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- PDB-7k26: Crystal structure of Human H-chain Ferritin variant infused with ... -

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基本情報

登録情報
データベース: PDB / ID: 7k26
タイトルCrystal structure of Human H-chain Ferritin variant infused with Sodium Acrylate
要素Ferritin heavy chainフェリチン
キーワードOXIDOREDUCTASE (酸化還元酵素) / Ferritin (フェリチン) / Polymer (重合体) / Hydrogel / Polymer Integrated Crystals / Crystal Hydrogel Hybrids / RAFT Polymerization
機能・相同性
機能・相同性情報


iron ion sequestering activity / : / オートファゴソーム / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / ferroxidase activity / intracellular sequestering of iron ion / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / : / オートファゴソーム / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / ferroxidase activity / intracellular sequestering of iron ion / negative regulation of fibroblast proliferation / ferric iron binding / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / iron ion transport / intracellular iron ion homeostasis / ficolin-1-rich granule lumen / 免疫応答 / iron ion binding / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / 生体膜 / identical protein binding / 細胞核 / 細胞質基質 / 細胞質
類似検索 - 分子機能
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / 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
: / Ferritin heavy chain
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.7 Å
データ登録者Bailey, J.B. / Zhang, L.
引用ジャーナル: J.Am.Chem.Soc. / 年: 2020
タイトル: Anisotropic Dynamics and Mechanics of Macromolecular Crystals Containing Lattice-Patterned Polymer Networks.
著者: Han, K. / Bailey, J.B. / Zhang, L. / Tezcan, F.A.
履歴
登録2020年9月8日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年11月11日Provider: repository / タイプ: Initial release
改定 1.12020年11月25日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
改定 1.22023年10月18日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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 heavy chain
B: Ferritin heavy chain
C: Ferritin heavy chain
D: Ferritin heavy chain
E: Ferritin heavy chain
F: Ferritin heavy chain
G: Ferritin heavy chain
H: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain
K: Ferritin heavy chain
L: Ferritin heavy chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)254,68138
ポリマ－253,02312
非ポリマー1,65826
水6,593366
1
A: Ferritin heavy chain
B: Ferritin heavy chain
C: Ferritin heavy chain
D: Ferritin heavy chain
E: Ferritin heavy chain
F: Ferritin heavy chain
G: Ferritin heavy chain
H: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain
K: Ferritin heavy chain
L: Ferritin heavy chain
ヘテロ分子

A: Ferritin heavy chain
B: Ferritin heavy chain
C: Ferritin heavy chain
D: Ferritin heavy chain
E: Ferritin heavy chain
F: Ferritin heavy chain
G: Ferritin heavy chain
H: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain
K: Ferritin heavy chain
L: Ferritin heavy chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)509,36376
ポリマ－506,04624
非ポリマー3,31752
水43224
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area96590 Å2
ΔGint-798 kcal/mol
Surface area141580 Å2
手法PISA
単位格子
Length a, b, c (Å)131.570, 131.570, 306.560
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDモデル要素
11K-202-

