643-0.00010.4423-0.0680.591627.1432148.5918143.165
220.9571-0.3299-1.09280.2516-0.74135.4696-0.0125-0.0648-0.04770.0444-0.12120.05380.2149-0.61770.19430.4665-0.12250.00590.5636-0.06840.589322.0868141.094146.3547
231.161-0.16740.40980.5921-0.6441.1193-0.0434-0.05740.32970.07360.0325-0.1142-0.3766-0.07280.05260.5386-0.0862-0.02750.4871-0.10050.625123.0537153.25143.8984
240.9737-0.0552-0.85860.9329-0.31561.8196-0.3984-0.3464-0.07290.1162-0.13530.01190.74990.20930.30060.4970.0017-0.00740.5711-0.07880.540811.7531149.1417146.4515
255.0028-1.4621-2.20743.007-1.81873.2978-0.2705-0.2680.1750.36040.09330.17780.4957-1.05780.24450.6711-0.06690.0441.0384-0.0640.52612.3916141.6771166.1888
265.3899-1.6297-2.03241.34210.64221.5802-0.2685-0.11190.29170.28010.1098-0.18120.10260.16920.2310.5999-0.0596-0.08750.5664-0.01640.41334.5789116.9458185.8877
273.021-2.2296-1.89772.15231.0471.40010.29740.13770.0137-0.2691-0.34290.0426-0.1297-0.01950.06430.577-0.0566-0.09420.5714-0.04470.469230.2704114.1245181.5909
281.8091-0.7792-0.89750.2370.51191.46680.1072-0.08230.47630.1794-0.0302-0.3232-0.30180.1116-0.07290.6586-0.0571-0.0560.6259-0.10380.524336.5839125.9091183.5104
294.1831-2.8411-1.04863.09850.82180.7880.1418-0.1431-0.229-0.03220.05570.4056-0.22720.04-0.21350.6196-0.0481-0.00930.57870.0060.498632.5611126.5379173.5824
303.0079-1.1325-0.72982.9452-0.2292.37290.56840.65410.0284-0.9019-0.66580.7036-0.1985-0.02710.02550.78430.149-0.04570.879-0.03540.60512.8455132.8092178.376
312.6282-0.2194-1.69711.49950.41142.1946-0.1556-0.3282-0.01330.3640.0371-0.03730.28440.08490.10630.58840.0103-0.06360.68710.03160.426822.0854109.6434196.6597
322.4117-1.5084-1.35593.13080.83640.605-0.2086-0.0403-0.3577-0.0620.06540.2443-0.0344-0.05570.09690.6539-0.0293-0.09270.6735-0.01490.462520.5408109.0231189.947
332.92691.16682.28570.50420.71693.6052-0.1976-1.0365-0.52390.6476-0.0018-0.036-0.26810.42240.32570.79720.0749-0.02580.89740.13680.619836.3916100.5985195.1064
343.1328-2.0693-1.29423.41630.67772.5195-0.095-0.1643-0.23410.2382-0.1885-0.15670.13350.18160.270.552-0.0561-0.05110.60650.07460.480617.6934100.5399201.6397
352.7984-2.7477-0.88844.10811.46690.64940.31620.027-0.0728-0.6297-0.2301-0.2663-0.1592-0.0193-0.07760.67740.02260.02570.67980.12430.554415.195195.4429193.5866
363.649-0.567-1.68856.13230.1874.3955-0.3736-0.3982-1.0677-1.10110.09260.18690.7301-0.04480.4830.9375-0.07080.2340.7341-0.08120.899128.620586.7707180.1348
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 66 )A36 - 66
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 115 )A67 - 115
4X-RAY DIFFRACTION4chain 'A' and (resid 116 through 146 )A116 - 146
5X-RAY DIFFRACTION5chain 'A' and (resid 147 through 164 )A147 - 164
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 35 )B1 - 35
7X-RAY DIFFRACTION7chain 'B' and (resid 36 through 66 )B36 - 66
8X-RAY DIFFRACTION8chain 'B' and (resid 67 through 164 )B67 - 164
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 35 )C1 - 35
10X-RAY DIFFRACTION10chain 'C' and (resid 36 through 65 )C36 - 65
11X-RAY DIFFRACTION11chain 'C' and (resid 66 through 115 )C66 - 115
12X-RAY DIFFRACTION12chain 'C' and (resid 116 through 146 )C116 - 146
13X-RAY DIFFRACTION13chain 'C' and (resid 147 through 164 )C147 - 164
14X-RAY DIFFRACTION14chain 'D' and (resid 1 through 35 )D1 - 35
15X-RAY DIFFRACTION15chain 'D' and (resid 36 through 146 )D36 - 146
16X-RAY DIFFRACTION16chain 'D' and (resid 147 through 164 )D147 - 164
17X-RAY DIFFRACTION17chain 'E' and (resid 1 through 35 )E1 - 35
18X-RAY DIFFRACTION18chain 'E' and (resid 36 through 66 )E36 - 66
19X-RAY DIFFRACTION19chain 'E' and (resid 67 through 146 )E67 - 146
20X-RAY DIFFRACTION20chain 'E' and (resid 147 through 164 )E147 - 164
21X-RAY DIFFRACTION21chain 'F' and (resid 1 through 36 )F1 - 36
22X-RAY DIFFRACTION22chain 'F' and (resid 37 through 65 )F37 - 65
23X-RAY DIFFRACTION23chain 'F' and (resid 66 through 115 )F66 - 115
24X-RAY DIFFRACTION24chain 'F' and (resid 116 through 146 )F116 - 146
25X-RAY DIFFRACTION25chain 'F' and (resid 147 through 164 )F147 - 164
26X-RAY DIFFRACTION26chain 'G' and (resid 1 through 36 )G1 - 36
27X-RAY DIFFRACTION27chain 'G' and (resid 37 through 75 )G37 - 75
28X-RAY DIFFRACTION28chain 'G' and (resid 76 through 115 )G76 - 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 35 )H1 - 35
32X-RAY DIFFRACTION32chain 'H' and (resid 36 through 75 )H36 - 75
33X-RAY DIFFRACTION33chain 'H' and (resid 76 through 84 )H76 - 84
34X-RAY DIFFRACTION34chain 'H' and (resid 85 through 115 )H85 - 115
35X-RAY DIFFRACTION35chain 'H' and (resid 116 through 146 )H116 - 146
36X-RAY DIFFRACTION36chain '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