MPD

21K-202-

MPD

31D-354-

HOH

41D-355-

HOH

非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRSERSER(chain 'A' and (resid 5 through 13 or (resid 14...AA5 - 595 - 59
12GLUGLULYSLYS(chain 'A' and (resid 5 through 13 or (resid 14...AA64 - 8764 - 87
13GLUGLUALAALA(chain 'A' and (resid 5 through 13 or (resid 14...AA90 - 16090 - 160
14SERSERLEULEU(chain 'A' and (resid 5 through 13 or (resid 14...AA163 - 175163 - 175
21THRTHRSERSER(chain 'B' and (resid 5 through 48 or (resid 49...BB5 - 595 - 59
22GLUGLULYSLYS(chain 'B' and (resid 5 through 48 or (resid 49...BB64 - 8764 - 87
23GLUGLUALAALA(chain 'B' and (resid 5 through 48 or (resid 49...BB90 - 16090 - 160
24SERSERLEULEU(chain 'B' and (resid 5 through 48 or (resid 49...BB163 - 175163 - 175
31THRTHRSERSER(chain 'C' and (resid 5 through 48 or (resid 49...CC5 - 595 - 59
32GLUGLULYSLYS(chain 'C' and (resid 5 through 48 or (resid 49...CC64 - 8764 - 87
33GLUGLUALAALA(chain 'C' and (resid 5 through 48 or (resid 49...CC90 - 16090 - 160
34SERSERLEULEU(chain 'C' and (resid 5 through 48 or (resid 49...CC163 - 175163 - 175
41THRTHRSERSER(chain 'D' and (resid 5 through 13 or (resid 14...DD5 - 595 - 59
42GLUGLULYSLYS(chain 'D' and (resid 5 through 13 or (resid 14...DD64 - 8764 - 87
43GLUGLUALAALA(chain 'D' and (resid 5 through 13 or (resid 14...DD90 - 16090 - 160
44SERSERLEULEU(chain 'D' and (resid 5 through 13 or (resid 14...DD163 - 175163 - 175
51THRTHRSERSER(chain 'E' and (resid 5 through 13 or (resid 14...EE5 - 595 - 59
52GLUGLULYSLYS(chain 'E' and (resid 5 through 13 or (resid 14...EE64 - 8764 - 87
53GLUGLUALAALA(chain 'E' and (resid 5 through 13 or (resid 14...EE90 - 16090 - 160
54SERSERLEULEU(chain 'E' and (resid 5 through 13 or (resid 14...EE163 - 175163 - 175
61THRTHRSERSER(chain 'F' and (resid 5 through 48 or (resid 49...FF5 - 595 - 59
62GLUGLULYSLYS(chain 'F' and (resid 5 through 48 or (resid 49...FF64 - 8764 - 87
63GLUGLUALAALA(chain 'F' and (resid 5 through 48 or (resid 49...FF90 - 16090 - 160
64SERSERLEULEU(chain 'F' and (resid 5 through 48 or (resid 49...FF163 - 175163 - 175
71THRTHRSERSER(chain 'G' and (resid 5 through 13 or (resid 14...GG5 - 595 - 59
72GLUGLULYSLYS(chain 'G' and (resid 5 through 13 or (resid 14...GG64 - 8764 - 87
73GLUGLUALAALA(chain 'G' and (resid 5 through 13 or (resid 14...GG90 - 16090 - 160
74SERSERLEULEU(chain 'G' and (resid 5 through 13 or (resid 14...GG163 - 175163 - 175
81THRTHRSERSER(chain 'H' and (resid 5 through 48 or (resid 49...HH5 - 595 - 59
82GLUGLULYSLYS(chain 'H' and (resid 5 through 48 or (resid 49...HH64 - 8764 - 87
83GLUGLUALAALA(chain 'H' and (resid 5 through 48 or (resid 49...HH90 - 16090 - 160
84SERSERLEULEU(chain 'H' and (resid 5 through 48 or (resid 49...HH163 - 175163 - 175
91THRTHRSERSER(chain 'I' and (resid 5 through 13 or (resid 14...II5 - 595 - 59
92GLUGLULYSLYS(chain 'I' and (resid 5 through 13 or (resid 14...II64 - 8764 - 87
93GLUGLUALAALA(chain 'I' and (resid 5 through 13 or (resid 14...II90 - 16090 - 160
94SERSERLEULEU(chain 'I' and (resid 5 through 13 or (resid 14...II163 - 175163 - 175
101THRTHRSERSER(chain 'J' and (resid 5 through 48 or (resid 49...JJ5 - 595 - 59
102GLUGLULYSLYS(chain 'J' and (resid 5 through 48 or (resid 49...JJ64 - 8764 - 87
103GLUGLUALAALA(chain 'J' and (resid 5 through 48 or (resid 49...JJ90 - 16090 - 160
104SERSERLEULEU(chain 'J' and (resid 5 through 48 or (resid 49...JJ163 - 175163 - 175
111THRTHRSERSER(chain 'K' and (resid 5 through 13 or (resid 14...KK5 - 595 - 59
112GLUGLULYSLYS(chain 'K' and (resid 5 through 13 or (resid 14...KK64 - 8764 - 87
113GLUGLUALAALA(chain 'K' and (resid 5 through 13 or (resid 14...KK90 - 16090 - 160
114SERSERLEULEU(chain 'K' and (resid 5 through 13 or (resid 14...KK163 - 175163 - 175
121THRTHRSERSER(chain 'L' and (resid 5 through 48 or (resid 49...LL5 - 595 - 59
122GLUGLULYSLYS(chain 'L' and (resid 5 through 48 or (resid 49...LL64 - 8764 - 87
123GLUGLUALAALA(chain 'L' and (resid 5 through 48 or (resid 49...LL90 - 16090 - 160
124SERSERLEULEU(chain 'L' and (resid 5 through 48 or (resid 49...LL163 - 175163 - 175

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要素

#1: タンパク質
Ferritin heavy chain / フェリチン / Ferritin H subunit / Cell proliferation-inducing gene 15 protein


分子量: 21085.248 Da / 分子数: 12 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P02794, ferroxidase
#2: 化合物
ChemComp-FE / FE (III) ION / 鉄


分子量: 55.845 Da / 分子数: 12 / 由来タイプ: 合成 / 式: Fe
#3: 化合物
ChemComp-NA / SODIUM ION / ナトリウムカチオン


分子量: 22.990 Da / 分子数: 7 / 由来タイプ: 合成 / 式: Na
#4: 化合物
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / (S)-2-メチル-2,4-ペンタンジオ-ル / 2-Methyl-2,4-pentanediol


分子量: 118.174 Da / 分子数: 7 / 由来タイプ: 合成 / 式: C6H14O2 / コメント: 沈殿剤*YM
#5: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 366 / 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: 3.03 Å3/Da / 溶媒含有率: 59.37 %
結晶化温度: 298 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: Reservoir: 525 uL total volume 100 uL of 500 mM HEPES pH 7.0, 125 uL of 1 M NH4OAc, 300 uL 2-Methyl-2,4-pentanediol Sitting drop: 5 uL reservoir, 5 uL of 25 uM dCs ferritin

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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: SSRL / ビームライン: BL9-2 / 波長: 0.9801 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2020年7月3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: 0.9801 Å / 相対比: 1
反射解像度: 2.7→91.44 Å / Num. obs: 85108 / % possible obs: 99.8 % / 冗長度: 18 % / Biso Wilson estimate: 49.66 Å2 / CC1/2: 0.996 / Net I/σ(I): 8.5
反射 シェル解像度: 2.7→2.75 Å / Num. unique obs: 4498 / CC1/2: 0.744

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解析

ソフトウェア
名称バージョン分類
PHENIX1.17.1_3660精密化
iMOSFLMデータ削減
Aimlessデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 6B8F

6b8f


解像度: 2.7→53.99 Å / SU ML: 0.3565 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 27.6792
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2537 4390 5.19 %
Rwork0.198 80118 -
obs0.2009 84508 99.14 %
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 mean: 59.36 Å2
精密化ステップサイクル: LAST / 解像度: 2.7→53.99 Å
タンパク質核酸リガンド溶媒全体
原子数16826 0 75 366 17267
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.005117261
X-RAY DIFFRACTIONf_angle_d0.733223349
X-RAY DIFFRACTIONf_chiral_restr0.04522481
X-RAY DIFFRACTIONf_plane_restr0.00453108
X-RAY DIFFRACTIONf_dihedral_angle_d10.23242288
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.730.37661290.3112709X-RAY DIFFRACTION99.86
2.73-2.760.33541370.32142619X-RAY DIFFRACTION99.78
2.76-2.80.34921590.30942675X-RAY DIFFRACTION99.68
2.8-2.830.40161280.29542605X-RAY DIFFRACTION99.49
2.83-2.870.31400.27182691X-RAY DIFFRACTION99.89
2.87-2.910.34441540.26842620X-RAY DIFFRACTION99.64
2.91-2.950.31281610.27262656X-RAY DIFFRACTION99.4
2.95-2.990.36051280.2562677X-RAY DIFFRACTION99.75
2.99-3.040.33631410.26562633X-RAY DIFFRACTION99.43
3.04-3.090.29781760.26612628X-RAY DIFFRACTION99.22
3.09-3.140.35031410.26612570X-RAY DIFFRACTION96.86
3.14-3.20.31781500.25732654X-RAY DIFFRACTION98.52
3.2-3.260.30141440.2432640X-RAY DIFFRACTION99.32
3.26-3.330.31291350.23632641X-RAY DIFFRACTION99.43
3.33-3.40.29451680.22772640X-RAY DIFFRACTION98.98
3.4-3.480.26011340.22592655X-RAY DIFFRACTION98.14
3.48-3.570.25041350.19772664X-RAY DIFFRACTION99.18
3.57-3.660.23151360.19012644X-RAY DIFFRACTION98.62
3.66-3.770.23571410.18162638X-RAY DIFFRACTION99.04
3.77-3.890.25861390.18732697X-RAY DIFFRACTION98.68
3.89-4.030.2181440.17362634X-RAY DIFFRACTION98.83
4.03-4.190.21321770.16012589X-RAY DIFFRACTION97.39
4.19-4.390.21411720.14652696X-RAY DIFFRACTION99.31
4.39-4.620.1831470.13982645X-RAY DIFFRACTION99.57
4.62-4.90.21431440.1432729X-RAY DIFFRACTION99.45
4.91-5.280.19851600.15552704X-RAY DIFFRACTION99.62
5.28-5.810.26081430.17662708X-RAY DIFFRACTION99.44
5.81-6.650.24261440.19512732X-RAY DIFFRACTION98.87
6.66-8.380.21881420.17312795X-RAY DIFFRACTION99.93
8.38-53.990.22791410.17882930X-RAY DIFFRACTION99.06
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)
10.4663314808050.0651267194222-0.12546059740.4517461128280.3503016360030.5751306043840.112231030559-0.4546242296060.02995973334340.28665511824-0.155804663864-0.09187574610520.2217576288140.09567188650920.02426615295810.517778846151-0.359781537314-0.1172686841250.9179322428890.1774525760520.35008350816815.638327566320.416872820348.0757733134
23.63274815556-2.180561718161.116128947541.78141662263-0.7980719022730.3758802821680.360911003789-0.05201061562140.1483051313760.0952036799289-0.296212504534-0.1275630828050.2180930119250.0451716843498-0.02502582281810.571957603121-0.278101020648-0.1023817540010.8659649063810.1280033661570.31419377923116.995896563520.713597288643.6113181374
30.784089418161-0.491315067098-0.009331670687881.63457177280.06698029857690.003774414162910.096465405101-0.60263023844-0.07778567641390.352001886561-0.04827547255770.2569409867590.109547056271-0.112953784772-0.02857837500330.577864056749-0.449244167833-0.02745009273350.9063714241480.03106081680250.33403565088213.788660819729.022243956654.1623644975
43.84983874561-2.368651860711.961126628183.89443448566-0.799643474414.46362355955-0.190420560912-0.09111289715890.08642939392440.4325822739120.0718398205118-0.41044276588-0.1184537955220.2839874548920.08262609313660.691656645701-0.354971248997-0.2486043973270.9951630051760.1727893030440.42347978446432.650618525523.981950592748.1024965959
56.81606082352-2.701187033092.515077245262.58526672272-0.9690201735391.114919933180.0361348414403-0.09253383756920.006822418857920.317645993786-0.1049126474610.231045527672-0.07217732235960.0973516799330.06673364270410.515971881012-0.3664597169080.0864846767520.810802776375-0.07928038034260.3507605575398.2955340397842.209316818145.8186307448
60.1848509798920.06123432310040.07605744775770.255891249773-0.08704898015830.2192116400310.00255331293314-0.04257945327510.06565583606860.202747011056-0.0567067524147-0.1305748545370.0124342835392-0.0305602294790.009851885456250.692420241121-0.514270107575-0.08377414757180.98236548148-0.08309723576310.28912875508635.541047733151.46182336450.0527041731
71.194755352920.554076324194-1.427099192890.593637413327-0.8414270723531.802827316940.0155712750020.0204279310207-0.00315359761239-0.001499517592680.0990659155964-0.249799441099-0.0135790083805-0.0413559314818-0.05365878418840.606135701322-0.487556726888-0.02078835768920.900143604492-0.07878416297560.39996784031339.213358388254.252754071838.5044814321
81.65468139041-0.00657258870691-0.1971859783761.10789219899-0.003760944919120.02405875803030.182811572832-0.3309487006540.01109270005510.147507760756-0.127130794032-0.090182450298-0.1420094221610.0320577062648-0.03047242803680.685469413679-0.5174634145320.05823098497961.00739966114-0.07467962121960.40045692652830.021145704555.833016197554.2940399213
90.1831836843710.114277647928-0.1051814032430.15332405965-0.07865462798790.06879328327090.100585704275-0.2317605825370.001268767668680.1362422920790.0528838837723-0.171914202346-0.04724123916440.1159517518940.09830849237010.626883726855-0.528919640982-0.1943869321941.11752144217-0.06859798056520.45938357501844.289587171847.31614996148.515440911
101.453098421410.65569819313-0.5912083743851.33979586377-1.381280239712.279410777040.04650861419270.0156769054844-0.01801222115040.02825467555640.0907830478495-0.253207372533-0.2247335644460.258338915665-0.01896663626960.418471650948-0.428082961081-0.1257253855490.8723603860490.001572210388180.57577278545156.005807534950.49631168532.7589054118
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322.32212195354-3.95792219257-2.050702077887.121946945223.234147160482.08899622890.153979963968-0.421167354066-0.07651902866940.36291486168-0.132303568755-0.4830546028950.06850256606750.488357609923-0.02566188909430.356073184705-0.20233860046-0.07359010074980.8916243143930.08251793851840.59416751778367.185225838139.019954911217.710886584
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340.4865724098580.233347736077-0.14428745830.379302655940.00478482985470.2148324174040.12307676528-0.2737213696880.188990473540.0840048175452-0.0482102957835-0.0329640983834-0.2596036115760.122709078962-0.020306471650.798637170419-0.4540401539910.1418296366040.862570580552-0.2756657239590.42588515147729.177057107870.535105789639.0382181264
351.619193027721.327507563571.119519810894.45208991530.9486765402150.7734233510160.198131786376-0.322815936482-0.0167261514210.277062561387-0.2115620536430.134017578749-0.20693994994-0.24565347380.04295178233050.684311040585-0.3175561095960.1604574647540.700415634778-0.2461695211020.4523761574579.9349903169763.044470799239.5389448434
360.914147603686-0.1127913229641.146898763020.021725488512-0.1804179694372.060602889430.0968445912904-0.2940800359810.551052916339-0.0616272496164-0.1274154880960.0792230455871-0.431828175878-0.1442462724260.1755502471670.955896014348-0.09006222958840.1397647656330.508407144744-0.2879067949150.690069606677.3605178631385.515950627921.0551225018
370.434471919620.3828420592410.8295672058270.3400812056580.491011575016.567333285030.403251118055-0.09540829132880.339716290908-0.084793978186-0.09718542535190.158420552508-0.0384475682750.126339652275-0.3080095298190.885093952976-0.01520963232930.1055716656510.359892141709-0.1020839625820.5858667985087.1450605610979.80930726969.76265619837
380.4208490876480.157511813586-0.2470681151430.0992160536363-0.02094456550250.267870828510.336933235609-0.198505297210.224391732788-0.00441842768041-0.02591549863950.209092764673-0.5601369567770.0163034291109-0.1813302385951.15321755043-0.08945152162590.1852403950150.405498045183-0.2010315389260.72233451819513.700299041388.641258921312.7457853597
397.706880229492.799478314251.123196971292.391366345563.428658521346.801897810030.1841167786160.07485823350690.679230836028-0.388391958467-0.05419213019480.167833792715-0.287697771033-0.273085203714-0.1386025897731.062199330570.0597065972566-0.0005624119820190.306440442068-0.0719917965940.64042497001911.321389669384.2720213236-11.7115611061
401.080374284880.08642817033620.08883351751150.5263412899660.05183262809570.105720888408-0.0427982273823-0.05378047990730.169808636428-0.02497425617630.01968678400480.0270119379614-0.2533009317750.246810305738-0.05646570123450.896640712792-0.5148241290530.2086111739050.497048589827-0.1806847008920.60950536748845.162746685984.84022352027.42362807473
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421.16991435782-0.8069749862170.1036977846830.7484029766150.01339634744640.307017292741-0.0381255370036-0.1369962837170.4405123987160.27899652756-0.08273968259630.0785069238768-0.288111805955-0.01871655636180.1254200901260.962635976192-0.5424028647480.1561456013340.570129824207-0.2358385401290.63021585406541.528627192685.315385569918.5488684167
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443.82311374553-2.62520943525-2.266978015074.92436256221-0.7931671734493.11284605256-0.1633779810240.574470015679-0.216001281278-0.2555433947450.238734801098-0.1508901190180.001658709215730.011533781991-0.03248836837280.668395552243-0.4701125712770.09293534934410.824361766706-0.0709970352580.47532871214459.516076151661.252397182715.3205785071
450.9423895053780.180456116349-0.0184042290540.496907348471-0.4200282248790.7883472421630.177685935968-0.173410337180.555686444385-0.119580565232-0.2514089935940.302476516188-0.687334297627-0.2797322605140.08779804177360.7868300982940.1582073486110.07799952493720.428591615055-0.2087530339130.837177228799-8.1466961935978.555253268713.1770356377
460.389475995546-0.4340997021921.327700639710.510495753407-1.510802842314.551603254570.5150729057970.06865272563380.349451106716-0.315851593875-0.2857394079240.3150652887280.276634378630.259602074299-0.2130566532440.6678088964370.07001089839690.1060573780550.412857453993-0.1603510282090.724399463651-4.3690222715672.163621876811.9293130972
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精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 48 )
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 86 )
3X-RAY DIFFRACTION3chain 'A' and (resid 87 through 123 )
4X-RAY DIFFRACTION4chain 'A' and (resid 124 through 137 )
5X-RAY DIFFRACTION5chain 'A' and (resid 138 through 176 )
6X-RAY DIFFRACTION6chain 'C' and (resid 5 through 41 )
7X-RAY DIFFRACTION7chain 'C' and (resid 42 through 76 )
8X-RAY DIFFRACTION8chain 'C' and (resid 77 through 86 )
9X-RAY DIFFRACTION9chain 'C' and (resid 87 through 137 )
10X-RAY DIFFRACTION10chain 'C' and (resid 138 through 176 )
11X-RAY DIFFRACTION11chain 'D' and (resid 5 through 48 )
12X-RAY DIFFRACTION12chain 'D' and (resid 49 through 81 )
13X-RAY DIFFRACTION13chain 'D' and (resid 82 through 95 )
14X-RAY DIFFRACTION14chain 'D' and (resid 96 through 137 )
15X-RAY DIFFRACTION15chain 'D' and (resid 138 through 176 )
16X-RAY DIFFRACTION16chain 'G' and (resid 5 through 41 )
17X-RAY DIFFRACTION17chain 'G' and (resid 42 through 158 )
18X-RAY DIFFRACTION18chain 'G' and (resid 159 through 176 )
19X-RAY DIFFRACTION19chain 'B' and (resid 5 through 48 )
20X-RAY DIFFRACTION20chain 'B' and (resid 49 through 75 )
21X-RAY DIFFRACTION21chain 'B' and (resid 76 through 137 )
22X-RAY DIFFRACTION22chain 'B' and (resid 138 through 176 )
23X-RAY DIFFRACTION23chain 'F' and (resid 5 through 41 )
24X-RAY DIFFRACTION24chain 'F' and (resid 42 through 86 )
25X-RAY DIFFRACTION25chain 'F' and (resid 87 through 126 )
26X-RAY DIFFRACTION26chain 'F' and (resid 127 through 176 )
27X-RAY DIFFRACTION27chain 'H' and (resid 5 through 40 )
28X-RAY DIFFRACTION28chain 'H' and (resid 41 through 137 )
29X-RAY DIFFRACTION29chain 'H' and (resid 138 through 176 )
30X-RAY DIFFRACTION30chain 'J' and (resid 5 through 41 )
31X-RAY DIFFRACTION31chain 'J' and (resid 42 through 137 )
32X-RAY DIFFRACTION32chain 'J' and (resid 138 through 176 )
33X-RAY DIFFRACTION33chain 'E' and (resid 5 through 48 )
34X-RAY DIFFRACTION34chain 'E' and (resid 49 through 137 )
35X-RAY DIFFRACTION35chain 'E' and (resid 138 through 176 )
36X-RAY DIFFRACTION36chain 'I' and (resid 5 through 41 )
37X-RAY DIFFRACTION37chain 'I' and (resid 42 through 76 )
38X-RAY DIFFRACTION38chain 'I' and (resid 77 through 158 )
39X-RAY DIFFRACTION39chain 'I' and (resid 159 through 176 )
40X-RAY DIFFRACTION40chain 'K' and (resid 5 through 48 )
41X-RAY DIFFRACTION41chain 'K' and (resid 49 through 95 )
42X-RAY DIFFRACTION42chain 'K' and (resid 96 through 137 )
43X-RAY DIFFRACTION43chain 'K' and (resid 138 through 163 )
44X-RAY DIFFRACTION44chain 'K' and (resid 164 through 176 )
45X-RAY DIFFRACTION45chain 'L' and (resid 5 through 48 )
46X-RAY DIFFRACTION46chain 'L' and (resid 49 through 76 )
47X-RAY DIFFRACTION47chain 'L' and (resid 77 through 137 )
48X-RAY DIFFRACTION48chain 'L' and (resid 138 through 176 )

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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